1,425 results on '"génomique"'
Search Results
2. Plankton biogeography in the 21st century and impacts of climate change: advances through genomics.
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Frémont, Paul, Gehlen, Marion, and Jaillon, Olivier
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TWENTY-first century , *BIOGEOGRAPHY , *GREENHOUSE gases , *CLIMATE change , *OCEAN currents - Abstract
This article summarizes recent advances in our knowledge of plankton biogeography obtained by genomic approaches and the impacts of global warming on it. Large-scale comparison of the genomic content of samples of different plankton size fractions revealed a partitioning of the oceans into genomic provinces and the impact of major oceanic currents on them. By defining ecological niches, these provinces are extrapolated to all oceans, with the exception of the Arctic Ocean. By the end of the 21st century, a major restructuring of these provinces is projected in response to a high emission greenhouse gas scenario over 50% of the surface of the studied oceans. Such a restructuring could lead to a decrease in export production by 4%. Finally, obtaining assembled sequences of a large number of plankton genomes defining this biogeography has allowed to better characterize the genomic content of the provinces and to identify the species structuring them. These genomes similarly enabled a better description of potential future changes of plankton communities under climate change. [ABSTRACT FROM AUTHOR]
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- 2023
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3. À propos du document de l’Agence nationale de la recherche Les apports de la génomique à l’agroécologie
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Hainzelin Étienne
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génomique ,agroécologie ,intégration des données ,diversité fonctionnelle ,Science ,Social Sciences - Abstract
Comment les outils de la génomique peuvent-ils concrètement contribuer à la transition agroécologique de la production agricole ? Cette question est traitée au travers de l’analyse d’un corpus des 1 200 projets de recherche dans les différents domaines de la génomique, financés par l’Agence nationale de la recherche (ANR) entre 2005 et 2019. L’analyse débouche sur une proposition de quatre pistes prioritaires pour les recherches futures en génomique pour l’agroécologie.
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- 2022
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4. La domestication des champignons Penicillium du fromage
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Ropars, Jeanne, Caron, Thibault, Lo, Ying-Chu, Bennetot, Bastien, and Giraud, Tatiana
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Domestication ,Fromage ,Champignon ,Penicillium ,Adaptation ,Génomique ,Biology (General) ,QH301-705.5 - Abstract
Domestication is the process of organism evolution under selection by humans, and as such has been a model for studying adaptation since Charles Darwin. Here we review recent studies on the genomics of adaptation and domestication syndrome in two cheese-making fungal lineages, Penicillium roqueforti used for maturing blue cheeses, and the Penicillium camemberti species complex used for making soft cheeses such as Camembert and Brie. Comparative genomics have revealed horizontal gene transfers involved in convergent adaptation to cheese. Population genomics have identified differentiated populations with contrasted traits, several populations having independently been domesticated for cheese making in both P. roqueforti and the Penicillium camemberti species complex, and having undergone bottlenecks. The different cheese populations have acquired traits beneficial for cheese making in comparison to non-cheese populations, regarding color, spore production, growth rates on cheese, salt tolerance, lipolysis, proteolysis, volatile compound or toxin production and/or competitive ability. The cheese populations also show degeneration for some unused functions such as decreased ability of sexual reproduction or of growth under harsh conditions. These recent findings have fundamental importance for our understanding of adaptation and have applied interest for strain improvement.
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- 2020
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5. Les propositions génomiques en oncopédiatrie: bouleversements des temporalités et des repères éthiques -- points de vue des patients, des parents et des professionnels.
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Droin-Mollard, M., Hervouet, L., Lahlou-Laforêt, K., and de Montgolfier, S.
- Abstract
Copyright of Psycho-Oncologie is the property of Tech Science Press and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2021
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6. Polyarthrite et maladie de Huntington.
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Massy, Emmanuel, Roudier, Jean, and Balandraud, Nathalie
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- 2023
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7. Economic potential of adopting genomic technology in Alberta's tree improvement sector.
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Shuo Wang, An, Henry, Wei-Yew Chang, Gaston, Chris, and Thomas, Barb R.
