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1. A Chimeric TGA Repressor Slows Down Fruit Maturation and Ripening in Tomato

Author: Carine Ferrand, Christophe Rothan, Martine Lemaire-Chamley, Takayuki Tohge, Joana Jorly, Hiroshi Ezura, Erika Asamizu, Marilise Nogueira, Lázaro Eustáquio Pereira Peres, Paul D Fraser, Takuya Yoshida, Claude Koutouan, Alisdair R. Fernie, Julien Assali, Mohammad-Reza Hajirezaei, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, The University of Tokyo (UTokyo), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Royal Holloway [University of London] (RHUL), University of São Paulo (USP), Université de Tsukuba = University of Tsukuba, Ryukoku University, and Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben)
Subjects: Crops, Agricultural, 0106 biological sciences, Genotype, Physiology, [SDV]Life Sciences [q-bio], Repressor, Plant Science, tomato, Biology, Genes, Plant, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, chloroplast, ripening competency, Solanum lycopersicum, Gene Expression Regulation, Plant, bZIP, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Transcription factor, Phylogeny, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, TOMATE, hormone regulation, Genetic Variation, food and beverages, Ripening, Cell Biology, General Medicine, Metabolism, biology.organism_classification, Cell biology, Chloroplast, Basic-Leucine Zipper Transcription Factors, chemistry, Fruit, développement du fruit, Mutation, Plant hormone, Salicylic acid, Systemic acquired resistance, 010606 plant biology & botany
Abstract: The bZIP transcription factor (TF) SlTGA2.2 was previously highlighted as a possible hub in a network regulating fruit growth and transition to ripening (maturation phase). It belongs to a clade of TFs well known for their involvement in the regulation of the salicylic acid–dependent systemic acquired resistance. To investigate if this TGA TF plays a role in tomato fruit growth and maturation, we took advantage of the fruit-specific SlPPC2 promoter (PPC2pro) to target the expression of a SlTGA2.2-SRDX chimeric repressor in a developmental window restricted to early fruit growth and maturation. Here, we show that this SlTGA2.2-SRDX repressor alters early fruit development and metabolism, including chloroplast number and structure, considerably extends the time necessary to reach the mature green stage and slows down fruit ripening. RNA sequencing and plant hormone analyses reveal that PPC2pro:SlTGA2.2-SRDX fruits are maintained in an immature stage as long as PPC2pro is active, through early modifications of plant hormonal signaling and down-regulation of MADS-RIN and NAC-NOR ripening regulators. Once PPC2pro becomes inactive and therefore SlTGA2.2-SRDX expression is reduced, ripening can proceed, albeit at a slower pace than normal. Altogether, this work emphasizes the developmental continuum between fruit growth, maturation and ripening and provides a useful tool to alter and study the molecular bases of tomato fruit transition to ripening.
Published: 2021

2. Metal crossroads in plants: modulation of nutrient acquisition and root development by essential trace metals

Author: Ricardo Fabiano Hettwer Giehl, Hélène Javot, Alexandra Lešková, Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Plant Environmental Physiology and Stress Signaling (PEPSS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), and ANR-19-CE13-0007,PHLOWZ,Approche systémique de l'interaction entre les voies de signalisation du Zinc et du Phosphate(2019)
Subjects: Crops, Agricultural, Micronutrient deficiency, Physiology, Chemistry, fungi, food and beverages, Metal toxicity, Plant Science, Root system, Trace Elements, Trace (semiology), Metal, Plant Breeding, Soil, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Nutrient, Metals, visual_art, Environmental chemistry, Soil water, visual_art.visual_art_medium, Trace metal
Abstract: The metals iron, zinc, manganese, copper, molybdenum, and nickel are essential for the growth and development of virtually all plant species. Although these elements are required at relatively low amounts, natural factors and anthropogenic activities can significantly affect their availability in soils, inducing deficiencies or toxicities in plants. Because essential trace metals can shape root systems and interfere with the uptake and signaling mechanisms of other nutrients, the non-optimal availability of any of them can induce multi-element changes in plants. Interference by one essential trace metal with the acquisition of another metal or a non-metal nutrient can occur prior to or during root uptake. Essential trace metals can also indirectly impact the plant’s ability to capture soil nutrients by targeting distinct root developmental programs and hormone-related processes, consequently inducing largely metal-specific changes in root systems. The presence of metal binding domains in many regulatory proteins also enables essential trace metals to coordinate nutrient uptake by acting at high levels in hierarchical signaling cascades. Here, we summarize the known molecular and cellular mechanisms underlying trace metal-dependent modulation of nutrient acquisition and root development, and highlight the importance of considering multi-element interactions to breed crops better adapted to non-optimal trace metal availabilities.
Published: 2022

3. Multilateral benefit-sharing from digital sequence information will support both science and biodiversity conservation

Author: Amber Hartman Scholz, Jens Freitag, Christopher H. C. Lyal, Rodrigo Sara, Martha Lucia Cepeda, Ibon Cancio, Scarlett Sett, Andrew Lee Hufton, Yemisrach Abebaw, Kailash Bansal, Halima Benbouza, Hamadi Iddi Boga, Sylvain Brisse, Michael W. Bruford, Hayley Clissold, Guy Cochrane, Jonathan A. Coddington, Anne-Caroline Deletoille, Felipe García-Cardona, Michelle Hamer, Raquel Hurtado-Ortiz, Douglas W. Miano, David Nicholson, Guilherme Oliveira, Carlos Ospina Bravo, Fabian Rohden, Ole Seberg, Gernot Segelbacher, Yogesh Shouche, Alejandra Sierra, Ilene Karsch-Mizrachi, Jessica da Silva, Desiree M. Hautea, Manuela da Silva, Mutsuaki Suzuki, Kassahun Tesfaye, Christian Keambou Tiambo, Krystal A. Tolley, Rajeev Varshney, María Mercedes Zambrano, Jörg Overmann, European Commission, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), The Natural History Museum [London] (NHM), One Planet Solutions, Montpellier, Universidad de los Andes [Bogota] (UNIANDES), European Marine Biological Resource Centre (EMBRC-ERIC), Ethiopian Biotechnology Institute, Addis Ababa, National Academy of Agricultural Science and Global Plant Council, New Delhi, National Council of Scientific Research and Technologies (NCSRT), Algiers (NCSRT), Ministry of Agriculture, Livestock, Fisheries and Cooperatives, Nairobi, Institut Pasteur [Paris] (IP), Cardiff University, The Wellcome Trust Sanger Institute [Cambridge], European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Global Genome Initiative, Smithsonian National Museum of Natural History, Washington, DC, Alexander von Humboldt Biological Resources Research Institute, Bogota, South African National Biodiversity Institute, University of Nairobi (UoN), Instituto Tecnológico Vale [Belém, Brazil] (ITV), Ministry of the Environment and Sustainable Developmentment, University of Lethbridge, Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of Freiburg [Freiburg], National Centre for Cell Science [Pune, India] (NCCS), Mariano Galvez University, Guatemala City, National Center for Biotechnology Information (NCBI), University of Johannesburg [South Africa] (UJ), University of the Philippines Los Baños (UP Los Baños), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP), National Institute of Genetics (NIG), Institute of Biotechnology [Vilnius], Life Science Center [Vilnius], Vilnius University [Vilnius]-Vilnius University [Vilnius], Centre for Tropical Livestock Genetics and Health [Edimburgh] (CTLGH), Murdoch University, Corporación CorpoGen, Bogota, Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig], This work was funded by the German Federal Ministry of Education and Research (BMBF) WiLDSI 031B0862 (A.H.S., J.O., and J.F.) and Horizon Europe EVA-GLOBAL 871029 (A.H.S.). I.K.M. was supported by the National Center for Biotechnology Information of the National Library of Medicine, National Institutes of Health., European Project: 871029,H2020,H2020-INFRAIA-2019-1,EVA-GLOBAL(2020), and European Project: 01UU1602A/C
Subjects: Conservation of Natural Resources, Multidisciplinary, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, General Physics and Astronomy, General Chemistry, Biodiversity, General Biochemistry, Genetics and Molecular Biology
Abstract: Open access to sequence data is a cornerstone of biology and biodiversity research, but has created tension under the United Nations Convention on Biological Diversity (CBD). Policy decisions could compromise research and development, unless a practical multilateral solution is implemented. This workwas funded by the German Federal Ministry of Education and Research (BMBF) WiLDSI 031B0862 (A.H.S., J.O., and J.F.) and Horizon Europe EVA-GLOBAL 871029 (A.H.S.). I.K.M. was supported by the National Center for Biotechnology Information of the National Library of Medicine, National Institutes of Health.
Published: 2022
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4. Inter-annual and spatial climatic variability have led to a balance between local fluctuating selection and wide-range directional selection in a perennial grass species

Author: Thomas Keep, Fabien Surault, Isabelle Litrico, E. Willner, Klaus J. Dehmer, Philippe Barre, Tom Ruttink, Isabel Roldán-Ruiz, R Veron, Mathew Hegarty, Jean-Paul Sampoux, Hilde Muylle, Thomas Ledauphin, José Luis Blanco-Pastor, S Rouet, Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Research Institute for Agricultural, Fisheries and Food (ILVO), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Institute of Biological, Environmental and Rural Sciences (IBERS), Biotechnology and Biological Sciences Research Council (BBSRC)-Aberystwyth University, ANR-14-JFAC-0004,GrassLandscape,Bridging landscape genomics and quantitative genetics for a regional adaptation of European grasslands to climate change(2014), European Project: 618105,EC:FP7:KBBE,FP7-ERANET-2013-RTD,FACCE ERA NET PLUS(2013), and Aberystwyth University
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Climate Change, Lolium perenne, Quantitative Trait Loci, Population, Climatic adaptation, Plant Science, Quantitative trait locus, Biology, adaptive diversity, 01 natural sciences, 03 medical and health sciences, Lolium, genome-wide genotyping, Selection, Genetic, Allele, education, Alleles, 2. Zero hunger, Functional ecology, education.field_of_study, natural genetic diversity, Directional selection, Phenology, Ecology, perennial ryegrass, Allele diversity, food and beverages, intra-specific variability, Original Articles, climatic adaptation, 15. Life on land, Adaptation, Physiological, Genetics, Population, Phenotype, 030104 developmental biology, fluctuating selection, Adaptation, grassland, 010606 plant biology & botany
Abstract: Background and Aims The persistence of a plant population under a specific local climatic regime requires phenotypic adaptation with underlying particular combinations of alleles at adaptive loci. The level of allele diversity at adaptive loci within a natural plant population conditions its potential to evolve, notably towards adaptation to a change in climate. Investigating the environmental factors that contribute to the maintenance of adaptive diversity in populations is thus worthwhile. Within-population allele diversity at adaptive loci can be partly driven by the mean climate at the population site but also by its temporal variability. Methods The effects of climate temporal mean and variability on within-population allele diversity at putatively adaptive quantitative trait loci (QTLs) were evaluated using 385 natural populations of Lolium perenne (perennial ryegrass) collected right across Europe. For seven adaptive traits related to reproductive phenology and vegetative potential growth seasonality, the average within-population allele diversity at major QTLs (HeA) was computed. Key Results Significant relationships were found between HeA of these traits and the temporal mean and variability of the local climate. These relationships were consistent with functional ecology theory. Conclusions Results indicated that temporal variability of local climate has likely led to fluctuating directional selection, which has contributed to the maintenance of allele diversity at adaptive loci and thus potential for further adaptation.
Published: 2021

5. Signatures of Transcription Factor Evolution and the Secondary Gain of Red Algae Complexity

Author: Petroll, Romy, Schreiber, Mona, Finke, Hermann, Cock, J. Mark, Gould, Sven B., Rensing, Stefan A., Philipps Universität Marburg, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], and University of Freiburg [Freiburg]
Subjects: [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Rhodophyta, evolution, Genetics, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, multicellularity, QH426-470, transcription factor, morphological complexity
Abstract: International audience; Red algae (Rhodophyta) belong to the superphylum Archaeplastida, and are a species-rich group exhibiting diverse morphologies. Theory has it that the unicellular red algal ancestor went through a phase of genome contraction caused by adaptation to extreme environments. More recently, the classes Porphyridiophyceae, Bangiophyceae, and Florideophyceae experienced genome expansions, coinciding with an increase in morphological complexity. Transcription-associated proteins (TAPs) regulate transcription, show lineage-specific patterns, and are related to organismal complexity. To better understand red algal TAP complexity and evolution, we investigated the TAP family complement of uni- and multi-cellular red algae. We found that the TAP family complement correlates with gain of morphological complexity in the multicellular Bangiophyceae and Florideophyceae, and that abundance of the C2H2 zinc finger transcription factor family may be associated with the acquisition of morphological complexity. An expansion of heat shock transcription factors (HSF) occurred within the unicellular Cyanidiales, potentially as an adaption to extreme environmental conditions.
Published: 2021

6. Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly

Author: Le Wang, Frédéric Choulet, Juan C Rodriguez, Kellye Eversole, Hélène Rimbert, Martin Mascher, Yong Q. Gu, Rudi Appels, Tingting Zhu, Romain De Oliveira, Gabriel Keeble-Gagnère, Josquin Tibbits, Karin R. Deal, Jan Dvorak, Jane Rogers, Ming-Cheng Luo, UCDavis (UCD), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Agriculture Victoria (AgriBio), International Wheat Genome Sequencing Consortium, Eau Claire (IWGS), United States Department of Agriculture (USDA), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), United States Department of Agriculture (USDA) : 2030-21430-014-00-D, National Science Foundation (NSF ) : IOS-1929053, and ANR-10-BTBR-0003,BREEDWHEAT,Développer de nouvelles variétés de blé pour une agriculture durable(2010)
Subjects: 0106 biological sciences, 0301 basic medicine, Resource, Chromosomes, Artificial, Bacterial, [SDV]Life Sciences [q-bio], Sequence assembly, gene collinearity, Plant Science, Computational biology, Biology, 01 natural sciences, Genome, DNA sequencing, Chromosomes, Plant, 03 medical and health sciences, Hi-C, Genetics, RefSeq, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Genome size, direct label and stain, Triticum, 2. Zero hunger, Comparative genomics, Whole genome sequencing, Contig, Hi‐C, pseudomolecule, Chromosome Mapping, food and beverages, Molecular Sequence Annotation, Cell Biology, transposable element, 030104 developmental biology, DNA Transposable Elements, Genome, Plant, 010606 plant biology & botany
Abstract: Summary Until recently, achieving a reference‐quality genome sequence for bread wheat was long thought beyond the limits of genome sequencing and assembly technology, primarily due to the large genome size and > 80% repetitive sequence content. The release of the chromosome scale 14.5‐Gb IWGSC RefSeq v1.0 genome sequence of bread wheat cv. Chinese Spring (CS) was, therefore, a milestone. Here, we used a direct label and stain (DLS) optical map of the CS genome together with a prior nick, label, repair and stain (NLRS) optical map, and sequence contigs assembled with Pacific Biosciences long reads, to refine the v1.0 assembly. Inconsistencies between the sequence and maps were reconciled and gaps were closed. Gap filling and anchoring of 279 unplaced scaffolds increased the total length of pseudomolecules by 168 Mb (excluding Ns). Positions and orientations were corrected for 233 and 354 scaffolds, respectively, representing 10% of the genome sequence. The accuracy of the remaining 90% of the assembly was validated. As a result of the increased contiguity, the numbers of transposable elements (TEs) and intact TEs have increased in IWGSC RefSeq v2.1 compared with v1.0. In total, 98% of the gene models identified in v1.0 were mapped onto this new assembly through development of a dedicated approach implemented in the MAGAAT pipeline. The numbers of high‐confidence genes on pseudomolecules have increased from 105 319 to 105 534. The reconciled assembly enhances the utility of the sequence for genetic mapping, comparative genomics, gene annotation and isolation, and more general studies on the biology of wheat., Significance Statement This new release of bread wheat cv. Chinese Spring reference genome sequence, IWGSC RefSeq v2.1, features correction of assembly errors affecting approximately 10% of the prior IWGSC RefSeq v1.0 release using genome‐wide optical maps and filling of gaps with single‐molecule long‐reads as well as incorporating re‐annotation of TEs and re‐computation of gene coordinates. These refinements enhance the sequence utility for breeding and research applications.
Published: 2021

7. To grow or survive: Which are the strategies of a perennial grass to face severe seasonal stress?

Author: E. Willner, Thomas Ledauphin, Matthew J. Hegarty, Tom Ruttink, Klaus J. Dehmer, Jean-Louis Durand, Hilde Muylle, Isabel Roldán-Ruiz, José Luis Blanco-Pastor, Jean-Paul Sampoux, Fabien Surault, Thomas Keep, Florence Volaire, Philippe Barre, Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Research Institute for Agricultural, Fisheries and Food (ILVO), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Perennial plant, Climate change, drought, Biology, 010603 evolutionary biology, 01 natural sciences, Intraspecific competition, Grassland, 03 medical and health sciences, frost, intraspecific variability, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Environmental gradient, 2. Zero hunger, Abiotic component, 0303 health sciences, geography, geography.geographical_feature_category, Ecology, Phenology, fungi, food and beverages, Lolium perenne (perennial ryegrass), 15. Life on land, climate change, growth-survival trade-off, Adaptation, grassland, climatic stress
Abstract: More severe seasonal stresses resulting from climate change affect the survival of perennial plant species. The growth–survival trade‐off exemplified in dormant species is a key issue to understand adaptation. As the validity of this trade‐off has yet to be tested in non‐dormant species, it was assessed by exploring the intraspecific variability of strategies to face drought and frost within perennial ryegrass. Three common gardens compared 385 European perennial ryegrass populations along a latitudinal environmental gradient over 3‐years. Persistence, productivity and physiological traits were recorded under contrasting seasonal environments. Decoupling plant responses, that is, growth under favourable summers/winters and plant survival under harsh summers/winters, showed a general trade‐off between growth potential and dehydration survival. Three groups of perennial ryegrass populations were identified according to their contrasting strategies: (a) year‐round productive but stress sensitive populations from wet areas; (b) drought‐tolerant populations with low summer growth potential from drought‐prone areas and (c) frost‐tolerant populations with low winter growth potential from frost‐prone areas. Overall, the populations surviving drought best were more resource conservative, whereas populations of the other groups were more resource acquisitive. However, such overall functional patterns were less meaningful than seasonal variations of resource acquisition potentials. The predicted potential biogeographical distribution of these groups suggests shifts of areas of suitability under climate change over the next decades in Europe. Dehydration escape and dehydration tolerance through reduction of growth potential in summer may become the strategies best adapted to an increasingly large area of Europe. The large intraspecific variability of phenological adaptations within perennial ryegrass reveals that the seasonal modulation of growth potential is crucial to plant adaptation under severe chronic abiotic stresses. The global plant economics spectrum cannot account for contrasting seasonal trade‐offs, which points out the importance of integrating phenological traits as key components of plant strategies. The identification of the trade‐off between growth potential and frost or drought stress survival in this non‐dormant species provides key knowledge to understand the future regional distribution of this major species for grassland ecosystem services. A free Plain Language Summary can be found within the Supporting Information of this article.
Published: 2021

8. Polymorphism in the short arm of 1R rye chromosomes in wheat lines with 1RS.1BL translocation and 1R(1B) substitution from different sources

Author: M. K. Toporash, A. Börner, Pierre Sourdille, I. I. Motsnyy, S. V. Chebotar, Odessa National I.I.Mechnikov University, National Center of Seed and Cultivar Investigations, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Génétique Diversité et Ecophysiologie des Céréales (GDEC), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
Subjects: 2. Zero hunger, 0106 biological sciences, 0301 basic medicine, Genetics, 1RS.1BL translocation, [SDV]Life Sciences [q-bio], food and beverages, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Chromosomal translocation, General Medicine, Biology, 01 natural sciences, polymorphism, microsatellites markers, 03 medical and health sciences, 030104 developmental biology, PCR analysis, Polymorphism (materials science), [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 010606 plant biology & botany
Abstract: Aim. The short arm of 1R rye (Secale cereale L.) chromosome is widely used in the breeding of bread wheat (Triticum aestivum L.), in particular 1RS.1BL, to introsgress genes of resistance to leaf (Lr26), stem (Sr31), striped (Yr9) rusts, as well as powdery mildew (Pm8); 1RS.1AL carries Gb2/Gb6 resistance genes to the wheat aphid (Schizaphis graminum Rondani), powdery mildew (Pm17), and the Cmc4 resistance gene to the Aceria tosichella Koifer mite, which is a vector for spreading of wheat mosaic virus. The aim of the research is to reveal molecular genetic polymorphisms of short arm rye 1RS chromosomes of different origins in bread wheat lines with 1RS.1BL translocation or 1R(1B) substitution from different sources. Methods. Genetic polymorphism of lines was analyzed by using PCR with a number of rye and wheat microsatellite markers. Results. It was shown that the CWXs line has a recombinant 1RS arm that contains the chromosomes parts of 1RS of the parental lines H242/97-2 and H273/97, due to crossover event, which led to the recombination of marked loci. Conclusions. Molecular genetic polymorphism has been reviled in 1RS.1BL translocations and 1R substituted rye chromosomes of different origins in H242/97-2, CWXs, H273/97, PavonMA1, Salmon lines, as there are different alleles present at loci: Xscm9, Xtsm422, Xgwm752, Xgwm18, Taglgap. Keywords: polymorphism, 1RS.1BL translocation, PCR analysis, microsatellites markers.
Published: 2019

9. The Evolutionary Dynamics of Genetic Incompatibilities Introduced by Duplicated Genes in Arabidopsis thaliana

Author: Vipul Patel, Ales Pecinka, Isabelle Gy, Olivier Loudet, Maarten Koornneef, Marina Ferrand, Fang Liu, Petra Pecinkova, Sigi Effgen, Christine Camilleri, Jonas R Klasen, Korbinian Schneeberger, Wen-Biao Jiao, Max Planck Institute for Plant Breeding Research (MPIPZ), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Palacky University Olomouc, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Wageningen University and Research [Wageningen] (WUR), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Ludwig Maximilian University [Munich] (LMU), Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germanys Excellence Strategy—EXC 2048/1—390686111, and European Project: 802629 ,INTERACT
Subjects: 0106 biological sciences, Reproductive Isolation, genetic incompatibility, Population, Arabidopsis, Genome-wide association study, Biology, AcademicSubjects/SCI01180, Laboratorium voor Erfelijkheidsleer, 01 natural sciences, Genome, Gene flow, 03 medical and health sciences, Gene Duplication, Genotype, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Allele, Evolutionary dynamics, education, Molecular Biology, Gene, Alleles, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, education.field_of_study, [SDV.GEN]Life Sciences [q-bio]/Genetics, genome-wide association study, AcademicSubjects/SCI01130, duplicated gene, Phylogeography, loss of function, Evolutionary biology, HPA, Fast Track, Laboratory of Genetics, 010606 plant biology & botany, TIM22
Abstract: Although gene duplications provide genetic backup and allow genomic changes under relaxed selection, they may potentially limit gene flow. When different copies of a duplicated gene are pseudofunctionalized in different genotypes, genetic incompatibilities can arise in their hybrid offspring. Although such cases have been reported after manual crosses, it remains unclear whether they occur in nature and how they affect natural populations. Here, we identified four duplicated-gene based incompatibilities including one previously not reported within an artificial Arabidopsis intercross population. Unexpectedly, however, for each of the genetic incompatibilities we also identified the incompatible alleles in natural populations based on the genomes of 1,135 Arabidopsis accessions published by the 1001 Genomes Project. Using the presence of incompatible allele combinations as phenotypes for GWAS, we mapped genomic regions that included additional gene copies which likely rescue the genetic incompatibility. Reconstructing the geographic origins and evolutionary trajectories of the individual alleles suggested that incompatible alleles frequently coexist, even in geographically closed regions, and that their effects can be overcome by additional gene copies collectively shaping the evolutionary dynamics of duplicated genes during population history.
Published: 2021

10. Ustilago maydis effector Jsi1 interacts with Topless corepressor, hijacking plant jasmonate/ethylene signaling

Author: Simon Uhse, Ivo Feussner, Khong-Sam Chia, Michael Borg, Armin Djamei, Indira Saado, Krzysztof Zienkiewicz, Yohann Petit-Houdenot, Luz Mayela Soto-Jiménez, Joana Marques, Martin Alejandro Darino, Ruben Betz, János Bindics, David Aleksza, Austrian Academy of Sciences (OeAW), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), University of Natural Resources and Life Sciences (BOKU), Institute of Molecular Biotechnology (IMBA), Goettingen Center for Molecular Biosciences (GZMB ), Univ Gottingen, Albrecht von Haller Inst, Dept Plant Biochem, BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of East Anglia [Norwich] (UEA), University of Bonn, Austrian Science Fund (FWF) I 3033-B22P27818-B22, Austrian Academy of Sciences, German Research Foundation (DFG) INST 186/822-1, European Project, Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), and Universität Bonn = University of Bonn
Subjects: 0106 biological sciences, 0301 basic medicine, Topless, Physiology, Ustilago, [SDV]Life Sciences [q-bio], Ustilago maydis, Plant Science, Cyclopentanes, jasmonate/ethylene (JA/ET) signaling, 01 natural sciences, Zea mays, Transcriptome, Fungal Proteins, 03 medical and health sciences, Ascomycota, ethylene (JA, Jasmonate, Oxylipins, Psychological repression, Transcription factor, Plant Diseases, biology, Full Paper, Effector, Basidiomycota, Research, fungi, food and beverages, ET) signaling, Ethylenes, Full Papers, biology.organism_classification, jasmonate, Cell biology, Jsi1, 030104 developmental biology, Signal transduction, EAR motif, ethylene response factor, Corepressor, Co-Repressor Proteins, 010606 plant biology & botany
Abstract: early access; International audience; Ustilago maydis is the causal agent of maize smut disease. During the colonization process, the fungus secretes effector proteins that suppress immune responses and redirect the host metabolism in favor of the pathogen. As effectors play a critical role during plant colonization, their identification and functional characterization are essential to understanding biotrophy and disease.Using biochemical, molecular, and transcriptomic techniques, we performed a functional characterization of the U. maydis effector Jasmonate/Ethylene signaling inducer 1 (Jsi1).Jsi1 interacts with several members of the plant corepressor family Topless/Topless related (TPL/TPR). Jsi1 expression in Zea mays and Arabidopsis thaliana leads to transcriptional induction of the ethylene response factor (ERF) branch of the jasmonate/ethylene (JA/ET) signaling pathway. In A. thaliana, activation of the ERF branch leads to biotrophic susceptibility. Jsi1 likely activates the ERF branch via an EAR (ET-responsive element binding-factor-associated amphiphilic repression) motif, which resembles EAR motifs from plant ERF transcription factors, that interacts with TPL/TPR proteins.EAR-motif-containing effector candidates were identified from different fungal species, including Magnaporthe oryzae, Sporisorium scitamineum, and Sporisorium reilianum. Interaction between plant TPL proteins and these effector candidates from biotrophic and hemibiotrophic fungi indicates the convergent evolution of effectors modulating the TPL/TPR corepressor hub.
Published: 2021

11. High-quality genome sequence of white lupin provides insight into soil exploration and seed quality

Author: Pierre-Marc Delaux, Romain Guyot, Martin Crespi, Erika Sallet, Malika Laguerre, Fanchon Divol, Sébastien Carrère, Benjamin Péret, Patrick Doumas, Cecile Huneau, Matthew R. Nelson, Jemma Taylor, Alexandre Soriano, Jérôme Salse, Laurence Marquès, Veit Schubert, Fernando Geu-Flores, Davide Mancinotti, Jérôme Gouzy, Sandrine Arribat, Karine Gallardo, André Marques, Thomas Blein, Barbara Hufnagel, William Marande, Delphine Aime, Hélène Bergès, Jean Keller, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Max Planck Institute for Plant Breeding Research (MPIPZ), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), University of Copenhagen = Københavns Universitet (KU), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Royal Botanic Garden , Kew, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), The University of Western Australia (UWA), Centre IRD de Montpellier (IRD), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Evolution des Interactions Plantes-Microorganismes, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Institut de Recherche pour le Développement (IRD), VILLUM Foundation : 15476, Innovate UK, FAPEAL/CNPq (Brasil), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-LABX-0032,LaSIPS,LABORATORY FOR SYSTEMS AND ENGINEERING OF PARIS SACLAY(2010), European Project: 0637420(2007), University of Copenhagen = Københavns Universitet (UCPH), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Royal Botanic Gardens [Kew], and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: 0106 biological sciences, 0301 basic medicine, Repetitive Sequences, Nucleic Acid/genetics, Plant Roots/genetics, [SDV]Life Sciences [q-bio], Plant genetics, Gene Dosage, General Physics and Astronomy, Sequence assembly, Alkaloids/chemistry, Plant Roots, 01 natural sciences, Genome, Lupinus, Soil, Nutrient, Gene Duplication, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Plant Proteins, Plant Proteins/metabolism, 2. Zero hunger, Multidisciplinary, Ecotype, food and beverages, Transcriptome/genetics, Polymorphism, Single Nucleotide/genetics, Seeds, Genome, Plant, Agricultural genetics, Synteny/genetics, Plant domestication, Science, Centromere, Biology, Lupinus/genetics, Polymorphism, Single Nucleotide, Synteny, Article, General Biochemistry, Genetics and Molecular Biology, Crop, Evolution, Molecular, 03 medical and health sciences, Alkaloids, Seeds/physiology, Centromere/genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Domestication, Repetitive Sequences, Nucleic Acid, Models, Genetic, fungi, Genetic Variation, Molecular Sequence Annotation, General Chemistry, Sequence Analysis, DNA, 15. Life on land, biology.organism_classification, Plant Leaves, 030104 developmental biology, Agronomy, Genomic Structural Variation, lcsh:Q, Plant Leaves/metabolism, Transcriptome, 010606 plant biology & botany
Abstract: White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n = 50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield., White lupin is an annual crop cultivated for protein rich seeds and can produce cluster roots for efficient phosphate acquisition. Here, the authors generate high quality genome assemblies of a cultivated accession, a landrace, and a wild relative and provides insight into soil exploration and seed quality.
Published: 2020

12. COMPOSITUM 1 contributes to the architectural simplification of barley inflorescence via meristem identity signals

Author: Michael Melzer, Nils Stein, Thomas Schmutzer, Ravi Koppolu, Marion Dalmais, Zhanguo Xin, Udda Lundqvist, Corinna Trautewig, Thorsten Schnurbusch, Naser Poursarebani, Thomas Nussbaumer, Abdelhafid Bendahmane, Twan Rutten, Richard Sibout, Helmy M. Youssef, Lothar Altschmied, Ronny Brandt, Axel Himmelbach, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Helmholtz Zentrum München (HMGU), German Research Center for Environmental Health, Institute of Network Biology (INET), Nordic Genetic Resource Center (NordGen), Technical University of Munich and Helmholtz Center Munich, Institute of Environmental Medicine, WIK Wissenschaftliches Institut für Infrastruktur und Kommunikationsdienste [Bad Honnef]-WIK Wissenschaftliches Institut für Infrastruktur und Kommunikationsdienste [Bad Honnef], Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin-Luther-University Halle-Wittenberg-Martin-Luther-University Halle-Wittenberg, Faculty of Agriculture, Cairo University, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS)-United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Martin-Luther-Universität Halle Wittenberg (MLU), Federal Ministry of Education & Research (BMBF) FKZ 0315954A 031B0201A, German Research Foundation (DFG) SCHN 768/8-1 SCHN 768/15-1, IPK core budget, and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], General Physics and Astronomy, Spike, 01 natural sciences, Plant evolution, Gene Expression Regulation, Plant, Inflorescence, lcsh:Science, Triticeae, Plant Proteins, 2. Zero hunger, Molecular breeding, Regulation of gene expression, Diversity, Multidisciplinary, Natural selection, food and beverages, Cell biology, [SDE]Environmental Sciences, Signal Transduction, Morphology, Agricultural genetics, Evolution, Science, Meristem, Biology, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, otorhinolaryngologic diseases, ddc:610, Transcription factor, Gene, Shoot apical meristem, Program, Hordeum, General Chemistry, 15. Life on land, biology.organism_classification, 030104 developmental biology, Mutation, lcsh:Q, [INFO.INFO-ET]Computer Science [cs]/Emerging Technologies [cs.ET], Format, 010606 plant biology & botany
Abstract: Grasses have varying inflorescence shapes; however, little is known about the genetic mechanisms specifying such shapes among tribes. Here, we identify the grass-specific TCP transcription factor COMPOSITUM 1 (COM1) expressing in inflorescence meristematic boundaries of different grasses. COM1 specifies branch-inhibition in barley (Triticeae) versus branch-formation in non-Triticeae grasses. Analyses of cell size, cell walls and transcripts reveal barley COM1 regulates cell growth, thereby affecting cell wall properties and signaling specifically in meristematic boundaries to establish identity of adjacent meristems. COM1 acts upstream of the boundary gene Liguleless1 and confers meristem identity partially independent of the COM2 pathway. Furthermore, COM1 is subject to purifying natural selection, thereby contributing to specification of the spike inflorescence shape. This meristem identity pathway has conceptual implications for both inflorescence evolution and molecular breeding in Triticeae., Grasses have diverse inflorescence morphologies, but the underlying genetic mechanisms are unclear. Here, the authors report a TCP transcription factor COM1 affects cell growth through regulation of cell wall properties and promotes branch formation in non-Triticeae grasses but branch inhibition in barley (Triticeae).
Published: 2020

13. The native acyltransferase-coding genes DGA1 and DGA2 affect lipid accumulation in Blastobotrys raffinosifermentans differently when overexpressed

Author: Cécile Neuvéglise, Daniel Ruben Akiola Sanya, Djamila Onésime, Gotthard Kunze, Anne-Marie Crutz-Le Coq, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), and DS received PhD funding from the IsDB (Islamic Development Bank).
Subjects: Blastobotrys raffinosifermentans, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Lipid accumulation, Biology, Arxula, Applied Microbiology and Biotechnology, Microbiology, DGAT, 03 medical and health sciences, Amino Acid Sequence, Diacylglycerol O-Acyltransferase, Gene, 030304 developmental biology, Diacylglycerol kinase, 2. Zero hunger, 0303 health sciences, Strain (chemistry), 030306 microbiology, Fatty Acids, lipid production, General Medicine, Lipid Metabolism, Yeast, Biochemistry, Acyltransferases, Acyltransferase, Saccharomycetales, diacylglycerol acyltransferase, Microorganisms, Genetically-Modified, triacylglycerol
Abstract: Blastobotrys raffinosifermentans is an ascomycetous yeast with biotechnological applications, recently shown to be an oleaginous yeast accumulating lipids under nitrogen limitation. Diacylglycerol acyltransferases (DGATs) act in the lipid storage pathway, in the last step of triacylglycerol biosynthesis. Two DGAT families are widespread in eukaryotes. We first checked that B. raffinosifermentans strain LS3 possessed both types of DGAT, and we then overexpressed the native DGAT-encoding genes, DGA1 and DGA2, separately or together. DGA2 (from the DGAT1 family) overexpression was sufficient to increase lipid content significantly in LS3, to up to 26.5% of dry cell weight (DCW), 1.6 times the lipid content of the parental strain (16.90% of DCW) in glucose medium under nitrogen limitation. By contrast, DGA1 (of the DGAT2 type) overexpression led to a large increase (up to 140-fold) in the amount of the corresponding transcript, but had no effect on overall lipid content relative to the parental strain. Analysis of the expression of the native genes over time in the parental strain revealed that DGA2 transcript levels quadrupled between 8 and 24 h in the N-limited lipogenic medium, whereas DGA1 transcript levels remained stable. This survey highlights the predominant role of the DGAT1 family in lipid accumulation and demonstrates the suitability of B. raffinosifermentans for engineering for lipid production.
Published: 2020

14. The Arabidopsis condensin CAP-D subunits arrange interphase chromatin

Author: Andrea Bräutigam, Celia Municio, Michiel Van Bel, Veit Schubert, Wojciech Antosz, Frederik Coppens, Ignacio Eguinoa, Klaus D. Grasser, Andreas Houben, Etienne Kornobis, Inna Lermontova, Katarzyna Zelkowska, Astrid Bruckmann, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), University of Regensburg, Biomics (plateforme technologique), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Mendel Centre for Plant Genomics and Proteomics [Brno, Czech Republic], Masaryk University [Brno] (MUNI)-CEITEC - Central European Institute of Technology [Brno, Czech Republic], and The work was supported by a Marie Curie Initial Training Network fellowship (FP7-PEOPLE-2013-ITN, CHIP-ET). The A. Bruckmann and KDG laboratories were supported by the German Research Foundation through grant SFB960. IL was supported by European Regional Development ‘Fund-Project MSCAfellow@MUNI’ (no. CZ.02.2.69/0.0/0.0/17_050/0008496).
Subjects: 0106 biological sciences, 0301 basic medicine, chromosomes, Euchromatin, Arabidopsis thaliana, Physiology, Heterochromatin, Condensin, Arabidopsis, Plant Science, macromolecular substances, 01 natural sciences, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Condensin complex, Animals, Interphase, Adenosine Triphosphatases, biology, Chemistry, condensin, Biology and Life Sciences, biology.organism_classification, Chromatin, Cell biology, DNA-Binding Proteins, SMC proteins, 030104 developmental biology, Histone, Multiprotein Complexes, biology.protein, 010606 plant biology & botany, chromatin organization, interphase nuclei
Abstract: International audience; Condensins are best known for their role in shaping chromosomes. Other functions such as organizing interphase chromatin and transcriptional control have been reported in yeasts and animals, but little is known about their function in plants. To elucidate the specific composition of condensin complexes and the expression of CAP-D2 (condensin I) and CAP-D3 (condensin II), we performed biochemical analyses in Arabidopsis. The role of CAP-D3 in interphase chromatin organization and function was evaluated using cytogenetic and transcriptome analysis in cap-d3 T-DNA insertion mutants. CAP-D2 and CAP-D3 are highly expressed in mitotically active tissues. In silico and pulldown experiments indicate that both CAP-D proteins interact with the other condensin I and II subunits. In cap-d3 mutants, an association of heterochromatic sequences occurs, but the nuclear size and the general histone and DNA methylation patterns remain unchanged. Also, CAP-D3 influences the expression of genes affecting the response to water, chemicals, and stress. The expression and composition of the condensin complexes in Arabidopsis are similar to those in other higher eukaryotes. We propose a model for the CAP-D3 function during interphase in which CAP-D3 localizes in euchromatin loops to stiffen them and consequently separates centromeric regions and 45S rDNA repeats.
Published: 2020

15. High-throughput genome-wide genotyping to optimize the use of natural genetic resources in the grassland species perennial ryegrass ( Lolium perenne L.)