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TREE breeding ,LOGGING ,WHITE spruce ,FORESTS & forestry ,LODGEPOLE pine ,TYPHA latifolia - Abstract
Copyright of Forestry Chronicle is the property of Canadian Institute of Forestry and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2021
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8. Reconstructing 50,000 years of human history from our DNA: lessons from modern genomics.
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Rotival, Maxime, Cossart, Pascale, and Quintana-Murci, Lluis
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NUCLEOTIDE sequencing , *HUMAN genetic variation , *GENETIC drift , *GENOMICS , *FOSSIL DNA - Abstract
The advent of high throughput sequencing approaches and ancient DNA techniques have enabled reconstructing the history of human populations at an unprecedented level of resolution. The symposium from the French Academy of Sciences "50,000 ans d'épopée humaine dans notre ADN" has reviewed some of the latest contributions from the fields of genomics, archaeology, and linguistics to our understanding of >300,000 years of human history. DNA has revealed the richness of the human journey, from the deep divergences between human populations in Africa, to the first encounters of Homo Sapiens with other hominins on their way to Eurasia and the peopling of Remote Oceania. The symposium has also emphasized how migrations, cultural practices, and environmental pathogens have contributed to shape the genetic diversity of modern humans, through admixture, genetic drift or genetic adaptation. Finally, special attention was also given to how human behaviours have shaped the genome of other species, through the spreading of microbes and pathogens, as in the case of Yersinia Pestis, or through domestication, as elegantly demonstrated for dogs, horses, and apples. Altogether, this conference illustrated how the complex history of human populations is tightly linked with their contemporary genetic diversity that, in turn, has direct effects on their identity and health. [ABSTRACT FROM AUTHOR]
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- 2021
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9. Application of genomics and transcriptomics to accelerate development of clubroot resistant canola.
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Zhou, Qinqin, Galindo-González, Leonardo, Hwang, Sheau-Fang, and Strelkov, Stephen E.
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PLASMODIOPHORA brassicae , *GENOME-wide association studies , *CLUBROOT , *CANOLA , *SINGLE nucleotide polymorphisms , *RAPESEED , *GENE expression - Abstract
Clubroot, a soil-borne disease caused by the obligate parasite Plasmodiophora brassicae Woronin, is a threat to canola (Brassica napus L.) production in western Canada. Genetic resistance represents the most effective tool to manage this disease. However, given the rapid spread of clubroot and the emergence of new virulent pathotypes of P. brassicae, it is important to accelerate the resistance breeding effort. The advent of genome-sequencing technologies has created a new toolbox that can aid in breeding strategies. Many genomic approaches, such as genotyping-by-sequencing, high-density single nucleotide polymorphism (SNP) arrays, genome-wide association studies, and transcriptomic approaches such as bulked segregant RNA-seq analysis and microarray/RNA-seq differential expression analysis have been applied to studies of clubroot resistance or susceptibility. Here, we review the impact of traditional marker-assisted selection-based breeding for clubroot resistance, and then discuss how omics approaches have contributed to the (1) detection and genotyping of genome-wide SNP markers linked with clubroot resistance genes or quantitative trait loci, (2) understanding of host resistance mechanisms upon P. brassicae infection, and (3) acceleration of resistance breeding by identifying and characterizing candidate genes, especially those with differential efficacy against new pathotypes of P. brassicae. We suggest that the use of different omics approaches together could improve the efficiency of clubroot-resistance breeding. Finally, we propose that the CRISPR/Cas9 system for genome editing is a promising tool to facilitate the validation and use of candidate genes for clubroot-resistance breeding. [ABSTRACT FROM AUTHOR]
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- 2021
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10. Adaptive Silviculture for Climate Change: From Concepts to Reality Report on a symposium held at Carrefour Forêts 2019.