Author: José Luis Blanco-Pastor, Isabel Roldán-Ruiz, Philippe Barre, Fabien Surault, Thomas Ledauphin, Hilde Muylle, Matthew J. Hegarty, Jean Paul Sampoux, E. Willner, Thomas Keep, Tom Ruttink, Isabelle Litrico, Klaus J. Dehmer, Anna M. Roschanski, Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Research Institute for Agricultural, Fisheries and Food (ILVO), and Bourse de thèse cofinancée INRAE-Région Nouvelle Aquitaine
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Genotype, forage species, Genome-wide association study, Biology, QH426-470, genebank, association study, 01 natural sciences, Lolium perenne, 03 medical and health sciences, Germany, Lolium, Genetics, GWAS, Ecosystem, Shared data resources, Genetic variability, Molecular Biology, Genotyping, Genetics (clinical), genomic prediction, 030304 developmental biology, 2. Zero hunger, natural diversity, 0303 health sciences, Genetic diversity, Ecotype, Ecology, business.industry, Genetic Variation, 15. Life on land, biology.organism_classification, Grassland, Europe, Plant Breeding, GenPred, Agriculture, business, 010606 plant biology & botany
Abstract: The natural genetic diversity of agricultural species is an essential genetic resource for breeding programs aiming to improve their ecosystem and production services. A large natural ecotype diversity is usually available for most grassland species. This could be used to recombine natural climatic adaptations and agronomic value to create improved populations of grassland species adapted to future regional climates. However describing natural genetic resources can be long and costly. Molecular markers may provide useful information to help this task. This opportunity was investigated for Lolium perenne L., using a set of 385 accessions from the natural diversity of this species collected right across Europe and provided by genebanks of several countries. For each of these populations, genotyping provided the allele frequencies of 189,781 SNP markers. GWAS were implemented for over 30 agronomic and/or putatively adaptive traits recorded in three climatically contrasted locations (France, Belgium, Germany). Significant associations were detected for hundreds of markers despite a strong confounding effect of the genetic background; most of them pertained to phenology traits. It is likely that genetic variability in these traits has had an important contribution to environmental adaptation and ecotype differentiation. Genomic prediction models calibrated using natural diversity were found to be highly effective to describe natural populations for almost all traits as well as commercial synthetic populations for some important traits such as disease resistance, spring growth or phenological traits. These results will certainly be valuable information to help the use of natural genetic resources of other species.
Published: 2020

16. Enabling reusability of plant phenomic datasets with MIAPPE 1.1

Author: François Tardieu, Cyril Pommier, Célia Michotey, Bruno Costa, Stephan Weise, Bert Droesbeke, Graham J.W. King, Astrid Junker, Philippe Rocca-Serra, Guillaume Cornut, Hanna Ćwiek-Kupczyńska, Markus Oppermann, Célia Miguel, Daniel Faria, Björn Usadel, Cristobal Uauy, Paweł Krajewski, Jochen C. Reif, Susanna-Assunta Sansone, Živa Ramšak, Uwe Scholz, Richard G. F. Visser, Evangelia Papoutsoglou, Ioannis N. Athanasiadis, Daniel Arend, Inês Chaves, Hendrik Poorter, Richard Finkers, Marie-Angélique Laporte, Kristina Gruden, Elizabeth Arnaud, Ricardo H. Ramirez-Gonzalez, Paul J. Kersey, Anne-Françoise Adam-Blondon, Frederik Coppens, Richard Ostler, Matthias Lange, Wageningen University and Research [Wageningen] (WUR), Instituto Gulbenkian de Ciência [Oeiras] (IGC), Fundação Calouste Gulbenkian, Instituto de Engenharia de Sistemas e Computadores (INESC), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Geo-Information Science and Remote Sensing Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Instituto de Biologia Experimental e Tecnológica (IBET), Department of plant Biotechnology and Bioinformatics, University of Gent, VIBUGent Center for Plant Systems Biology, Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), BioISI, Universidade de Lisboa (ULISBOA), Polish Academy of Sciences, Institute of Plant Genetics, Department of Integrative Plant Biology, Partenaires INRAE, Department of Biotechnology and Systems Biology, National Institute of Biology [Ljubljana] (NIB), Southern Cross Plant Science, Southern Cross University (SCU), Computational and Analytical Sciences, Rothamsted Research, Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, University North Ryde, John Innes Centre [Norwich], University of Oxford [Oxford], Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), RWTH Aachen University, Royal Botanic Gardens, Kew Richmond, European Project: 676559,H2020,H2020-INFRADEV-1-2015-1,ELIXIR-EXCELERATE(2015), European Project: 739514,EMPHASIS-PREP, European Project: 634107,H2020,H2020-PHC-2014-two-stage,MULTIMOT(2015), European Project: 654241,H2020,H2020-EINFRA-2014-2,PhenoMeNal(2015), Universiteit Gent = Ghent University (UGENT), Universidade de Lisboa = University of Lisbon (ULISBOA), Biotechnology and Biological Sciences Research Council (BBSRC)-Biotechnology and Biological Sciences Research Council (BBSRC), Biotechnology and Biological Sciences Research Council (BBSRC), University of Oxford, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Rheinisch-Westfälische Technische Hochschule Aachen University (RWTH)
Subjects: 0106 biological sciences, 0301 basic medicine, Computer science, Physiology, Interoperability, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, WASS, interoperability, Plant Science, MINIMUM INFORMATION, 01 natural sciences, Domain (software engineering), law.invention, 03 medical and health sciences, plant phenotyping, Laboratorium voor Plantenveredeling, Knowledge extraction, Laboratory of Geo-information Science and Remote Sensing, law, Methods, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Laboratorium voor Geo-informatiekunde en Remote Sensing, Implementation, Reusability, Research, metadata, Biology and Life Sciences, phenomics, Plants, findability, PE&RC, Data science, ONTOLOGIES, Metadata, Plant Breeding, 030104 developmental biology, ddc:580, Data model, VOCABULARY, CLARITY, reusability, standards, EPS, 010606 plant biology & botany, REPOSITORY
Abstract: The new phytologist 227(1), 260-273 (2020). doi:10.1111/nph.16544, Published by Wiley-Blackwell, Oxford [u.a.]
Published: 2020

17. SBML Level 3: an extensible format for the exchange and reuse of biological models

Author: Edda Klipp, Marco Antoniotti, Frank Bergmann, James C. Schaff, Peter D. Karp, Daniel Lucio, Kedar Nath Natarajan, Thomas M. Hamm, Leandro Watanabe, Henning Hermjakob, David Tolnay, John Wagner, Joerg Stelling, Alida Palmisano, Falk Schreiber, Yukiko Matsuoka, Harold F. Gómez, Huaiyu Mi, Carole J. Proctor, Ulrike Wittig, Neil Swainston, Jan Červený, Denis Thieffry, Piero Dalle Pezze, Julio Saez-Rodriguez, Maciej J. Swat, Bin Hu, Martina Kutmon, Thomas Pfau, Bas Teusink, Sarah M. Keating, Fedor A. Kolpakov, Andreas Dräger, Pedro Mendes, Martin Scharm, Emek Demir, Ioannis Xenarios, Christoph Flamm, Axel von Kamp, Darren J. Wilkinson, Nick Juty, Fengkai Zhang, Leonard A. Harris, Michael Schubert, Dagmar Waltemath, Lucian P. Smith, Steffen Klamt, Herbert M. Sauro, Ali Ebrahim, Wolfram Liebermeister, Christian Knüpfer, Nicolas Rodriguez, Tramy Nguyen, Naoki Tanimura, Christopher Cox, Stuart C. Sealfon, Nicholas Alexander Allen, Clemens Wrzodek, Bastian R. Angermann, Martin Meier-Schellersheim, Anna Zhukova, Jean-Baptiste Pettit, Hovakim Grabski, Devin P. Sullivan, Claudine Chaouiya, Michael L. Blinov, John Doyle, Ilya Kiselev, Roman Schulte, Alex Gutteridge, Mélanie Courtot, Eric Mjolsness, Finja Wrzodek, Rahuman S Malik-Sheriff, Ronan M. T. Fleming, Bruce E. Shapiro, Kimberly Begley, Leslie M. Loew, Colin S. Gillespie, Ibrahim Vazirabad, Michael Hucka, Akira Funahashi, Bernhard O. Palsson, Hamid Bolouri, Tomáš Helikar, Camille Laibe, William S. Denney, Chris T. Evelo, Florian Mittag, William S. Hlavacek, Ron Henkel, Harish Dharuri, Julien Dorier, Karthik Raman, Martina Fröhlich, Conor Lawless, Rainer Machné, Falko Krause, Damon Hachmeister, Matthias König, Clifford A. Shaffer, Benjamin D. Heavner, Douglas B. Kell, Jonathan R. Karr, Mihai Glont, Lukas Endler, Melanie I. Stefan, Robert Phair, Lu Li, Henning Schmidt, Dirk Drasdo, Johan Elf, Allyson L. Lister, Hiroaki Kitano, Richard R. Adams, Oliver A. Ruebenacker, Roland Keller, Sven Sahle, Ion I. Moraru, Gary D. Bader, Poul M. F. Nielsen, Johann M. Rohwer, Johannes Eichner, Daniel R. Hyduke, James R. Faeder, Stefan Hoops, Emanuel Gonçalves, Yuichiro Inagaki, Aurélien Naldi, Koichi Takahashi, Sylvain Soliman, Brett G. Olivier, Kieran Smallbone, Stuart L. Moodie, Pedro T. Monteiro, Chris J. Myers, Martin Golebiewski, Tomas Radivoyevitch, Jeremy Zucker, Hidde de Jong, Andrew Finney, Keating, S, Waltemath, D, König, M, Zhang, F, Dräger, A, Chaouiya, C, Bergmann, F, Finney, A, Gillespie, C, Helikar, T, Hoops, S, Malik-Sheriff, R, Moodie, S, Moraru, I, Myers, C, Naldi, A, Olivier, B, Sahle, S, Schaff, J, Smith, L, Swat, M, Thieffry, D, Watanabe, L, Wilkinson, D, Blinov, M, Begley, K, Faeder, J, Gómez, H, Hamm, T, Inagaki, Y, Liebermeister, W, Lister, A, Lucio, D, Mjolsness, E, Proctor, C, Raman, K, Rodriguez, N, Shaffer, C, Shapiro, B, Stelling, J, Swainston, N, Tanimura, N, Wagner, J, Meier-Schellersheim, M, Sauro, H, Palsson, B, Bolouri, H, Kitano, H, Funahashi, A, Hermjakob, H, Doyle, J, Hucka, M, Adams, R, Allen, N, Angermann, B, Antoniotti, M, Bader, G, Červený, J, Courtot, M, Cox, C, Dalle Pezze, P, Demir, E, Denney, W, Dharuri, H, Dorier, J, Drasdo, D, Ebrahim, A, Eichner, J, Elf, J, Endler, L, Evelo, C, Flamm, C, Fleming, R, Fröhlich, M, Glont, M, Gonçalves, E, Golebiewski, M, Grabski, H, Gutteridge, A, Hachmeister, D, Harris, L, Heavner, B, Henkel, R, Hlavacek, W, Hu, B, Hyduke, D, Jong, H, Juty, N, Karp, P, Karr, J, Kell, D, Keller, R, Kiselev, I, Klamt, S, Klipp, E, Knüpfer, C, Kolpakov, F, Krause, F, Kutmon, M, Laibe, C, Lawless, C, Li, L, Loew, L, Machne, R, Matsuoka, Y, Mendes, P, Mi, H, Mittag, F, Monteiro, P, Natarajan, K, Nielsen, P, Nguyen, T, Palmisano, A, Jean-Baptiste, P, Pfau, T, Phair, R, Radivoyevitch, T, Rohwer, J, Ruebenacker, O, Saez-Rodriguez, J, Scharm, M, Schmidt, H, Schreiber, F, Schubert, M, Schulte, R, Sealfon, S, Smallbone, K, Soliman, S, Stefan, M, Sullivan, D, Takahashi, K, Teusink, B, Tolnay, D, Vazirabad, I, Kamp, A, Wittig, U, Wrzodek, C, Wrzodek, F, Xenarios, I, Zhukova, A, Zucker, J, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Heidelberg University Hospital [Heidelberg], Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), European Molecular Biology Laboratory (EMBL), University of Connecticut (UCONN), National Institutes of Health [Bethesda] (NIH), Chercheur indépendant, Amazon Web Services [Seattle] (AWS), Università degli Studi di Milano-Bicocca = University of Milano-Bicocca (UNIMIB), University of Toronto, Masaryk University [Brno] (MUNI), Terry Fox Laboratory, BC Cancer Agency (BCCRC)-British Columbia Cancer Agency Research Centre, The University of Tennessee [Knoxville], The Babraham Institute [Cambridge, UK], Oregon Health and Science University [Portland] (OHSU), Human Predictions LLC, Illumina, Swiss-Prot Group, Swiss Institute of Bioinformatics [Genève] (SIB), Modelling and Analysis for Medical and Biological Applications (MAMBA), Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University of California [San Diego] (UC San Diego), University of California (UC), Center for Bioinformatics (ZBIT), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Uppsala University, Institut für Populationsgenetik [Vienna], Veterinärmedizinische Universität Wien, Maastricht University [Maastricht], Alpen-Adria-Universität Klagenfurt [Klagenfurt, Austria], Medizinische Universität Wien = Medical University of Vienna, German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Heidelberg Institute for Theoretical Studies (HITS ), Russian-Armenian University (RAU), GlaxoSmithKline [Stevenage, UK] (GSK), GlaxoSmithKline [Headquarters, London, UK] (GSK), Microsoft Technology Licensing (MTL), Microsoft Corporation [Redmond, Wash.], Vanderbilt University School of Medicine [Nashville], University of Washington [Seattle], University of Rostock, Los Alamos National Laboratory (LANL), Lorentz Institute, Universiteit Leiden, Tegmine Therapeutics, Modeling, simulation, measurement, and control of bacterial regulatory networks (IBIS), Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Jean Roget, SRI International [Menlo Park] (SRI), Icahn School of Medicine at Mount Sinai [New York] (MSSM), University of Liverpool, Universitätsklinikum Tübingen - University Hospital of Tübingen, Institute of Information and Computational Technologies (IICT), Max Planck Institute for Dynamics of Complex Technical Systems, Max-Planck-Gesellschaft, Max-Planck-Institut für Molekulare Genetik (MPIMG), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Humboldt University Of Berlin, Newcastle University [Newcastle], École polytechnique (X), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], The Systems Biology Institute [Tokyo] (SBI), Centro de Quimica Estrutural (CQE), Instituto Superior Técnico, Universidade Técnica de Lisboa (IST), University of Southern California (USC), Instituto Gulbenkian de Ciência [Oeiras] (IGC), Fundação Calouste Gulbenkian, University of Southern Denmark (SDU), University of Auckland [Auckland], University of Utah, Virginia Tech [Blacksburg], University of Luxembourg [Luxembourg], Integrative Bioinformatics Inc [Mountain View], Cleveland Clinic, Stellenbosch University, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Universität Heidelberg [Heidelberg] = Heidelberg University, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Mount Sinai School of Medicine, Department of Psychiatry-Icahn School of Medicine at Mount Sinai [New York] (MSSM), University of Manchester [Manchester], Computational systems biology and optimization (Lifeware), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), California Institute of Technology (CALTECH), Encodia Inc [San Diego], Shinshu University [Nagano], University of Amsterdam [Amsterdam] (UvA), Versiti Blood Center of Wisconsin, Greifswald University Hospital, Bioinformatique évolutive - Evolutionary Bioinformatics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Pacific Northwest National Laboratory (PNNL), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), Department of Bioengineering, University of California (UC)-University of California (UC), ANSYS, Virginia Polytechnic Institute and State University [Blacksburg], Eight Pillars Ltd, Center for Integrative Genomics - Institute of Bioinformatics, Génopode (CIG), Université de Lausanne = University of Lausanne (UNIL)-Université de Lausanne = University of Lausanne (UNIL), Universität Heidelberg, Bioquant, Applied Biomathematics [New York], SimCYP Ltd, Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Utah School of Medicine [Salt Lake City], University of Pittsburgh School of Medicine, Pennsylvania Commonwealth System of Higher Education (PCSHE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Mizuho Information and Research Institute, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Oxford, Computer Science (North Carolina State University), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), University of California [Irvine] (UC Irvine), Indian Institute of Technology Madras (IIT Madras), California State University [Northridge] (CSUN), Biotechnology and Biological Sciences Research Council (BBSRC), IBM Research [Melbourne], Benaroya Research Institute [Seattle] (BRI), Okinawa Institute of Science and Technology Graduate University, Keio University, Department of Computing and Mathematical sciences, members, SBML Level 3 Community, Université de Lausanne (UNIL), Università degli Studi di Milano-Bicocca [Milano] (UNIMIB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), University of California, Universiteit Leiden [Leiden], Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Inria Grenoble - Rhône-Alpes, Humboldt University of Berlin, Universität Heidelberg [Heidelberg], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Humboldt-Universität zu Berlin, University of California-University of California, Université de Lausanne (UNIL)-Université de Lausanne (UNIL), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Oxford [Oxford], University of California [Irvine] (UCI), Biotechnology and Biological Sciences Research Council, Computer Science, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)
Subjects: computational modeling, Medicine (General), Markup language, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, INFORMATION, Interoperability, interoperability, Review, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], ANNOTATION, 0302 clinical medicine, Software, file forma, Models, Biology (General), 0303 health sciences, Computational model, Applied Mathematics, Systems Biology, systems biology, File format, 3. Good health, Networking and Information Technology R&D, Networking and Information Technology R&D (NITRD), Computational Theory and Mathematics, SIMULATION, General Agricultural and Biological Sciences, STANDARDS, REPOSITORY, Information Systems, QH301-705.5, Bioinformatics, Systems biology, Software ecosystem, Reviews, Bioengineering, Methods & Resources, Biology, MARKUP LANGUAGE, Models, Biological, SBML Level 3 Community members, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, R5-920, Animals, Humans, SBML, reproducibility, 030304 developmental biology, ENVIRONMENT, General Immunology and Microbiology, file format, business.industry, Computational Biology, Biological, ONTOLOGY, Metabolism, Logistic Models, Biochemistry and Cell Biology, Other Biological Sciences, Software engineering, business, 030217 neurology & neurosurgery
Abstract: Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction‐based models and packages that extend the core with features suited to other model types including constraint‐based models, reaction‐diffusion models, logical network models, and rule‐based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single‐cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution., Over the past two decades, scientists from different fields have been developing SBML, a standard format for encoding computational models in biology and medicine. This article summarizes recent progress and gives perspectives on emerging challenges.
Published: 2020

18. Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass

Author: Philippe Barre, Abraham J. Escobar-Gutiérrez, Elisabeth Veeckman, Klaas Vandepoele, Evelyn Willner, Matthew J. Hegarty, Thomas Keep, Tom Ruttink, Isabel Roldán-Ruiz, Klaus J. Dehmer, Hilde Muylle, Jean-Paul Sampoux, Thomas Ledauphin, José Luis Blanco-Pastor, Stéphanie Manel, Anna M. Roschanski, Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Research Institute for Agricultural, Fisheries and Food (ILVO), Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, Germplasm, SELECTION, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, quantitative genetics, Ecological selection, LEAF-AREA, Climate, adaptation, 01 natural sciences, R PACKAGE, agriculture, 2. Zero hunger, QUANTITATIVE TRAIT LOCI, Ecology, Ecological genetics, Adaptation, Physiological, L, Phenotype, climate change, Biotechnology, FLOWERING TIME, Genotype, Evolution, ecological genetics, Gene prediction, Quantitative trait locus, Biology, 010603 evolutionary biology, 03 medical and health sciences, Behavior and Systematics, Genetics, Lolium, GENOME-WIDE ASSOCIATION, Ecology, Evolution, Behavior and Systematics, LOLIUM-PERENNE, Biology and Life Sciences, landscape genetics, Phenotypic trait, Quantitative genetics, 15. Life on land, Plant Breeding, 030104 developmental biology, 13. Climate action, Evolutionary biology, Genetic Loci, Multivariate Analysis, Adaptation, COLLECTION
Abstract: International audience; Germplasm from perennial ryegrass (Lolium perenne L.) natural populations is useful for breeding because of its adaptation to a wide range of climates. Climate-adaptive genes can be detected from associations between genotype, phenotype and climate but an integrated framework for the analysis of these three sources of information is lacking. We used two approaches to identify adaptive loci in perennial ryegrass and their effect on phenotypic traits. First, we combined Genome-Environment Association (GEA) and GWAS analyses. Then, we implemented a new test based on a Canonical Correlation Analysis (CANCOR) to detect adaptive loci. Furthermore, we improved the previous perennial ryegrass gene set by de novo gene prediction and functional annotation of 39,967 genes. GEA-GWAS revealed eight outlier loci associated with both environmental variables and phenotypic traits. CANCOR retrieved 633 outlier loci associated with two climatic gradients, characterized by cold-dry winter versus mild-wet winter and long rainy season versus long summer, and pointed out traits putatively conferring adaptation at the extremes of these gradients. Our CANCOR test also revealed the presence of both polygenic and oligogenic climatic adaptations. Our gene annotation revealed that 374 of the CANCOR outlier loci were positioned within or close to a gene. Co-association networks of outlier loci revealed a potential utility of CANCOR for investigating the interaction of genes involved in polygenic adaptations. The CANCOR test provides an integrated framework to analyse adaptive genomic diversity and phenotypic responses to environmental selection pressures that could be used to facilitate the adaptation of plant species to climate change.
Published: 2020

19. Gene banks for wild and cultivated sunflower genetic resources☆

Author: M. Sujatha, Sini sa Jocić, Loren H. Rieseberg, Stéphane Muños, Gerald J. Seiler, Daniel Alvarez, Marie-Claude Boniface, Brent S. Hulke, Sreten Terzić, Leonardo Velasco, Vera Gavrilova, Karin Baumann, Maria Joita-Pacureanu, Daniela Valkova, Laura Marek, Nicolas B. Langlade, Felicity Vear, University of Novi Sad, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Iowa State University (ISU), United States Department of Agriculture (USDA), Instituto Nacional de Tecnología Agropecuaria (INTA), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), N.I. Vavilov Research Institute of Plant Industry (VIR (BИP)), National Agricultural Research and Development Institute (NARDI), Indian Council of Agricultural Research (ICAR), Dobroudja Agricultural Institute (DAI), Instituto de Agricultura Sostenible - Institute for Sustainable Agriculture (IAS CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), University of British Columbia (UBC), and USDA Agricultural Research Service [Maricopa, AZ] (USDA)
Subjects: 0106 biological sciences, 0301 basic medicine, Germplasm, sunflower, lcsh:TP670-699, lignées, 01 natural sciences, Biochemistry, Open pollination, Crop, 03 medical and health sciences, Inbred strain, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Helianthus annuus, cultivated, wild, Helianthus, perennial, 2. Zero hunger, biology, Ecotype, populations à pollinisation libre, food and beverages, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Helianthus annuus L, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, accessions, biology.organism_classification, Sunflower, tournesol, genetic resources, 030104 developmental biology, Agronomy, inbred lines, variétés, breeding, open pollinated varieties, annual, gene banks, lcsh:Oils, fats, and waxes, écotypes, Agronomy and Crop Science, 010606 plant biology & botany, Food Science
Abstract: Modern breeding of sunflower (Helianthus annuus L.), which started 100 years ago, increased the number and the diversity of cultivated forms. In addition, for more than 50 years, wild sunflower and other Helianthus species have been collected in North America where they all originated. Collections of both cultivated and wild forms are maintained in gene banks in many countries where sunflower is an important crop, with some specificity according to the availability of germplasm and to local research and breeding programmes. Cultivated material includes land races, open pollinated varieties, synthetics and inbred lines. The majority of wild accessions are ecotypes of wild Helianthus annuus, but also 52 other species of Helianthus and a few related genera. The activities of three gene banks, in USA, France and Serbia, are described in detail, supplemented by data from seven other countries. Past and future uses of the genetic resources for environmental adaptation and breeding are discussed in relation to genomic and improved phenotypic knowledge of the cultivated and wild accessions available in the gene banks. L’amélioration moderne du tournesol (Helianthus annuus L.) a débuté il y a un siècle, diversifiant et augmentant le nombre des formes cultivées du tournesol. De plus, des collectes de tournesols sauvages et d’espèces du genre Helianthus ont lieu depuis 50 ans en Amérique du Nord d’où ils sont tous originaires. Ainsi, des collections de tournesols cultivés et sauvages sont conservées par des centres de ressources génétiques dans de nombreux pays où le tournesol est une culture importante. Chacun d’eux présente des spécificités par rapport aux ressources génétiques maintenues, en fonction des programmes de recherche ou de sélection variétale locales. Le matériel génétique cultivé comprend des écotypes, des populations et des lignées tandis que les accessions sauvages correspondent eux écotypes d’Helianthus annuus sauvages et des 52 autres espèces apparentées du genre Helianthus. Les activités de trois centres de ressources génétiques des États-Unis, de la France et de la Serbie sont décrites en détail, complétées par des données provenant des centres de sept autres pays. L’historique de l’utilisation des ressources génétiques et les perspectives futures pour l’adaptation des variétés à l’environnement sont discutés ainsi que leur caractérisation au niveau génomique et phénotypique. The Supplementary Material is available at [https://www.ocljournal.org/10.1051/ocl/2020004/olm].
Published: 2020

20. Absolute Configuration of Mycosporine-Like Amino Acids, Their Wound Healing Properties and In Vitro Anti-Aging Effects

Author: Maria Orfanoudaki, Anja Hartmann, Mostafa Alilou, Thomas Gelbrich, Patricia Planchenault, Séverine Derbré, Andreas Schinkovitz, Pascal Richomme, Andreas Hensel, Markus Ganzera, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Substances d'Origine Naturelle et Analogues Structuraux (SONAS), and Université d'Angers (UA)
Subjects: Glycation End Products, Advanced, Circular Dichroism, anti-aging, stereochemistry, wound healing, In Vitro Techniques, mycosporine-like amino acids, Article, Skin Aging, lcsh:Biology (General), X-Ray Diffraction, Humans, [CHIM]Chemical Sciences, ECD, Collagenases, Amino Acids, [CHIM.OTHE]Chemical Sciences/Other, lcsh:QH301-705.5, X-ray crystallography
Abstract: Mycosporine-like amino acids (MAAs) are water-soluble metabolites, reported to exhibit strong UV-absorbing properties. They have been found in a wide range of marine organisms, especially those that are exposed to extreme levels of sunlight, to protect them against solar radiation. In the present study, the absolute configuration of 14 mycosporine-like-amino acids was determined by combining the results of electronic circular dichroism (ECD) experiments and that of advanced Marfey&rsquo, s method using LC-MS. The crystal structure of a shinorine hydrate was determined from single crystal X-ray diffraction data and its absolute configuration was established from anomalous-dispersion effects. Furthermore, the anti-aging and wound-healing properties of these metabolites were evaluated in three different assays namely the inhibition of collagenase, inhibition of advanced glycation end products (AGEs) and wound healing assay (scratch assay).
Published: 2019
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21. Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops

Author: Evangelia V. Avramidou, Stéphane Maury, Philippe Gallusci, Efi Sarri, Federico Martinelli, Eleni M. Abraham, Maria Gerakari, Eleni Tani, Na'ama Segal, Chiara Vergata, Mateo Gašparović, Valya Vassileva, Pilar S. Testillano, Glória Pinto, Eirini Kaiserli, Vasileios Fotopoulos, Miroslav Baránek, Hans Hoenicka, Erna Karalija, Dragana Miladinović, Aliki Kapazoglou, Velimir Mladenov, Manuela Nagel, European Cooperation in Science and Technology, Mladenov, Velimir, Fotopoulos, Vasileios, Kaiserli, Eirini, Karalija, Erna, Maury, Stéphane, Baránek, Miroslav, Segal, Na’ama, Testillano, P. S., Vassileva, Valya, Pinto, Glória, Nagel, Manuela, Hoenicka, Hans, Miladinovic, Dragana, Gallusci, Philippe, Vergata, Chiara, Kapazoglou, Aliki, Abraham, Eleni, Tani, Eleni, Sarri, Efi, Avramidou, Evangelia V., Gašparović, Mateo, Martinelli, Federico, Mladenov, Velimir [0000-0002-2182-6579], Fotopoulos, Vasileios [0000-0003-1205-2070], Kaiserli, Eirini [0000-0003-1517-4591], Karalija, Erna [0000-0001-7262-0645], Maury, Stéphane [0000-0003-0481-0847], Baránek, Miroslav [0000-0002-1583-3588], Segal, Na’ama [0000-0002-4133-6411, Testillano, P. S. [0000-0003-4509-7646], Vassileva, Valya [0000-0002-9055-8002], Pinto, Glória [0000-0001-7735-5131], Nagel, Manuela [0000-0003-0396-0333], Hoenicka, Hans [0000-0001-7226-3772], Miladinovic, Dragana [0000-0001-9555-9162], Gallusci, Philippe [0000-0003-1163-8299], Vergata, Chiara [0000-0003-2727-7977], Kapazoglou, Aliki [0000-0002-7584-5994], Abraham, Eleni [0000-0003-4032-5830], Tani, Eleni [0000-0001-6178-0459], Sarri, Efi [0000-0003-4816-2167], Avramidou, Evangelia V. [0000-0002-5932-1189], Gašparović, Mateo [0000-0003-2345-7882], Martinelli, Federico [0000-0002-8502-767X], University of Novi Sad, Cyprus University of Technology, University of Glasgow, University of Sarajevo, UNIVERZITET U SARAJEVU, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans (UO)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mendel University in Brno (MENDELU), National Center for Mariculture, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Bulgarian Academy of Sciences (BAS), Universidade de Aveiro, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Thünen Institute of Forest Genetics, Institute of Field and Vegetable Crops [Novi Sad], Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Institute for Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organisation 'DEMETER', Aristotle University of Thessaloniki, Agricultural University of Athens, and University of Zagreb
Subjects: Epigenomics, 0106 biological sciences, 0301 basic medicine, Acclimatization, Inheritance Patterns, Review, 01 natural sciences, Epigenesis, Genetic, Biotic stress, Gene Expression Regulation, Plant, Biology (General), Stress memory, Spectroscopy, 2. Zero hunger, Agricultural Sciences, Epigenetic, food and beverages, General Medicine, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Adaptation, Physiological, Computer Science Applications, Chemistry, Identification (biology), abiotic stress, biotic stress, epigenetic, methodology, stress memory, transgenerational memory, Crops, Agricultural, QH301-705.5, Biology, Catalysis, Inorganic Chemistry, 03 medical and health sciences, Transgenerational epigenetics, Stress, Physiological, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Epigenetics, Physical and Theoretical Chemistry, QD1-999, Molecular Biology, Abiotic stress, fungi, Organic Chemistry, Methodology, Agriculture Forestry and Fisheries, Transgenerational memory, DNA Methylation, Plant Breeding, 030104 developmental biology, 13. Climate action, Evolutionary biology, Alphabet, Adaptation, 010606 plant biology & botany
Abstract: 20 p.-3 fig., Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics, This finalization of the review was funded by COST Action CA19125—EPIgenetic mechanisms of Crop Adaptation to Climate cHange.
Published: 2021

22. A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan

Author: Robert Larocque, Jan-Hendrik Hehemann, Gurvan Michel, Marcus Bäumgen, Dörte Becher, Aurélie Préchoux, Mihovilovic, Thomas Schweder, Stephanie Markert, Thomas Roret, Uwe T. Bornscheuer, Christian Stanetty, Frank Unfried, Lukas Reisky, Tao Song, N. Gerlach, Marie-Katherin Zühlke, Craig S. Robb, Anke Trautwein-Schult, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Universität Greifswald - University of Greifswald, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Max Planck Institute for Marine Microbiology, and Max-Planck-Gesellschaft
Subjects: Models, Molecular, Protein Conformation, [SDV]Life Sciences [q-bio], Biomass, Polysaccharide, Algal bloom, Gene Expression Regulation, Enzymologic, 03 medical and health sciences, Bacterial Proteins, Algae, Polysaccharides, Botany, [CHIM.CRIS]Chemical Sciences/Cristallography, Glycoside hydrolase, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, Chemistry, fungi, 030302 biochemistry & molecular biology, food and beverages, Gene Expression Regulation, Bacterial, Genomics, Cell Biology, biology.organism_classification, Metabolic pathway, Carbohydrate Metabolism, Fermentation, Sulfatases, Flavobacteriaceae, Genome, Bacterial, Flavobacterium
Abstract: Marine seaweeds increasingly grow into extensive algal blooms, which are detrimental to coastal ecosystems, tourism and aquaculture. However, algal biomass is also emerging as a sustainable raw material for the bioeconomy. The potential exploitation of algae is hindered by our limited knowledge of the microbial pathways-and hence the distinct biochemical functions of the enzymes involved-that convert algal polysaccharides into oligo- and monosaccharides. Understanding these processes would be essential, however, for applications such as the fermentation of algal biomass into bioethanol or other value-added compounds. Here, we describe the metabolic pathway that enables the marine flavobacterium Formosa agariphila to degrade ulvan, the main cell wall polysaccharide of bloom-forming Ulva species. The pathway involves 12 biochemically characterized carbohydrate-active enzymes, including two polysaccharide lyases, three sulfatases and seven glycoside hydrolases that sequentially break down ulvan into fermentable monosaccharides. This way, the enzymes turn a previously unexploited renewable into a valuable and ecologically sustainable bioresource.
Published: 2019

23. A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate

Author: Ranjan Swarup, Meredith T. Hanlon, Darren M. Wells, Bipin K. Pandey, Anja Hartmann, Richard Traini, Ute Voß, Jeonga Yun, Nicola Leftley, Kamal Swarup, Kathleen M. Brown, Malcolm J. Bennett, Nicolaus von Wirén, Jonathan P. Lynch, Teva Vernoux, Anna Stepanova, Ricardo Fabiano Hettwer Giehl, Jose M. Alonso, Anthony Bishopp, Liam Dolan, Jekaterina Truskina, Rahul Bhosale, Karin Ljung, Jitender Giri, Afaf Rashed, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre for Plant Integrative Biology, University of Nottingham, UK (UON), Department of Genetics, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Umea Plant Science Center, Swedish University of Agricultural Sciences (SLU)-Department of Forest Genetics and Plant Physiology, Department of Plant Science, Pennsylvania State University (Penn State), Penn State System-Penn State System, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Umea Plant Science Center (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Biotechnology and Biological Sciences Research Council BB/G023972/1 BB/R013748/1 BB/L026848/1 BB/M018431/1 BB/PO16855/1 BB/M001806/1 BB/P010520/1, European Research Council FUTUREROOTS Advanced Investigator grant 294729, Leverhulme Trust RPG-2016-409, Royal SocietyWM130021 NA140281, Newton International Fellowship NF140287, British Council Newton Bhabha 228144076, University of Nottingham Future Food Beacon of Excellence Nottingham Research and PhD+ fellowship schemes, Interuniversity Attraction Poles Program, Belgian Science Policy Office P7/29, Swedish Governmental Agency for Innovation Systems (VINNOVA), Swedish Research Council (V.R.), University of Nottingham, Institut National de la Recherche Agronomique (INRA), and NSF-MCB1158181
Subjects: 0106 biological sciences, 0301 basic medicine, Science, Mutant, General Physics and Astronomy, Organogenesis, Root hair, Root hair elongation, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Auxin, Arabidopsis, heterocyclic compounds, lcsh:Science, Transcription factor, ComputingMilieux_MISCELLANEOUS, phosphate, chemistry.chemical_classification, Multidisciplinary, biology, integumentary system, auxine, plasticité, Lateral root, fungi, food and beverages, General Chemistry, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, croissance cellulaire, Cell biology, racine, arabidopsis, 030104 developmental biology, chemistry, plante, lcsh:Q, 010606 plant biology & botany
Abstract: Phosphate (P) is an essential macronutrient for plant growth. Roots employ adaptive mechanisms to forage for P in soil. Root hair elongation is particularly important since P is immobile. Here we report that auxin plays a critical role promoting root hair growth in Arabidopsis in response to low external P. Mutants disrupting auxin synthesis (taa1) and transport (aux1) attenuate the low P root hair response. Conversely, targeting AUX1 expression in lateral root cap and epidermal cells rescues this low P response in aux1. Hence auxin transport from the root apex to differentiation zone promotes auxin-dependent hair response to low P. Low external P results in induction of root hair expressed auxin-inducible transcription factors ARF19, RSL2, and RSL4. Mutants lacking these genes disrupt the low P root hair response. We conclude auxin synthesis, transport and response pathway components play critical roles regulating this low P root adaptive response.
Published: 2018

24. Developmental programmed cell death during asymmetric microsporogenesis in holocentric species of Rhynchospora (Cyperaceae)

Author: Danilo M. Rocha, Andrea Pedrosa-Harand, Jeffrey L. Bennetzen, André Luís Laforga Vanzela, Srinivasa R. Chaluvadi, Andreas Houben, Romain Guyot, Célia Guadalupe Tardeli de Jesus Andrade, André Marques, State University of Londrina = Universidade Estadual de Londrina, Federal University of Pernambuco [Recife], UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), University of Georgia [USA], Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), and Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
Subjects: 0106 biological sciences, 0301 basic medicine, mitotic disorder, Programmed cell death, Cytoplasm, Cell division, Physiology, Cell, Plant Science, Biology, Asymetric cell plate, 01 natural sciences, 03 medical and health sciences, Meiosis, Asymmetric cell plate, holocentromeres, Botany, medicine, Mitosis, Vacuolar cell death, [SDV.BDD.GAM]Life Sciences [q-bio]/Development Biology/Gametogenesis, Cytoskeleton, In Situ Hybridization, Gametogenesis, Plant, electron microscopy, Cell Death, vacuolar cell death, fungi, pollen development, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, meiotic drive, Cell biology, Microscopy, Electron, 030104 developmental biology, medicine.anatomical_structure, Holocentric, DNA fragmentation, Cyperaceae, Cell Division, 010606 plant biology & botany, Research Paper
Abstract: Highlight The functional cell of an asymmetric tetrad is selected according to its replication capability, while degenerative cells progress to multistep PCD, including mitotic disorder and DNA elimination., Members of the Cyperaceae family exhibit an asymmetric microsporogenesis that results in the degeneration of three out of four meiotic products. Efforts have been made previously to describe the resulting structure, named the pseudomonad, but mechanisms concerning the establishment of cell domains, nuclear development, and programmed cell death are largely unknown. Using the Rhynchospora genus as a model, evidence for cell asymmetry, cytoplasmic isolation, and programmed cell death was obtained by a combination of electron microscopic, cytochemical, immunocytochemical, in situ hybridization, and flow cytometric methods. Degenerative cells were identified at the abaxial region, with the cytoskeleton marking their delimitation from the functional domain after meiosis. After attempting to initiate cell division with an unreplicated genome and abnormal spindle assembly, these cells exhibited a gradual process of cytoplasmic contraction associated with hypermethylation of cytosines and differential loss of DNA. These results indicate that the asymmetric tetrad establishes a functional cell, where one nucleus is preferentially selected to survive. Degenerative haploid cells are then eliminated in a multistep process associated with mitotic disorder, non-random elimination of repetitive DNA, vacuolar cell death, and DNA fragmentation.
Published: 2016

25. BrAPI-an application programming interface for plant breeding applications

Author: Guilhem Sempere, Patrick König, Bruno Costa, Jan Erik Backlund, Jack Elendil B. Lagare, Viana C. Calaminos, Jeremy D. Edwards, Gordon Stephen, Omar Eduardo Benites-Alfaro, Pierre Carceller, Martin Basterrechea Salido, David LeBauer, Maikel P. H. Verouden, Guillaume Cornut, Nicolas Morales, Philip Glaser, David Marshall, Evangelia Papoutsoglou, Cyril Pommier, Guillaume Bauchet, Valentin Guignon, Kelly R. Robbins, Iain Milne, David A. Lyon, Pascal Neveu, Brian Pearce, Chaitanya Sarma, Qi Sun, Nahuel Soldevilla, Sebastian Raubach, Peter Selby, Clarysabel Tovar, Grzegorz Uszynski, Rafael Abbeloos, Reinhard Simon, Paul Shaw, Marie-Angélique Laporte, Mathieu Rouard, Star Yanxin Gao, Naymesh Mistry, Puthick Hok, Uwe Scholz, Trevor W. Rife, Ricardo H. Ramirez-Gonzalez, Dave Matthews, Mehmood Ghaffar, Pierre Larmande, Matthias Lange, Andrzej Kilian, Clayton Birkett, Ivan Perez-Masias, Angel Manica Raquel, Abhishek Rathore, Lukas A. Mueller, Richard Finkers, Wren, Jonathan, Flanders Institute for Biotechnology, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Boyce Thompson Institute [Ithaca], International Potato Center, USDA-ARS : Agricultural Research Service, International Rice Research Institute [Philippines] (IRRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Instituto de Biologia Experimental e Tecnológica (IBET), Wageningen University and Research Centre (WUR), Cornell University [New York], CGIAR, Diversity Arrays Technology Pty Ltd (DArT P/L), Institut de Recherche pour le Développement (IRD), University of Arizona, The James Hutton Institute, LeafNode Technology, Partenaires INRAE, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), International Crops Research Institute for the Semi-Arid Tropics [Inde] (ICRISAT), Kansas State University, Leafnode Technolog, Biometris, Gates Foundation, Bioversity International, Federal Ministry of Education & Research (BMBF) : FKZ 031A536A, 031B0190A, Boyce Thompson Institute for Plant Research CGIAR Research Program on Roots, Tubers and Bananas, Cornell University Excellence in Breeding Platform, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and John Innes Centre
Subjects: 0106 biological sciences, Germplasm, programme informatique, Computer science, [SDV]Life Sciences [q-bio], Data management, computer.software_genre, 01 natural sciences, Biochemistry, F30 - Génétique et amélioration des plantes, User-Computer Interface, Software, Laboratorium voor Plantenveredeling, [MATH]Mathematics [math], 0303 health sciences, Application programming interface, U10 - Informatique, mathématiques et statistiques, Genomics, Original Papers, Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, Web service, sélection végétale, Statistics and Probability, Technology and Engineering, Databases and Ontologies, génomique, 03 medical and health sciences, Bioinformatique, application informatique, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Life Science, [INFO]Computer Science [cs], Plant breeding, Genotyping, Molecular Biology, 030304 developmental biology, business.industry, Biology and Life Sciences, Amélioration des plantes, Data science, Plant Breeding, business, computer, 010606 plant biology & botany
Abstract: Motivation Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. Results To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases. Availability and implementation More information on BrAPI, including links to the specification, test suites, BrAPPs, and sample implementations is available at https://brapi.org/. The BrAPI specification and the developer tools are provided as free and open source.
Published: 2018

26. Novel loci and a role for nitric oxide for seed dormancy and preharvest sprouting in barley

Author: Ahmad M. Alqudah, Marlène Bailly, Loïc Rajjou, Manuela Nagel, Gabriele Matzig, Ilse Kranner, Andreas Börner, Sibylle Pistrick, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), and University of Innsbruck
Subjects: 0106 biological sciences, 0301 basic medicine, hordeum vulgare, Physiology, [SDV]Life Sciences [q-bio], Germination, Plant Science, Biology, Genes, Plant, Nitric Oxide, 01 natural sciences, 03 medical and health sciences, Anthesis, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, 2. Zero hunger, after-ripening, Arabidopsis Proteins, Seed dormancy, food and beverages, Hordeum, Plant Dormancy, Horticulture, 030104 developmental biology, Dormancy, Preharvest, Gibberellin, Hordeum vulgare, 010606 plant biology & botany, Sprouting, Genome-Wide Association Study
Abstract: International audience; Barley is used for food and feed, and brewing. Nondormant seeds are required for malting, but the lack of dormancy can lead to preharvest sprouting (PHS), which is also undesired. Here, we report several new loci that modulate barley seed dormancy and PHS. Using genome-wide association mapping of 184 spring barley genotypes, we identified four new, highly significant associations on chromosomes 1H, 3H, and 5H previously not associated with barley seed dormancy or PHS. A total of 71 responsible genes were found mostly related to flowering time and hormone signalling. A homolog of the well-known Arabidopsis Delay of Germination 1 (DOG1) gene was annotated on the barley chromosome 3H. Unexpectedly, DOG1 appears to play only a minor role in barley seed dormancy. However, the gibberellin oxidase gene HvGA20ox1 contributed to dormancy alleviation, and another seven important loci changed significantly during after-ripening. Furthermore, nitric oxide release correlated negatively with dormancy and shared 27 associations. Origin and growth environment affected seed dormancy and PHS more than did agronomic traits. Days to anthesis and maturity were shorter when seeds were produced under drier conditions, seeds were less dormant, and PHS increased, with a heritability of 0.57-0.80. The results are expected to be useful for crop improvement.
Published: 2018

27. Immersive Analytics: An Introduction

Author: Tim Dwyer, Wolfgang Stuerzlinger, Karsten Klein, Kim Marriott, Bruce H. Thomas, Tobias Isenberg, Nathalie Henry Riche, Falk Schreiber, Monash University [Clayton], Analysis and Visualization (AVIZ), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), The University of Sydney, Microsoft Research [Redmond], Microsoft Corporation [Redmond, Wash.], Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Department of Computer Science and Engineering [York], York University [Toronto], Centre Européen de Réalité Virtuelle (CERV), École Nationale d'Ingénieurs de Brest (ENIB), Dwyer, Tim, Marriott, Kim, Isenberg, Tobias, Klein, Karsten, Riche, Nathalie, Schreiber, Falk, Stuerzlinger, Wolfgang, Thomas, Bruce H., and University of South Australia [Adelaide]
Subjects: Computer science, 05 social sciences, ComputingMilieux_PERSONALCOMPUTING, [SCCO.COMP]Cognitive science/Computer science, Multi-sensory, 020207 software engineering, 02 engineering and technology, Research initiative, Data science, Immersive analytics, Multi sensory, Data analytics, 2D and 3D, ComputerApplications_MISCELLANEOUS, 0202 electrical engineering, electronic engineering, information engineering, 0501 psychology and cognitive sciences, Decision making, 050107 human factors, ComputingMethodologies_COMPUTERGRAPHICS
Abstract: International audience; Immersive Analytics is a new research initiative that aims to remove barriers between people, their data and the tools they use for analysis and decision making. Here we clarify the aims of immersive analytics research, its opportunities and historical context, as well as providing a broad research agenda for the field. In addition, we review how the term immersion has been used to refer to both technological and psychological immersion, both of which are central to immersive analytics research.
Published: 2018

28. The transcriptional landscape of polyploid wheat

Author: Christopher J. Ridout, Henk-jan Schoonbeek, F. van Ex, Caroline Juery, Jemima Brinton, Yogendra Khedikar, Brande B. H. Wulff, Mark W. Davey, Andrew G. Sharpe, Aron T. Cory, Nicholas J. Provart, Burkhard Steuernagel, Daniel Lang, Asher Pasha, Cristobal Uauy, David Latrasse, Daoquan Xiang, Luca Venturini, Andrea Bräutigam, Ricardo H. Ramirez-Gonzalez, Manuel Spannagl, Sophie A. Harrington, Raju Datla, Lorenzo Concia, Abdelhafid Bendahmane, Moussa Benhamed, Rudi Appels, Vijay K. Tiwari, Curtis J. Pozniak, Tobin Florio, Klaus F. X. Mayer, Stephen J. Robinson, Boulos Chalhoub, Etienne Paux, John Jacobs, Frédéric Choulet, Philippa Borrill, John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), Plant Genome and Systems Biology, Helmholtz Diabetes Center at Helmholtz Zentrum, Earlham Institute, Norwich Research Park, Innovation Center®, Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Saskatoon Research and Development Centre, Agriculture and Agri-Food (AAFC), University of Saskatchewan [Saskatoon] (U of S), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Aquatic and Crop Resource Development, National Research Council of Canada (NRC), Institut National de la Recherche Agronomique (INRA), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), School of Biosciences, University of Birmingham [Birmingham], AgriBio, School of Veterinary and Life Sciences, Murdoch University, University of Maryland [College Park], University of Maryland System, Global Institute for Food Security, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Agriculture and Agri-Food [Ottawa] (AAFC), and University of Saskatchewan
Subjects: 0106 biological sciences, 0301 basic medicine, Candidate gene, Transcription, Genetic, 01 natural sciences, Genome, Polyploidy, 03 medical and health sciences, Polyploid, Gene Expression Regulation, Plant, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, Triticum, 2. Zero hunger, Regulation of gene expression, Multidisciplinary, Sequence Analysis, RNA, Gene Expression Profiling, Gene Expression Regulation, Developmental, food and beverages, Bread, Phenotype, Gene expression profiling, 030104 developmental biology, Evolutionary biology, RNA, Plant, Subfunctionalization, Genome, Plant, 010606 plant biology & botany
Abstract: Insights from the annotated wheat genome Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Examples of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat.; International audience; The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes of many of the world's major crops. Here we combine extensive gene expression datasets to produce a comprehensive, genome-wide analysis of homoeolog expression patterns in hexaploid bread wheat. Bias in homoeolog expression varies between tissues, with ~30% of wheat homoeologs showing nonbalanced expression. We found expression asymmetries along wheat chromosomes, with homoeologs showing the largest inter-tissue, inter-cultivar, and coding sequence variation, most often located in high-recombination distal ends of chromosomes. These transcriptionally dynamic genes potentially represent the first steps toward neo- or subfunctionalization of wheat homoeologs. Coexpression networks reveal extensive coordination of homoeologs throughout development and, alongside a detailed expression atlas, provide a framework to target candidate genes underpinning agronomic traits in wheat.nonbalanced expression patterns, with higher or lower expression from a single homoeolog with respect to the other two. These differences between homoeologs were associated with epigenetic changes affecting DNA methylation and histone modifications. Although nonbalanced homoeolog expression could be partially predicted by expression in diploid ancestors, large changes in relative homoeolog expression were observed owing to polyploidization. Our results suggest that the transposable elements in promoters relate more closely to the variation in the relative expression of homoeologs across tissues than to a ubiquitous effect across all tissues. We found that homoeologs with the highest inter-tissue variation had promoters with more frequent transposable element insertions and more varied cis-regulatory elements than homoeologs that were stable across tissues. We also identified expression asymmetry along wheat chromosomes. Homoeologs with the largest inter-tissue, inter-cultivar, and coding sequence variation were most often located in the highly recombinogenic distal ends of chromosomes. These transcriptionally dynamic homoeologs are under more relaxed selection pressure, potentially representing the first steps toward functional innovation through neo- or subfunctionalization. We generated tissue- and stress-specific coexpression networks that reveal extensive coordination of homoeolog expression throughout development. These networks, alongside detailed gene expression atlases (www.wheat-expression.com and http://bar.utoronto.ca), lay the groundwork to identify candidate genes influencing agronomic traits in wheat. CONCLUSION This study provides detailed insights into the transcriptional landscape of bread wheat, an evolutionarily young polyploid. Our work shows that homoeolog expression patterns in bread wheat have been shaped by polyploidy and are associated with both epigenetic modifications and variation in transposable elements within promoters of homoeologous genes. The extensive datasets and analyses presented here provide a framework that can help researchers and breeders develop strategies to improve crops by manipulating individual or multiple homoeologs to modulate trait responses.
Published: 2018

29. Functions of maize genes encoding pyruvate phosphate dikinase in developing endosperm

Author: Jon D. Stewart, Hardy Rolletschek, Qiaohui Lin, Fabrice Wattebled, Tracie A. Hennen-Bierwagen, Ljudmilla Borisjuk, John Baier, Alan M. Myers, M. Paul Scott, Ryan D. Huffman, Susan K. Boehlein, A. Mark Settles, L. Curtis Hannah, Ryan R. Lappe, Iowa State University (ISU), University of Florida [Gainesville] (UF), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), and Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Pyruvate, Transgene, Orthophosphate Dikinase, maize, 01 natural sciences, Zea mays, Endosperm, 03 medical and health sciences, Pyruvate, phosphate dikinase, Storage protein, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Glycolysis, Energy charge, Gene, Plant Proteins, 2. Zero hunger, chemistry.chemical_classification, Multidisciplinary, Chemistry, fungi, PPDK, food and beverages, Starch, Cell biology, Pyruvate, Orthophosphate Dikinase, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, 030104 developmental biology, PNAS Plus, opaque, Mutation, Phosphoenolpyruvate carboxykinase, Energy Metabolism, metabolism, 010606 plant biology & botany, Transcription Factors
Abstract: Maize opaque2 (o2) mutations are beneficial for endosperm nutritional quality but cause negative pleiotropic effects for reasons that are not fully understood. Direct targets of the bZIP transcriptional regulator encoded by o2 include pdk1 and pdk2 that specify pyruvate phosphate dikinase (PPDK). This enzyme reversibly converts AMP, pyrophosphate, and phosphoenolpyruvate to ATP, orthophosphate, and pyruvate and provides diverse functions in plants. This study addressed PPDK function in maize starchy endosperm where it is highly abundant during grain fill. pdk1 and pdk2 were inactivated individually by transposon insertions, and both genes were simultaneously targeted by endosperm-specific RNAi. pdk2 accounts for the large majority of endosperm PPDK, whereas pdk1 specifies the abundant mesophyll form. The pdk1- mutation is seedling-lethal, indicating that C4 photosynthesis is essential in maize. RNAi expression in transgenic endosperm eliminated detectable PPDK protein and enzyme activity. Transgenic kernels weighed the same on average as nontransgenic siblings, with normal endosperm starch and total N contents, indicating that PPDK is not required for net storage compound synthesis. An opaque phenotype resulted from complete PPDK knockout, including loss of vitreous endosperm character similar to the phenotype conditioned by o2-. Concentrations of multiple glycolytic intermediates were elevated in transgenic endosperm, energy charge was altered, and starch granules were more numerous but smaller on average than normal. The data indicate that PPDK modulates endosperm metabolism, potentially through reversible adjustments to energy charge, and reveal that o2- mutations can affect the opaque phenotype through regulation of PPDK in addition to their previously demonstrated effects on storage protein gene expression.
Published: 2018