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Thiffault, Nelson, Raymond, Patricia, Lussier, Jean-Martin, Aubin, Isabelle, Royer-Tardif, Samuel, D'Amato, Anthony W., Doyon, Frédérik, Lafleur, Benoit, Perron, Martin, Bousquet, Jean, Isabel, Nathalie, Carles, Sylvie, Lupien, Patrick, and Malenfant, Annie
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FORESTS & forestry ,FOREST landowners ,CLIMATE change ,NATURAL resources ,FOREST management ,HARDWOOD forests ,ECOSYSTEM management - Abstract
Copyright of Forestry Chronicle is the property of Canadian Institute of Forestry and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2021
- Full Text
- View/download PDF
11. Unraveling the role of non-coding rare variants in epilepsy and its subtypes with deep learning
- Abstract
The discovery of new variants has slowed down in recent years in epilepsy studies, despite the use of very large cohorts. Consequently, most of the heritability is still unexplained. Rare non-coding variants have been largely ignored in studies on epilepsy, although non-coding single nucleotide variants can have a significant impact on gene expression. We had access to whole genome sequencing (WGS) from 247 epilepsy patients and 377 controls. To assess the functional impact of non-coding variants, ExPecto, a deep learning algorithm was used to predict expression change in brain tissues. We compared the burden of rare non-coding deleterious variants between cases and controls. Rare non-coding highly deleterious variants were significantly enriched with Genetic Generalized Epilepsy (GGE), but not with Non-Acquired Focal Epilepsy (NAFE) or all epilepsy cases when compared with controls. In this study, we showed that rare non-coding deleterious variants are associated with epilepsy, specifically with GGE. Larger WGS epilepsy cohort will be needed to investigate those effects at a greater resolution. Nevertheless, we demonstrated the importance of studying non-coding regions in epilepsy, a disease where new discoveries are scarce.
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- 2023
12. Global transcriptome profiling reveals differential regulatory, metabolic and hormonal networks during somatic embryogenesis in Coffea arabica
- Abstract
Background: Somatic embryogenesis (SE) is one of the most promising processes for large-scale dissemination of elite varieties. However, for many plant species, optimizing SE protocols still relies on a trial and error approach. We report the first global scale transcriptome profiling performed at all developmental stages of SE in coffee to unravel the mechanisms that regulate cell fate and totipotency. Results: RNA-seq of 48 samples (12 developmental stages × 4 biological replicates) generated 90 million high quality reads per sample, approximately 74% of which were uniquely mapped to the Arabica genome. First, the statistical analysis of transcript data clearly grouped SE developmental stages into seven important phases (Leaf, Dedifferentiation, Primary callus, Embryogenic callus, Embryogenic cell clusters, Redifferentiation and Embryo) enabling the identification of six key developmental phase switches, which are strategic for the overall biological efficiency of embryo regeneration. Differential gene expression and functional analysis showed that genes encoding transcription factors, stress-related genes, metabolism-related genes and hormone signaling-related genes were significantly enriched. Second, the standard environmental drivers used to control SE, i.e. light, growth regulators and cell density, were clearly perceived at the molecular level at different developmental stages. Third, expression profiles of auxin-related genes, transcription factor-related genes and secondary metabolism-related genes were analyzed during SE. Gene co-expression networks were also inferred. Auxin-related genes were upregulated during dedifferentiation and redifferentiation while transcription factor-related genes were switched on from the embryogenic callus and onward. Secondary metabolism-related genes were switched off during dedifferentiation and switched back on at the onset of redifferentiation. Secondary metabolites and endogenous IAA content were tightly linked with the
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- 2023
13. Les études moléculaires sur le palmier dattier (Phoenix dactylifera L.) : Article de synthèse.
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Hammadi Hamza and Ali Ferchichi
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Palmier dattier ,Moléculaire ,Génomique ,Post-génomique ,Agriculture - Abstract
Le palmier dattier possède certaines caractéristiques qui en font des organismes difficiles à étudier pour la localisation et l’identification des gènes. L’amélioration de la productivité, la qualité du fruit et la résistance aux stress biotiques et abiotiques est le principal objectif des analyses moléculaires chez le palmier dattier. Dans ce papier, nous examinons les progrès considérables dans ce domaine et leur état. On a passé en revue les progrès des études de la génomique chez le palmier dattier afin de fournir une référence utile aux chercheurs travaillant dans ce domaine. Le progrès des techniques moléculaires facilitera les programmes d'amélioration au moyen de la sélection moléculaire