30. Using a Full Spectral Raytracer for Calculating Light Microclimate in Functional-Structural Plant Modelling

Author: Gerhard Buck-Sorlin, Michael Henke, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Climate-KIC (Knowledge and Innovation Community), AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)
Subjects: 0106 biological sciences, Computer Networks and Communications, Computer science, GPU, GroIMP, Full spectral raytracing, light modelling, FSPM, GPU, photosynthesis, GroIMP, 01 natural sciences, Spectral line, Full spectral raytracing, Light beam, Representation (mathematics), Absorption (electromagnetic radiation), FSPM, photosynthesis, other areas of Computing and Informatics, 04 agricultural and veterinary sciences, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, light modelling, Transformation (function), Computational Theory and Mathematics, Transmission (telecommunications), Hardware and Architecture, 040103 agronomy & agriculture, Reflection (physics), 0401 agriculture, forestry, and fisheries, Monochromatic color, Biological system, Software, 68-U05, 010606 plant biology & botany
Abstract: International audience; Raytracers that allow the spatially explicit calculation of the fate of light beams in a 3D scene allow the consideration of shading, reected and transmitted light in functional-structural plant models (FSPM). However, the spectrum of visible light also has an e ect on cellular and growth processes. This recently created the interest to extend this modelling paradigm allowing the representation of detailed spectra instead of monochromatic or white light and to extend existing FSPM platforms accordingly. In this study a raytracer is presented which supports the full spectrum of light and which can be used to compute spectra from arbitrary light sources and their transformation at the organ level by absorption,reection and transmission in a virtual canopy. The raytracer was implemented as an extension of the FSPM platform GroIMP.
Published: 2017

31. In-flight photometry extraction of PLATO targets

Author: Juan Cabrera, N. Kutrowski, Martin Pertenais, A. Monsky, Carsten Paproth, Anko Börner, R. Samadi, F. Fialho, A. Santerne, V. Marchiori, Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA (UMR_8109)), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centro de Astrofísica da Universidade do Porto (CAUP), Universidade do Porto, Deutsches Zentrum für Luft- und Raumfahrt [Berlin] (DLR), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), and Institut de Radioprotection et de Sûreté Nucléaire (IRSN)
Subjects: Extrasolare Planeten und Atmosphären, planets and satellites: detection, FOS: Physical sciences, Context (language use), Astrophysics, 01 natural sciences, Asteroseismology, methods: numerical, Photometry (optics), techniques: photometric, Apparent magnitude, Planet, 0103 physical sciences, Instrumentation and Methods for Astrophysics (astro-ph.IM), 010303 astronomy & astrophysics, Institut für Optische Sensorsysteme, Earth and Planetary Astrophysics (astro-ph.EP), Physics, 010308 nuclear & particles physics, zodiacal dust, Astrophysics::Instrumentation and Methods for Astrophysics, Astronomy and Astrophysics, Planetary system, Exoplanet, instrumentation: photometers, Space and Planetary Science, Astrophysics::Earth and Planetary Astrophysics, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], Astrophysics - Instrumentation and Methods for Astrophysics, Circumstellar habitable zone, catalogs, Astrophysics - Earth and Planetary Astrophysics
Abstract: The ESA PLATO space mission is devoted to unveiling and characterizing new extrasolar planets and their host stars. This mission will encompass a very large field of view, granting it the potential to survey up to one million stars depending on the final observation strategy. The telemetry budget of the spacecraft cannot handle transmitting individual images for such a huge stellar sample at the right cadence, so the development of an appropriate strategy to perform on-board data reduction is mandatory. We employ aperture photometry to produce stellar light curves in flight. Our aim is thus to find the mask model that optimizes the scientific performance of the reduced data. We considered three distinct aperture models: binary mask, weighted Gaussian mask, and weighted gradient mask giving lowest noise-to-signal ratio, computed through a novel direct method. An innovative criterion was adopted for choosing between different mask models. We designated as optimal the model providing the best compromise between sensitivity to detect true and false planet transits. We determined the optimal model based on simulated noise-to-signal ratio and frequency of threshold crossing events. Our results show that, although the binary mask statistically presents a few percent higher noise-to-signal ratio compared to weighted masks, both strategies have very similar efficiency in detecting legitimate planet transits. When it comes to avoiding spurious signals from contaminant stars however the binary mask statistically collects considerably less contaminant flux than weighted masks, thereby allowing the former to deliver up to $\sim$30\% less false transit signatures at $7.1\sigma$. Our proposed approach for choosing apertures has been proven to be decisive for the determination of a mask model capable to provide near maximum planet yield and substantially reduced occurrence of false positives., Comment: 20 pages, 22 figures, Astronomy & Astrophysics (accepted)
Published: 2019

32. FSPM-P: towards a general functional-structural plant model for robust and comprehensive model development

Author: Gerhard Buck-Sorlin, Michael Henke, Winfried Kurth, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Mathematisches Institut Georg-August-Universität Göttingen (MATHEMATISCHES INSTITUT GOETTINGEN), Georg-August-University [Göttingen]-Mathematisches Institut-Göttingen, Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)
Subjects: 0106 biological sciences, State variable, General Computer Science, Computer science, Generalization, Process (engineering), Reuse, Machine learning, computer.software_genre, 01 natural sciences, Theoretical Computer Science, Production (economics), 2. Zero hunger, Structure (mathematical logic), business.industry, 04 agricultural and veterinary sciences, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Range (mathematics), Tree (data structure), 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Biochemical engineering, Artificial intelligence, business, computer, 010606 plant biology & botany
Abstract: International audience; In the last decade, functional-structural plant modelling (FSPM) has become a more widely accepted paradigm in crop and tree production, as 3D models for the most important crops have been proposed. Given the wider portfolio of available models, it is now appropriate to enter the next level in FSPM development, by introducing more efficient methods for model development. This includes the consideration of model reuse (by modularisation), combination and comparison, and the enhancement of existing models. To facilitate this process, standards for design and communication need to be defined and established. We present a first step towards an efficient and general, i.e., not speciesspecific FSPM, presently restricted to annual or bi-annual plants, but with the potential for extension and further generalization.Model structure is hierarchical and object-oriented, with plant organs being the base-level objects and plant individual and canopy the higher-level objects. Modules for the majority of physiological processes are incorporated, more than in other platforms that have a similar aim (e.g., photosynthesis, organ formation and growth). Simulation runs with several general parameter sets adopted from the literature show that the present prototypewas able to reproduce a plausible output range for different crops (rapeseed, barley, etc.) in terms of both the dynamics and final values (at harvest time) of model state variables such as assimilate production, organ biomass, leaf area and architecture.
Published: 2016

33. Nitrite–nitric oxide control of mitochondrial respiration at the frontier of anoxia

Author: Ljudmilla Borisjuk, David Macherel, Marie-Hélène Avelange-Macherel, Abdelilah Benamar, H. Ahmed Mostefai, Gilles Curien, Ramaroson Andriantsitohaina, Hardy Rolletschek, Physiologie Moléculaire des Semences (PMS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-Institut National d'Horticulture, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Laboratoire de physiologie cellulaire végétale (LPCV), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Biologie Neurovasculaire Intégrée (BNVI), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Institut für Pflanzengenetik und Kulturpflanzenforschung, Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut National d'Horticulture-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: 0106 biological sciences, Bioenergetics, Nitrite, Cell Respiration, Biophysics, plant, Mitochondrion, bioenergetics, 01 natural sciences, Biochemistry, mathematical analysis, Nitric oxide, 03 medical and health sciences, chemistry.chemical_compound, Oxygen homeostasis, Respiration, Animals, Cytochrome c oxidase, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Nitrites, Pisum sativum, 030304 developmental biology, 0303 health sciences, biology, hypoxia, Electron Spin Resonance Spectroscopy, Peas, anoxia, Cell Biology, Plants, Cell biology, Oxygen, mitochondria, chemistry, germination, Coenzyme Q – cytochrome c reductase, Seeds, Mammalia, biology.protein, Oxidation-Reduction, seed, respiration, 010606 plant biology & botany
Abstract: International audience; Actively respiring animal and plant tissues experience hypoxia because of mitochondrial O(2) consumption. Controlling oxygen balance is a critical issue that involves in mammals hypoxia-inducible factor (HIF) mediated transcriptional regulation, cytochrome oxidase (COX) subunit adjustment and nitric oxide (NO) as a mediator in vasodilatation and oxygen homeostasis. In plants, NO, mainly derived from nitrite, is also an important signalling molecule. We describe here a mechanism by which mitochondrial respiration is adjusted to prevent a tissue to reach anoxia. During pea seed germination, the internal atmosphere was strongly hypoxic due to very active mitochondrial respiration. There was no sign of fermentation, suggesting a down-regulation of O(2) consumption near anoxia. Mitochondria were found to finely regulate their surrounding O(2) level through a nitrite-dependent NO production, which was ascertained using electron paramagnetic resonance (EPR) spin trapping of NO within membranes. At low O(2), nitrite is reduced into NO, likely at complex III, and in turn reversibly inhibits COX, provoking a rise to a higher steady state level of oxygen. Since NO can be re-oxidized into nitrite chemically or by COX, a nitrite-NO pool is maintained, preventing mitochondrial anoxia. Such an evolutionarily conserved mechanism should have an important role for oxygen homeostasis in tissues undergoing hypoxia.
Published: 2008
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34. Identification of Early Nuclear Target Genes of Plastidial Redox Signals that Trigger the Long-Term Response of Arabidopsis to Light Quality Shifts

Author: Christine Gläßer, Klaus F. X. Mayer, Florence Courtois, Thomas Börner, Monique Liebers, Hagen Schlicke, Olaf Czarnecki, Bernhard Grimm, Stefan Hiekel, Lars Dietzel, Yan O. Zubo, Thomas Pfannschmidt, Institut für Allgemeine Botanik und Pflanzenphysiologie, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], InstitutfürMolekulare Biowissenschaften,Pflanzliche Zellphysiologie, Goethe-Universität Frankfurt am Main, Institute of Developmental Genetics [Neuherberg], Helmholtz-Zentrum München (HZM), Zentrum für Molekulare Biologie (ZMBH), Universität Heidelberg [Heidelberg], Laboratoire de physiologie cellulaire végétale (LPCV), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), KWS SAAT SE & Co.KGaA, Humboldt-Universität zu Berlin, Dartmouth College [Hanover], German Research Center for Environmental Health (GmbH), Scientific Computing and Imaging Institute (SCI Institute), University of Utah, Grants from the Deutsche Forschungsgemeinschaft- Deutsche Forschungsgemeinschaft research group FOR 804., Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Friedrich-Schiller-Universität Jena, Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), KWS Saat AG, Humboldt Universität zu Berlin, Helmholtz Zentrum München = German Research Center for Environmental Health, Universität Heidelberg [Heidelberg] = Heidelberg University, Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Humboldt University Of Berlin
Subjects: 0106 biological sciences, Time Factors, Light, Transcription, Genetic, Acclimatization, Arabidopsis, Plant Science, Regulatory Sequences, Nucleic Acid, 01 natural sciences, Gene Expression Regulation, Plant, Arabidopsis thaliana, Plastids, Photosynthesis, Early redox regulated genes, 0303 health sciences, Tetrapyrrole biosynthesis, Mitochondria, Cell biology, Chloroplast, Redox signals, Dibromothymoquinone, Biochemistry, Light acclimation, Oxidation-Reduction, Signal Transduction, Arabidopis thaliana, Nuclear gene, Biology, Bioenergetics, Genes, Plant, Redox, Nucleus, Electron Transport, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, RNA, Messenger, Molecular Biology, 030304 developmental biology, Photosynthetic electron transport chain, Cell Nucleus, Mitochondrial electron transport, Plant, Chromatin Assembly and Disassembly, biology.organism_classification, Electron transport chain, Light intensity, Tetrapyrroles, Mutation, Gene expression, Reactive Oxygen Species, 010606 plant biology & botany
Abstract: Natural illumination conditions are highly variable and because of their sessile life style, plants are forced to acclimate to them at the cellular and molecular level. Changes in light intensity or quality induce changes in the reduction/oxidation (redox) state of the photosynthetic electron chain that acts as a trigger for compensatory acclimation responses comprising functional and structural adjustments of photosynthesis and metabolism. Such responses include redox-controlled changes in plant gene expression in the nucleus and organelles. Here we describe a strategy for the identification of early redox-regulated genes (ERGs) in the nucleus of the model organism Arabidopsis thaliana that respond significantly 30 or 60 min after the generation of a reduction signal in the photosynthetic electron transport chain. By comparing the response of wild-type plants with that of the acclimation mutant stn7, we could specifically identify ERGs. The results reveal a significant impact of chloroplast redox signals on distinct nuclear gene groups including genes for the mitochondrial electron transport chain, tetrapyrrole biosynthesis, carbohydrate metabolism, and signaling lipid synthesis. These expression profiles are clearly different from those observed in response to the reduction of photosynthetic electron transport by high light treatments. Thus, the ERGs identified are unique to redox imbalances in photosynthetic electron transport and were then used for analyzing potential redox-responsive cis-elements, trans-factors, and chromosomal regulatory hot spots. The data identify a novel redox-responsive element and indicate extensive redox control at transcriptional and chromosomal levels that point to an unprecedented impact of redox signals on epigenetic processes.
Published: 2015

35. Bridging landscape genomics and quantitative genetics for a regional adaptation of European grasslands to climate-change

Author: Sampoux, Jean-Paul, Manel, Stéphanie, Hegarty, Matthew J., Dehmer, Klaus J., Willner, Evelin, ProdInra, Migration, Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National de la Recherche Agronomique (INRA), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Aberystwyth University, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), and GrassLandscape
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, ComputingMilieux_MISCELLANEOUS
Abstract: National audience
Published: 2015

36. Plant proteome analysis: A 2004–2006 update

Author: Andrea Matros, Jesús Jorrín, Michel Rossignol, Hans-Peter Mock, Ana M. Maldonado, Jean-Benoît Peltier, Unité de Recherche Protéomique (PROTEOMIQUE), Institut National de la Recherche Agronomique (INRA), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), and University of Córdoba [Córdoba]
Subjects: Proteomics, 0106 biological sciences, Proteome, [SDV]Life Sciences [q-bio], Arabidopsis, Computational biology, 01 natural sciences, Biochemistry, Mass Spectrometry, 03 medical and health sciences, Cell Wall, Stable isotope labeling by amino acids in cell culture, Protein Interaction Mapping, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, Electrophoresis, Gel, Two-Dimensional, Molecular Biology, Plant Proteins, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Oryza sativa, biology, food and beverages, Oryza, 15. Life on land, biology.organism_classification, Plant development, Plant species, Metaproteomics, Protein Processing, Post-Translational, Subcellular Fractions, 010606 plant biology & botany
Abstract: Since the appearance of the review entitled "Plant Proteome Analysis" in Proteomics in February 2004 (Cánovas, F. M., Dumas-Gaudot, E., Recorbert, G., Jorrín, J. et al., Proteomics 2004, 4, 285-298), about 200 original articles focusing on plant proteomics have been published. Although this represents less than 1% of the global proteomics output during this period, it nevertheless reflects an increase in activity over the period 1999-2004. These papers concern the proteome of at least 35 plant species but have concentrated mainly on thale cress (Arabidopsis thaliana) and rice (Oryza sativa). The scientific objectives have ranged from a proteomic analysis of organs, tissues, cell suspensions, or subcellular fractions to the study of plant development and response to various stresses. A number of contributions have covered PTMs and protein interactions. The dominant analytical platform has been 2-DE coupled to MS, but "second generation" techniques such as DIGE, multidimensional protein identification technology, isotope-coded affinity tags, and stable isotope labeling by amino acids in cell culture have begun to make an impact. This review aims to provide an update of the contribution of proteomics to plant biology during the period 2004-2006, and is divided into six sections: introduction, subcellular proteomes, plant development, responses to biotic and abiotic stresses, PTMs, and protein interactions. The conclusions summarize a view of the major pitfalls and challenges of plant proteomics.
Published: 2006

37. bZIP transcription factors in Arabidopsis

Author: Marc Jakoby, Bernd Weisshaar, Wolfgang Dröge-Laser, Jesus Vicente-Carbajosa, Jens Tiedemann, Thomas Kroj, François Parcy, Max Planck Institute for Plant Breeding Research (MPIPZ), Albrecht-von-Haller-Institut, Laboratorio de Bioquimica y Biologia Molecular. Dept Biotecnologia - Centro de Biotecnologia y Genomica de Plantas, ETSIA Universidad Politecnica, Institut für Pflanzengenetik und Kulturpflanzenforschung, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Institut des sciences du végétal (ISV), and Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Arabidopsis, Plant Science, MESH: Basic-Leucine Zipper Transcription Factors, 01 natural sciences, 03 medical and health sciences, Gene Expression Regulation, Plant, MESH: Zinc Fingers, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Arabidopsis, MESH: Gene Expression Regulation, Plant, 030304 developmental biology, Leucine Zippers, 0303 health sciences, MESH: G-Box Binding Factors, food and beverages, Zinc Fingers, MESH: Transcription Factors, MESH: Leucine Zippers, DNA-Binding Proteins, Basic-Leucine Zipper Transcription Factors, G-Box Binding Factors, Multigene Family, MESH: Multigene Family, MESH: DNA-Binding Proteins, Transcription Factors, 010606 plant biology & botany
Abstract: In plants, basic region/leucine zipper motif (bZIP) transcription factors regulate processes including pathogen defence, light and stress signalling, seed maturation and flower development. The Arabidopsis genome sequence contains 75 distinct members of the bZIP family, of which approximately 50 are not described in the literature. Using common domains, the AtbZIP family can be subdivided into ten groups. Here, we review the available data on bZIP functions in the context of subgroup membership and discuss the interacting proteins. This integration is essential for a complete functional characterization of bZIP transcription factors in plants, and to identify functional redundancies among AtbZIP factors.
Published: 2002

38. Genome interplay in the grain transcriptome of hexaploid bread wheat

Author: Pfeifer, Matthias, Kugler, Karl, Sandve, Simen, Zhan, Bujie, Rudi, Heidi, Hvidsten, Torgeir, Mayer, Klaus, Rogers, Jane, Doležel, Jaroslav, Pozniak, Curtis, Eversole, Kellye, Feuillet, Catherine, Gill, Bikram, Friebe, Bernd, Lukaszewski, Adam, Sourdille, Pierre, Endo, Takashi, Kubaláková, Marie, Číhalíková, Jarmila, Dubská, Zdeňka, Vrána, Jan, Šperková, Romana, Šimková, Hana, Febrer, Melanie, Clissold, Leah, Mclay, Kirsten, Singh, Kuldeep, Chhuneja, Parveen, Singh, Nagendra K, Khurana, Jitendra, Akhunov, Eduard, Choulet, Frédéric, Alberti, Adriana, Barbe, Valérie, Wincker, Patrick, Kanamori, Hiroyuki, Kobayashi, Fuminori, Itoh, Takeshi, Matsumoto, Takashi, Sakai, Hiroaki, Tanaka, Tsuyoshi, Wu, Jianzhong, Ogihara, Yasunari, Handa, Hirokazu, Maclachlan, P Ron, Sharpe, Andrew, Klassen, Darrin, Edwards, David, Batley, Jacqueline, Olsen, Odd-Arne, Lien, Sigbjørn, Steuernagel, Burkhard, Wulff, Brande, Caccamo, Mario, Ayling, Sarah, Ramirez-Gonzalez, Ricardo H, Clavijo, Bernardo J, Wright, Jonathan, Spannagl, Manuel, Martis, Mihaela M, Mascher, Martin, Chapman, Jarrod, Poland, Jesse A, Scholz, Uwe, Barry, Kerrie, Waugh, Robbie, Rokhsar, Daniel S, Muehlbauer, Gary J, Stein, Nils, Gundlach, Heidrun, Zytnicki, Matthias, Jamilloux, Véronique, Quesneville, Hadi, Wicker, Thomas, Faccioli, Primetta, Colaiacovo, Moreno, Stanca, Antonio Michele, Budak, Hikmet, Cattivelli, Luigi, Glover, Natasha, Pingault, Lise, Paux, Etienne, Sharma, Sapna, Appels, Rudi, Bellgard, Matthew, Chapman, Brett, Nussbaumer, Thomas, Bader, Kai Christian, Rimbert, Hélène, Wang, Shichen, Knox, Ron, Kilian, Andrzej, Alaux, Michael, Alfama, Françoise, Couderc, Loïc, Guilhot, Nicolas, Viseux, Claire, Loaec, Mikael, Keller, Beat, Praud, Sébastien, Plant Genome and Systems Biology, Helmholtz Diabetes Center at Helmholtz Zentrum, Norwegian University of Life Sciences (NMBU), University of Norway, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Norwegian Research Council 199387, Deutsche Forschungsgemeinschaft (DFG) SFB924, German Federal Ministry of Education and Research (BMBF), European Commission's 7th Framework Program, Plant Genome and Systems Biology (PGSB), Helmholtz Zentrum München = German Research Center for Environmental Health, Centre for Integrative Genetics, Department of Chemistry, Biotechnology and Food Science, Eversole Associates, Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), University of Saskatchewan [Saskatoon] (U of S), Bayer Crop Science, Kansas State Univ, Dept Plant Pathol, Manhattan, KS 66506 USA, Partenaires INRAE, Department of Botany and Plant Sciences [Riverside], University of California [Riverside] (UC Riverside), University of California (UC)-University of California (UC), Graduate School of Agriculture, Kyoto University, Kyoto, Japan, Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Centre of the Region Haná for Biotechnological and Agricultural Research, Fraunhofer Institute for Intelligent Analysis and Information Systems (Fraunhofer IAIS), Fraunhofer (Fraunhofer-Gesellschaft), National Research Centre Plant Biotechnology, Dept Plant Pathol, Kansas State University, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Bayer Cropscience, Institute of Crop Sciences of CAAS [Beijing] (ICS CAAS), Chinese Academy of Agricultural Sciences (CAAS), National Institute of Agrobiological Sciences (NIAS), National Institute of Agrobiological Sciences, Natl Inst Agrobiol Sci, JST-CREST, Japan Science and Technology Agency, Global Institute of Food Security, School of Agriculture and Food Sciences, Australian Centre for Plant Functional Genomics, University of Queensland [Brisbane], Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, The Sainsbury Laboratory [Norwich] (TSL), Genome Analysis Centre, John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), European Synchrotron Radiation Facility (ESRF), German Research Center for Environmental Health - Helmholtz Center München (GmbH), MIPS/IBIS, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), DOE Joint Genome Institute [Walnut Creek], United States Department of Energy, The James Hutton Institute, Inst Bioinformat & Syst Biol, Munich Informat Ctr Prot Sequences, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institute of Plant Biology, Universität Zürich [Zürich] = University of Zurich (UZH), Fac Engn & Nat Sci, Sabanci University [Istanbul], Genomics Research Centre, Consiglio per la Ricerca e Sperimentazione in Agricoltura, York University, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Centre for Comparative Genomics, Murdoch University, CUBE Division of Computational Systems Biology, University of Vienna [Vienna], Department of Plant Pathology, Shizuoka University, Diversity Arrays Technology Pty Ltd (DArT P/L), Centre de Recherche de Chappes, BIOGEMMA, Research Council of Norway [199387], German Research Foundation (DFG) [SFB924], German Federal Ministry of Education and Research (BMBF), European Project: 283496,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2011-2,TRANSPLANT(2011), Helmholtz-Zentrum München (HZM), Univ Saskatchewan, Dept Plant Sci, Saskatoon, SK, Canada, University of California [Riverside] (UCR), University of California-University of California, Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, University of Saskatchewan, John Innes Centre, and University of Zurich
Subjects: MESH: Genome, Plant, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, [SDV]Life Sciences [q-bio], Gene Dosage, 01 natural sciences, Genome, MESH: Gene Dosage, Endosperm, Transcriptome, Gene Expression Regulation, Plant, Triticum, Cancer, Plant Proteins, International Wheat Genome Sequencing Consortium, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, MESH: Plant Proteins, food and beverages, alignment, Bread, MESH: Edible Grain, starchy endosperm, reveals, Genome, Plant, Biotechnology, profiles, General Science & Technology, Cereals, MESH: Triticum, Biology, Gene dosage, MESH: Endosperm, Polyploidy, MESH: Bread, 03 medical and health sciences, Polyploid, MESH: Polyploidy, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MD Multidisciplinary, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene family, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Gene Expression Regulation, Plant, Gene, Metabolic and endocrine, 030304 developmental biology, Whole genome sequencing, triticum, MESH: Transcriptome, Human Genome, Plant, Gene Expression Regulation, germination, gene expression, RNA, identification, Edible Grain, protein, 010606 plant biology & botany
Abstract: Allohexaploid bread wheat ( Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type–specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type– and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome.
Published: 2014

39. Void space inside the developing seed of Brassica napus and the modelling of its function

Author: Hardy Rolletschek, Lukas Helfen, Henning Tschiersch, Ljudmilla Borisjuk, Els Herremans, Pieter Verboven, Bart Nicolai, Johannes Fuchs, Quang Tri Ho, BIOSYST - MeBioS, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), and European Synchrotron Radiation Facility (ESRF)
Subjects: 0106 biological sciences, Void (astronomy), Physiology, [SDV]Life Sciences [q-bio], Cell Respiration, chemistry.chemical_element, Plant Science, gas exchange, Biology, Thermal diffusivity, Models, Biological, 01 natural sciences, Oxygen, Diffusion, 03 medical and health sciences, mitochondrial respiration, Botany, Respiration, Plant Oils, Storage protein, Computer Simulation, oxygen diffusivity, Porosity, Water content, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Brassica napus, Reproducibility of Results, food and beverages, X-Ray Microtomography, Hypocotyl, Cell Compartmentation, chemistry, Seeds, Biophysics, Gases, synchrotron X-ray computed tomography, Oxygen sensor, 010606 plant biology & botany
Abstract: International audience; The developing seed essentially relies on external oxygen to fuel aerobic respiration, but it is currently unknown how oxygen diffuses into and within the seed, which structural pathways are used and what finally limits gas exchange. By applying synchrotron X-ray computed tomography to developing oilseed rape seeds we uncovered void spaces, and analysed their three-dimensional assembly. Both the testa and the hypocotyl are well endowed with void space, but in the cotyledons, spaces were small and poorly interconnected. In silico modelling revealed a three orders of magnitude range in oxygen diffusivity from tissue to tissue, and identified major barriers to gas exchange. The oxygen pool stored in the voids is consumed about once per minute. The function of the void space was related to the tissue-specific distribution of storage oils, storage protein and starch, as well as oxygen, water, sugars, amino acids and the level of respiratory activity, analysed using a combination of magnetic resonance imaging, specific oxygen sensors, laser micro-dissection, biochemical and histological methods. We conclude that the size and inter-connectivity of void spaces are major determinants of gas exchange potential, and locally affect the respiratory activity of a developing seed.
Published: 2013

40. La diversité naturelle des graminées fourragères : une ressource génétique à mieux connaître, préserver et valoriser depuis l’échelle locale jusqu’à l’échelle continentale

Author: Sampoux, Jean-Paul, Barre, Philippe, Litrico, Isabelle, Fourtier, Stéphane, Willner, E., Nehrlich, S., Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National de la Recherche Agronomique (INRA), Genebank. Research Group Satellite Collections North, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), and Institute of Plant Genetics and Crop Plant Research (IPK)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, prairie naturelle, spatial distribution, temporary meadow, perennial ryegrass, distribution spatiale, adaptative value, prairie temporaire, ray-grass anglais, valeur adaptative, valeur agronomique, natural meadow, agronomic value, graminée fourragère, lolium pérenne, Agricultural sciences, diversité génétique, campagne de prélèvement, Sciences agricoles, sélection végétale
Abstract: Les graminées fourragères font l’objet de programmes de sélection depuis plusieurs décennies afin d’offrir des semences de haute valeur agronomique pour la création de prairies temporaires. La diversité de ces espèces présente dans les prairies naturelles a fourni le matériel génétique qui a permis d’initier les premiers programmes d’amélioration puis d’enrichir régulièrement les pools de sélection. Pour cela, des campagnes de collecte de diversité naturelle ont été entreprises sur de vastes territoires. Nous montrons que la diversité naturelle des graminées fourragères reste encore une ressource génétique importante, notamment dans l’objectif de répondre à de nouveaux enjeux agro-environnementaux. La distribution spatiale de cette diversité est esquissée à trois échelles géographiques (locale, régionale et continentale) et les modalités de sa collecte sont discutées. L’importance du maintien in situ de cette diversité naturelle est soulignée. Il est montré que les collections des centres de ressources génétiques peuvent fournir un support pour développer des modèles permettant d’évaluer les risques potentiels qui pèsent sur le maintien in situ de la diversité naturelle. Ces différents points sont développés en s’appuyant sur deux études de la diversité du ray-grass anglais, l’une à l’échelle locale, l’autre combinant les échelles régionale et continentale., Forage grasses have been bred for several decades to create high performance cultivars to seed temporary meadows. The natural diversity existing for these species in natural meadows has provided the genetic material to start the first breeding programs and afterwards to reintroduce original diversity in breeding pools. Collection campaigns have hence been carried out to sample the natural diversity of forage grasses over wide territories. We emphasize that the natural diversity of forage grasses is still an important genetic resource, especially to meet agro-environmental goals with breeding.The spatial distribution of this natural diversity is outlined at three spatial scales (local, regional and continental). Methods to sample this diversity are discussed at these three spatial scales. It is emphasized that preservation of diversity in natural conditions is of key importance. It is pointed out that gene bank collections may provide material to set up models for predicting situations in which the natural diversity of forage grasses is endangered. These different issues are exemplified by two studies investigating the distribution of perennial ryegrass diversity, one at local scale and the other one combining regional and continental scales.
Published: 2013

41. Characterisation of yeast microbial fuel cell with the yeast Arxula adeninivorans as the biocatalyst

Author: Keith Baronian, Frédéric Barrière, Nicholas D. Haslett, Gotthard Kunze, Neil Pasco, Frankie J. Rawson, Ravi Gooneratne, Faculty of Agriculture and Life Sciences, Institut des Sciences Chimiques de Rennes (ISCR), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Lincoln Ventures Ltd., School of Biological Sciences, University of Canterbury, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and University of Canterbury [Christchurch]
Subjects: 0106 biological sciences, Microbial fuel cell, Bioelectric Energy Sources, Mediated transfer, Biomedical Engineering, Biophysics, 02 engineering and technology, Biosensing Techniques, 01 natural sciences, Catalysis, Mediator-less transfer, Electron Transport, Electron transfer, 010608 biotechnology, Electrochemistry, Extracellular, biology, Chemistry, Secreted redox molecule, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Substrate (chemistry), General Medicine, 021001 nanoscience & nanotechnology, biology.organism_classification, Yeast, Biochemistry, Arxula adeninivorans, Saccharomycetales, Cyclic voltammetry, 0210 nano-technology, Biotechnology
Abstract: International audience; Yeast microbial fuel cells have received little attention to date. Yeast should be ideal MFC catalyst because they are robust, easily handled, mostly non-pathogenic organisms with high catabolic rates and in some cases a broad substrate spectrum. Here we show that the non-conventional yeast Arxula adeninvorans transfers electrons to an electrode through the secretion of a reduced molecule that is not detectable when washed cells are first resuspended but which accumulates rapidly in the extracellular environment. It is a single molecule that accumulates to a significant concentration. The occurrence of mediatorless electron transfer was first established in a conventional microbial fuel cell and that phenomenon was further investigated by a number of techniques. Cyclic voltammetry (CV) on a yeast pellet shows a single peak at 450mV, a scan rate study showed that the peak was due to a solution species. CVs of the supernatant confirmed a solution species. It appears that, given its other attributes, A. adeninivorans is a good candidate for further investigation as a MFC catalyst.
Published: 2011

42. Structural analysis of metabolic networks based on flux centrality

Author: Jörg Schwender, Dirk Koschützki, Falk Schreiber, Björn H. Junker, Department of Computer and Electrical Engineering, Hochschule Furtwangen University [Furtwangen] (HFU), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Biology Department, and Martin-Luther-Universität Halle Wittenberg (MLU)
Subjects: Statistics and Probability, Biochemical Phenomena, Flux balance analysis, Metabolite, Metabolic network, Biology, Models, Biological, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Network centralities, Escherichia coli, Cluster Analysis, Fluxomics, 030304 developmental biology, 0303 health sciences, General Immunology and Microbiology, Applied Mathematics, General Medicine, Metabolic network modelling, Metabolism, chemistry, Biochemistry, Modeling and Simulation, Weighted network, Network analysis, General Agricultural and Biological Sciences, Centrality, Flux (metabolism), Metabolic Networks and Pathways, 030217 neurology & neurosurgery
Abstract: Metabolic reactions are fundamental to living organisms, and a large number of reactions simultaneously occur at a given time in living cells transforming diverse metabolites into each other. There has been an ongoing debate on how to classify metabolites with respect to their importance for metabolic performance, usually based on the analysis of topological properties of genome scale metabolic networks. However, none of these studies have accounted quantitatively for flux in metabolic networks, thus lacking an important component of a cell's biochemistry. We therefore analyzed a genome scale metabolic network of Escherichia coli by comparing growth under 19 different growth conditions, using flux balance analysis and weighted network centrality investigation. With this novel concept of flux centrality we generated metabolite rankings for each particular growth condition. In contrast to the results of conventional analysis of genome scale metabolic networks, different metabolites were top-ranking dependent on the growth condition. At the same time, several metabolites were consistently among the high ranking ones. Those are associated with pathways that have been described by biochemists as the most central part of metabolism, such as glycolysis, tricarboxylic acid cycle and pentose phosphate pathway. The values for the average path length of the analyzed metabolite networks were between 10.5 and 12.6, supporting recent findings that the metabolic network of E. coli is not a small-world network.
Published: 2010

43. Expression and immunogenicity of the mycobacterial Ag85B/ESAT-6 antigens produced in transgenic plants by elastin-like peptide fusion strategy

Author: Valérie Rodrigues, Udo Conrad, Edwin Garzon, Doreen M. Floss, Claire Chevaleyre, Marie Diogon, Henri Salmon, Mustapha Berri, Damien Brosson, Roger Frutos, Galliano Zanello, Michael Mockey, Timothée Bruel, Laurence Dedieu, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), IPK, Institute of Biochemistry [Kiel], Christian-Albrechts-Universität zu Kiel (CAU), UMR Trypanosomes, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD), Infectiologie Animale et Santé Publique, Institut National de la Recherche Agronomique (INRA), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Infectiologie Animale et Santé Publique (UR IASP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), EU [LSHB-CT-2003-503565], Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA)
Subjects: 0106 biological sciences, Swine, Health, Toxicology and Mutagenesis, lcsh:Medicine, Fusion de gènes, 01 natural sciences, Epitope, F30 - Génétique et amélioration des plantes, Mice, Antigène, Expression des gènes, Hypersensitivity, Delayed, 2. Zero hunger, Mice, Inbred BALB C, Vaccines, Synthetic, 0303 health sciences, Immunogenicity, General Medicine, Flow Cytometry, Plants, Genetically Modified, Antibodies, Bacterial, Extrait d'origine végétale, S50 - Santé humaine, ESAT-6, [SDE]Environmental Sciences, Molecular Medicine, Research Article, Genre humain, Biotechnology, Article Subject, Cell Survival, Vaccin, lcsh:Biotechnology, Recombinant Fusion Proteins, F60 - Physiologie et biochimie végétale, Transgene, Blotting, Western, Enzyme-Linked Immunosorbent Assay, Cell Growth Processes, Biology, Mycobacterium, Mycobacterium tuberculosis, Sciences de l'environnement, Production végétale, 03 medical and health sciences, Immune system, Bacterial Proteins, Antigen, lcsh:TP248.13-248.65, Tobacco, Plante médicinale, Genetics, Animals, Tuberculose, Molecular Biology, 030304 developmental biology, Génie génétique, Antigens, Bacterial, Bovin, Nicotiana tabacum, Immunogénétique, lcsh:R, Plante transgénique, biology.organism_classification, Fusion protein, Virology, Elastin, Plant Leaves, Cattle, Peptides, Spleen, Environmental Sciences, 010606 plant biology & botany
Abstract: International audience; This study explored a novel system combining plant-based production and the elastin-like peptide (ELP) fusion strategy to produce vaccinal antigens against tuberculosis. Transgenic tobacco plants expressing the mycobacterial antigens Ag85B and ESAT-6 fused to ELP (TBAg-ELP) were generated. Purified TBAg-ELP was obtained by the highly efficient, cost-effective, inverse transition cycling (ICT) method and tested in mice. Furthermore, safety and immunogenicity of the crude tobacco leaf extracts were assessed in piglets. Antibodies recognizing mycobacterial antigens were produced in mice and piglets. A T-cell immune response able to recognize the native mycobacterial antigens was detected in mice. These findings showed that the native Ag85B and ESAT-6 mycobacterial B- and T-cell epitopes were conserved in the plant-expressed TBAg-ELP. This study presents the first results of an efficient plant-expression system, relying on the elastin-like peptide fusion strategy, to produce a safe and immunogenic mycobacterial Ag85B-ESAT-6 fusion protein as a potential vaccine candidate against tuberculosis.
Published: 2010