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- 2020
14. Evolutions et perspectives des formations pour la génétique et la sélection animale.
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ROGNON, Xavier, HEAMS, Thomas, Ducos, Alain, Charpentier, Régis, MAGNOL, Laetitia, RESTOUX, Gwendal, RIGAL, Joël, and VERRIER, Étienne
- Abstract
Copyright of Ethnozootechnie is the property of Societe d Ethnozootechnie and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2021
15. Comment faire entrer la médecine de précision dans la décision thérapeutique de routine au lit du malade ?
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Lemaitre F, Florentin V, Blin O, Bayle A, Benito S, Chauny JV, Galaup A, Korchagina D, Lang M, Le Tourneau C, Pelloux H, Picard N, and Guilhaumou R
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- Humans, Precision Medicine, Artificial Intelligence
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- 2024
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16. Nouvelles techniques génétiques de dépistage et diagnostic anténatals : quels enjeux ?
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Désir, J., Meunier, C., Billard, J.-M., Marichal, A., Rombout, S., and Grisart, B.
- Abstract
New genomic techniques are revolutionizing the prenatal screening and diagnosis, by allowing access to diagnoses of fetal and/or parental conditions whose penetrance is not always complete. These techniques raise many questions, in a sensitive context, ethically different from postnatal follow-up. The creation of multidisciplinary national and international think tanks is fundamental to consider about the important diagnoses or susceptibility factors to relate to the couple during pregnancy. [ABSTRACT FROM AUTHOR]
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- 2020
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17. A different paradigm for the initial colonisation of Sahul.
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ALLEN, JIM and O'CONNELL, JAMES F.
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COLONIZATION , *MITOCHONDRIAL DNA , *INDIGENOUS Australians - Abstract
The questions of when and how humans reached Sahul, the Pleistocene continent of Australia and New Guinea, has remained a central issue of Australian archaeology since its development as an academic discipline in the mid‐twentieth century. Modelling this event has persistently appealed to minimal assumptions – the simplest watercraft, the shortest routes, the smallest viable colonising groups. This paper argues that Australian archaeology can no longer ignore the way our understanding of this initial colonisation is being reshaped by current genomic research. It reviews this evidence and concludes that a colonising wave of hundreds or perhaps low thousands of people was involved. If correct, it suggests that we need to rethink our models, modify or discard the minimalist assumptions that have so far driven them and consider how this different paradigm affects our understanding of early settlement in Sahul. [ABSTRACT FROM AUTHOR]
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- 2020
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18. RNA expression dataset of 384 sunflower hybrids in field condition.
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Penouilh-Suzette, Charlotte, Pomiès, Lise, Duruflé, Harold, Blanchet, Nicolas, Bonnafous, Fanny, Dinis, Romain, Brouard, Céline, Gody, Louise, Grassa, Christopher, Heudelot, Xavier, Laporte, Marion, Larroque, Marion, Marage, Gwenola, Mayjonade, Baptiste, Mangin, Brigitte, de Givry, Simon, and Langlade, Nicolas B.
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SUNFLOWERS , *RNA , *FIELD crops , *SUNFLOWER growing , *SUNFLOWER seeds , *HETEROSIS - Abstract
This article describes how RNA expression data of 173 genes were produced on 384 sunflower hybrids grown in field conditions. Sunflower hybrids were selected to represent genetic diversity within cultivated sunflower. The RNA was extracted from mature leaves at one time seven days after anthesis. These data allow to differentiate the different genotype behaviours and constitute a valuable resource to the community to study the adaptation of crops to field conditions and the molecular basis of heterosis. It is available on data.inra.fr repository. [ABSTRACT FROM AUTHOR]
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- 2020
- Full Text
- View/download PDF
19. From genomes to forest management – tackling invasive Phytophthora species in the era of genomics.
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Keriö, S., Daniels, H. A., Gómez-Gallego, M., Tabima, J. F., Lenz, R. R., Søndreli, K. L., Grünwald, N. J., Williams, N., Mcdougal, R., and LeBoldus, J. M.