44. Iron dynamics in the rhizosphere as a case study for analyzing interactions between soils, plants and microbes

Author: Stephan M. Kraemer, Philippe Lemanceau, Jean-François Briat, Petra Bauer, Microbiologie du Sol et de l'Environnement (MSE), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Institute for Plant Genetics and Crop Plant Research, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), University of Vienna [Vienna], Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), IPK, Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Microbiologie du Sol et de l'Environnement ( MSE ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ), Biochimie et Physiologie Moléculaire des Plantes ( BPMP ), and Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro )
Subjects: 0106 biological sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Siderophore, media_common.quotation_subject, Microorganism, Soil Science, Siderophores, Plant Science, Biology, Plant health, 01 natural sciences, ron, Competition (biology), Reductases, 03 medical and health sciences, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant nutrition, 030304 developmental biology, media_common, 2. Zero hunger, Mutualism (biology), 0303 health sciences, Rhizosphere, Competition, ACL, Plant physiology, food and beverages, 15. Life on land, Phytosiderophores, 13. Climate action, Soil water, 010606 plant biology & botany
Abstract: International audience; Iron is an essential element for plants and microbes. However, in most cultivated soils, the concentration of iron available for these living organisms is very low because its solubility is controlled by stable hydroxides, oxyhydroxides and oxides. In the rhizosphere, there is a high demand of iron because of the iron uptake by plants, and microorganisms which density and activity are promoted by the release of root exudates. Plants and microbes have evolved active strategies of iron uptake. Iron incorporation by these organisms lead to complex interactions ranging from competition to mutualism. These complex interactions are under the control of physico-chemical properties of the soils in which they occur, and reciprocally iron uptake strategies of plants and microbes impact these soil properties. These iron-mediated nteractions between soils, plants and microbes impact the plant growth and health and their analysis, together with that of the resulting iron dynamics, is of a major agronomic interest. Analysis of the complex interactions soils, plants and microbes represent also a unique opportunity to progress in our knowledge of the rhizosphere ecology. This progression requires merging complementary expertises and study strategies in soil science, plant biology and microbiology. This review provides information on (i) iron status in soil and rhizosphere, iron uptake by plants and microbes, and on (ii) the corresponding study strategies. Finally, illustrations of how integration of these approaches allows gaining knowledge in the complex interactions occurring in the rhizosphere are given.
Published: 2009

45. Mapping and diagnostic marker development for soil-borne cereal mosaic virus resistance in wheat

Author: Perovic, Dragan, Forster, Jutta, Devaux, Pierre, Hariri, Djabbar, Guilleroux, Morgane, Kanyuka, Kostya, Lyons, Rebecca, Weyen, Jens, Feuerhelm, David, Kastirr, Ute, Sourdille, Pierre, Roder, Marion, Ordon, Franck, Institut for resistance research and stress tolerance, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants, BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Centre for Sustainable Pest and Disease Management - Department of Plant Pathology and Microbiology, Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC)-Biotechnology and Biological Sciences Research Council (BBSRC), Institute for Epidemiology and Pathogen Diagnostics, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), AgroParisTech-Institut National de la Recherche Agronomique (INRA), IPK, and Leibniz Institute of Plant Genetics and Crop Plant Research
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, FUROVIRUS, AFLP, CEREAL MOSAIC VIRUS, POLYMYXA GRAMINIS, SOIL-BORNE, RESISTANCE, EXPRESSION GENETIQUE
Abstract: absent
Published: 2008

46. Cereal science and technology for feeding ten billion people: genomics era and beyond

Author: Molina-Cano, J.L., Christou, P., Graner, A., Hammer, K., Jouve, N., Keller, B., Lasa, J.M., Powell, W., Royo, C., Shewry, P., Stanca, A.M., Universitat de Lleida, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), University of Kassel, Universidad de Alcalá - University of Alcalá (UAH), Institute of plant biology, Universität Zürich [Zürich] = University of Zurich (UZH), Spanish National Research Council (CSIC), National Institute of Agricultural Botany (NIAB), Centre UdL-IRTA, Rothamsted Research, and Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA)
Subjects: GENETIC VARIATION, GENE EXPRESSION, STRESS, VARIATION GENETIQUE, PHYSIOLOGIE VEGETALE, QUALITE, PRODUCTION VEGETALE, [SHS]Humanities and Social Sciences, SUSTAINABILITY, MARQUEUR GENETIQUE, QUALITY, BREEDING, CEREALS, GENETIQUE MOLECULAIRE, MOLECULAR GENETICS, AMELIORATION GENETIQUE, PLANT PRODUCTION, BIODIVERSITE, CEREALE, [SDV.SA.AEP]Life Sciences [q-bio]/Agricultural sciences/Agriculture, economy and politics, DURABILITE, EXPRESSION DES GENES, GENOMIQUE, PLANT PHYSIOLOGY, GENETIC MARKERS, GRAINE, BIODIVERSITY, SEEDS, GENOMICS
Abstract: International audience; At the beginning of the 21 st Century, Mankind faces the challenge of feeding a growing population with increasing demande in quantity and quality of food. Land and water resources are limited and threatened by degradation worldwide, and the previsions related to climate change seem to indicate additional incertitude on the future of the global capacity of natural resources to bear the needed production of food. Statistics indicate that it is becoming more and more difficult to increase yields sustainably and that the goal of eliminating hunger is not on the way to being met in the medium term. In this context, Genomics applied to agriculture and more specifically to cereal production has to play an important rote in the effort to balance the world's food supply and demand sustainably by developing varieties that are adapted to the different environmental conditions, make better use of inputs and that can be integrated in environmentally and economically viable agricultural systems. With the boost in advances made in Genomics and Plant Physiology since the last part of 20th century, plant breeding has evolved to a complex science, integrating molecular and cell biology and bioinformatics tools into classical selection methods. We are now in a better position to exploit biodiversity in order to efficiently develop cereal varieties that are able to produce good quality grains in a avide range of environments, under different stresses, and are adapted to different production systems. The Meeting of the Eucarpia Cereal Section in Lieida (Spain) from 13 to 17 November 2006 brought together more than 170 scientiste and technicians dealing with cereal genomics, breeding and production from 28 countries of Europe and ail over the world, to present and diseuse advances in cereal science and technology. The Meeting was structured in eight Scientific Sessions covering the following topics: (i) Biodiversity for useful genes, (ii) Integration of molecular assisted selection into conventional cereal breeding, (iii) Genetic control of limiting factors for cereal production, (iv) New concept of healthy grains for high quality food, (v) Genetics and breeding for sustainable cereal production (vi) New strategies for better understanding Bene expression, (vii) The colloquium between the genome and the metabolome to understand plant growth and development and (viii) Forecasting the future. This publication contains 113 articles and abstracts that were presented in the different scientific sessions of the Meeting.
Published: 2008

47. The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest

Author: Rüdiger Bode, Martin Mascher, Serge Casaregola, Anasua Sarkar, Guilhem Savel, Patrick Wincker, Valérie Barbe, Martin Giersberg, Marina Marcet-Houben, Keith Baronian, Nils Stein, Véronique Leh-Louis, Christine Sacerdot, Guy-Franck Richard, Jan Riechen, Ingrid Lafontaine, Jean Luc Souciet, Urs Hähnel, Eric Westhof, Joseph Schacherer, Uwe Scholz, Sebastian Worch, Sebastian Beier, Pascal Durrens, Erik Böer, Anke Trautwein-Schult, Christian Marck, Toni Gabaldón, Cécile Fairhead, Anja Hartmann, Claire Jubin, Bernard Dujon, Cécile Neuvéglise, Małgorzata Czernicka, Claudine Bleykasten, David James Sherman, Laurence Despons, Marie Laure Straub, Paul P. Jung, Marc Lemaire, Dagmara Jankowska, Tiphaine Martin, Benoit Vacherie, Emmanuel Talla, Agnès Thierry, José Almeida Cruz, André Goffeau, Gotthard Kunze, Claude Gaillardin, Philippe Baret, Guillaume Morel, Przemysław Piotr Gierski, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Yeast Genetics, Leibniz Institute of Plant Research (IPK), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institute of Plant Biology and Biotechnology, University of Agriculture in Krakow, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Models and Algorithms for the Genome ( MAGNOME), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra [Barcelona], Architecture et Réactivité de l'ARN (ARN), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie et de Technologies de Saclay (IBITECS), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université catholique de Louvain, Institut des Sciences de la Vie, Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Earth and Life Institute [Louvain-La-Neuve] (ELI), Université Catholique de Louvain (UCL), School of Biological Sciences, University of Canterbury, Institute of Biochemistry, Universität Greifswald - University of Greifswald, Université de Strasbourg (UNISTRA), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Génétique moléculaire, génomique, microbiologie (GMGM), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire des levures (YMG), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), This work was supported in part by funding from the Consortium National de Recherche en Génomique (CNRG) to Génoscope, from CNRS (GDR 2354, Génolevures), ANR (ANR-05-BLAN-0331, GENARISE). The computing framework was supported by the funding of the University of Bordeaux 1, the Aquitaine Région in the program ' Génotypage et Génomique Comparée ' , the ACI IMPBIO ' Génolevures En Ligne ' and INRIA. We thank the System and Network Administration team in LaBRI for excellent help and advice. J.A.C. is supported by the PhD Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA, and Fundação para a Ciência e Tecnologia, SFRH/BD/33528/2008). M.C. research was supported by a grant of the Deutscher Akademischer Austauschdienst (DAAD). T.G. research was partly supported by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161)., Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona] (UPF), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Université Catholique de Louvain = Catholic University of Louvain (UCL), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Canterbury [Christchurch], International Institute of Molecular and Cell Biology [Warsaw] (IIMCB), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Kunze, Gotthard, Neuvéglise, Cécile, UCL - SST/ELI/ELIA - Agronomy, Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)
Subjects: Yarrowia lipolytica, n-butanol, yeast, genome, tannic acid, metabolism, biotechnology, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Technological development, Butyric acid, Applied Microbiology and Biotechnology, Genome, Blastobotrys, Saccharomycotina, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, N-butanol, 2. Zero hunger, 0303 health sciences, biology, Segmental duplications, Genomics, Phylogenetics, General Energy, Biochemistry, Biotechnology, Nitrogen, Saccharomyces cerevisiae, Biotecnologia agrícola, Computational biology, Management, Monitoring, Policy and Law, Biotechnological potentials, Arxula, Arxula adeninivorans, 03 medical and health sciences, Carbon and nitrogen, 030304 developmental biology, Saccharomycetes, Comparative genomics, Tannic acid, 030306 microbiology, Renewable Energy, Sustainability and the Environment, Protein, Research, Fundamental studies, Yarrowia, Llevats -- Genètica, biology.organism_classification, Yeast, Carbon, Metabolism, Genes, Organic acid
Abstract: Background: The industrially important yeast Blastobotrys (Arxula) adeninivorans is an asexual hemiascomycete phylogenetically very distant from Saccharomyces cerevisiae. Its unusual metabolic flexibility allows it to use a wide range of carbon and nitrogen sources, while being thermotolerant, xerotolerant and osmotolerant./nResults: The sequencing of strain LS3 revealed that the nuclear genome of A. adeninivorans is 11.8 Mb long and consists of four chromosomes with regional centromeres. Its closest sequenced relative is Yarrowia lipolytica, although mean conservation of orthologs is low. With 914 introns within 6116 genes, A. adeninivorans is one of the most intron-rich hemiascomycetes sequenced to date. Several large species-specific families appear to result from multiple rounds of segmental duplications of tandem gene arrays, a novel mechanism not yet described in yeasts. An analysis of the genome and its transcriptome revealed enzymes with biotechnological potential, such as two extracellular tannases (Atan1p and Atan2p) of the tannic-acid catabolic route, and a new pathway for the assimilation of n-butanol via butyric aldehyde and butyric acid. Conclusions: The high-quality genome of this species that diverged early in Saccharomycotina will allow further fundamental studies on comparative genomics, evolution and phylogenetics. Protein components of different pathways for carbon and nitrogen source utilization were identified, which so far has remained unexplored in yeast, offering clues for further biotechnological developments. In the course of identifying alternative microorganisms for biotechnological interest, A. adeninivorans has already proved its strengthened competitiveness as a promising cell factory for many more applications. This work was supported in part by funding from the Consortium National de Recherche en Génomique (CNRG) to Génoscope, from CNRS (GDR 2354, Génolevures), ANR (ANR-05-BLAN-0331, GENARISE). The computing framework was supported by the funding of the University of Bordeaux 1, the Aquitaine Région in the program “Génotypage et Génomique Comparée”, the ACI IMPBIO “Génolevures En Ligne” and INRIA. We thank the System and Network Administration team in LaBRI for excellent help and advice. J.A.C. is supported by the PhD Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA, and Fundação para a Ciência e Tecnologia; SFRH/BD/33528/2008). M.C. research was supported by a grant of the Deutscher Akademischer Austauschdienst (DAAD). T.G. research was partly supported by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161). B.D. is a member of Institut Universitaire de France
Published: 2014

48. High-resolution genetic mapping of the pepper resistancelocus Bs3 governing recognition of the Xanthomonascampestris pv vesicatora AvrBs3 protein

Author: Michèle Pierre, J. Veuskens, Thomas Lahaye, Laurent D. Noël, Ulla Bonas, Martin W. Ganal, Ballvora A, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Institut für Genetik, Martin-Luther-Universität Halle Wittenberg (MLU), and Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben)
Subjects: 0106 biological sciences, Genetics, 0303 health sciences, biology, Positional cloning, Bulked segregant analysis, Xanthomonas campestris pv. Vesicatoria, food and beverages, Locus (genetics), General Medicine, biology.organism_classification, 01 natural sciences, Xanthomonas campestris, 03 medical and health sciences, Gene mapping, Genetic marker, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Amplified fragment length polymorphism, Agronomy and Crop Science, 030304 developmental biology, 010606 plant biology & botany, Biotechnology
Abstract: The pepper (Capsicum annuum) Bs3 gene confers resistance to Xanthomonas campestris pv vesicatoria strains expressing the avirulence protein AvrBs3. Using amplified fragment length polymorphism (AFLP) and bulked DNA templates from resistant and susceptible plants we identified markers linked to Bs3 and defined a 2.1-cM interval containing the target gene. Bs3-linked AFLP fragments were cloned and conformity of isolated PCR products with the desired markers was determined by hybridisation to membrane-bound AFLP reactions. AFLP markers flanking the target gene were converted into locus-specific PCR-based markers. These markers were employed for the analysis of 790 plants segregating for Bs3, resulting in a linkage map with a genetic resolution of 0.13 cM. Mapping of Bs3-linked markers in tomato placed them to a syntenic interval on tomato chromosome 2.
Published: 2000

49. Location and mapping of the powdery mildew resistance gene MIRE and detection of a resistance QTL by bulked segregant analysis (BSA) with microsatellites in wheat

Author: G. Doussinault, Pierre Sourdille, M. Tavaud, Michel Bernard, Marion S. Röder, Nathalie Chantret, UMR 0118 UMR INRA / ENSAR : Génétique et amélioration des plantes, Institut National de la Recherche Agronomique (INRA)-Génétique et amélioration des plantes (G.A.P.)-UMR INRA / ENSAR : Génétique et amélioration des plantes (RENN UMR GENET AMELIOR PLANTES), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, disease resistance, molecular markers, Population, Triticum aestivum, Blumeria graminis, Quantitative trait locus, Biology, Plant disease resistance, 01 natural sciences, 03 medical and health sciences, Genetics, education, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, education.field_of_study, [SDV.GEN]Life Sciences [q-bio]/Genetics, QT mapping, Bulked segregant analysis, food and beverages, General Medicine, GENETIQUE, biology.organism_classification, Genetic marker, Microsatellite, Agronomy and Crop Science, Powdery mildew, 010606 plant biology & botany, Biotechnology, Blumeria graminis f. sp.tritici
Abstract: Powdery mildew (Blumeria graminis f. sp. tritici) is one of the most damaging diseases of wheat (Triticum aestivum). The objective of this study was to locate and map a recently identified powdery mildew resistance gene, MlRE, carried by the resistant line RE714 using microsatellites uniformly distributed among the whole genome together with a bulked segregant analysis (BSA). The bulks consisted of individuals with an extreme phenotype taken from a population of 140 F-3 families issued from the cross between RE714 (resistant) and Hardi (susceptible). The population had been tested with three powdery mildew isolates at the seedling stage. Qualitative interpretation of the resistance tests located the MlRE gene on the distal part of the long arm of chromosome 6A. A subsequent quantitative interpretation of the resistance permitted us to detect another resistance factor on a linkage group assigned to chromosome 5D, which was constructed with microsatellites for which a polymorphism of intensity between bulks was observed. This quantitative trait locus (QTL) explained 16.8-25.34% of the total variation. An interaction between both the resistant factor (MlRE and the QTL) was found for only one of the isolates tested. This study shows the advantage of making a quantitative interpretation of resistant tests and that the use of microsatellites combined with BSA is a powerful strategy to locate resistance genes in wheat.
Published: 2000

50. Genome-wide view of natural antisense transcripts in Arabidopsis thaliana.

Author: Yuan C, Wang J, Harrison AP, Meng X, Chen D, and Chen M
Subjects: DNA Methylation, Gene Regulatory Networks, Histones metabolism, Protein Processing, Post-Translational, RNA, Small Interfering genetics, RNA, Small Interfering metabolism, Arabidopsis genetics, Genome, Plant, RNA, Antisense genetics
Abstract: Natural antisense transcripts (NATs) are endogenous transcripts that can form double-stranded RNA structures. Many protein-coding genes (PCs) and non-protein-coding genes (NPCs) tend to form cis-NATs and trans-NATs, respectively. In this work, we identified 4,080 cis-NATs and 2,491 trans-NATs genome-widely in Arabidopsis. Of these, 5,385 NAT-siRNAs were detected from the small RNA sequencing data. NAT-siRNAs are typically 21nt, and are processed by Dicer-like 1 (DCL1)/DCL2 and RDR6 and function in epigenetically activated situations, or 24nt, suggesting these are processed by DCL3 and RDR2 and function in environment stress. NAT-siRNAs are significantly derived from PC/PC pairs of trans-NATs and NPC/NPC pairs of cis-NATs. Furthermore, NAT pair genes typically have similar pattern of epigenetic status. Cis-NATs tend to be marked by euchromatic modifications, whereas trans-NATs tend to be marked by heterochromatic modifications., (© The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.)
Published: 2015
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