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INTRODUCED species , *FOREST surveys , *FOREST health , *PHYTOPHTHORA cinnamomi , *DISEASE resistance of plants , *BIOLOGICAL invasions , *COMPARATIVE genomics , *DNA fingerprinting - Abstract
Species of Phytophthora pose one of the most serious biosecurity threats to forest ecosystems worldwide. Despite management efforts and increased awareness of forest pathogens, there is continued introduction and spread of Phytophthora species. Uncertainty about the center of origin for many of the invasive species hampers disease control efforts. Additionally, the management efforts are often made impossible either by the vast host range or the extreme susceptibility of naïve hosts. In this review, we discuss how genomics has shed light on the extent of spread and destruction caused by invasive Phytophthora species, and how approaches leveraged by genomics can be applied to enhance the management of these invasive forest pathogens. Four case studies, Phytophthora ramorum, Phytophthora lateralis, Phytophthora cinnamomi, and Phytophthora pluvialis are used to illustrate how genomics can be applied to forest management. We urge researchers, governmental research institutes, private companies, and citizens to collaborate in order to stop the spread of invasive Phytophthora species. To accomplish this, we see the following themes as critical parts of resolving this forest health crisis: i) integration of DNA-based pathogen detection into forest inventory programs; ii) development of practical and affordable DNA-based diagnostic methods; iii) sequence hosts as models for resistance gene identification; iv) prediction of pathogen impact based on genomic data; and v) increase collaborative projects and outreach to raise awareness of forest diseases. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
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20. Dynamique des génomes et évolution moléculaire des récepteurs chimiosensoriels des vecteurs de la maladie de Chagas du genre Rhodnius
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Merle, Marie, Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, Myriam Harry, and Florence Mougel
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Hemiptera ,Génomique ,Vecteurs de la maladie de Chagas ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,Vectors of Chagas disease ,Phylogenomics ,Chemosensory genes ,Gènes chimiosensoriels ,Genomics ,Adaptation ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,Phylogénomique - Abstract
Triatominae are haematophagous bugs that can transmit Trypanosoma cruzi, the causative agent of Chagas disease, endemic to Latin America. In the wild, species belonging to the genus Rhodnius mainly infest palm trees, feeding on a wide range of vertebrate hosts that find refuge in this habitat. However, some Rhodnius species are domiciliary, i.e. they have left their natural habitat (sylvatic environment) and have come into close contact with human populations by colonising their dwellings, and can then transmit T. cruzi to humans. The evolutionary history of species belonging to Rhodnius genus was assessed using a phylogenomic strategy based on whole mitogenome sequences and a set of 51 nuclear genes, characterized for 36 samples representing 16 species out of the 24 described in the genus. This approach allowed us to determine the evolutionary relationship between the 3 major groups of species (pallescens, pictipes and prolixus), to integrate species from Psammolestes genus inside the genus one, and to describe multiple introgression events between species. A comparative genomic approach was conducted between species living in different habitats. The genome size was estimated using flow cytometry and analysis of high throughput sequencing data. Genomes from 11 Rhodnius species (including 4 domiciliary species) were assembled and used to build a calibrated phylogeny including sequences from published genomes and fossil records. The divergence times inferred from this phylogeny allowed us to study genome dynamics. It revealed that the rate of gains and losses per gene per million years is 7.5 times faster in domiciliary species compared to sylvatic ones. This study has made it possible to propose candidate genes including chemosensory receptors involved in the domiciliation of species of the genus Rhodnius. Chemosensory genes belong to multigene families with rapid evolutionary dynamics that cause changes in sensory sensitivity. Their study is especially relevant when searching for genes involved in the recognition of a new environment. The chemosensory receptors were annotated (from 49 to 135 ORs and from 21 to 32 GRs depending on the species studied) and analyzed to detect evidence of selection pressure: 4 candidate genes (OR1, OR38, OR102 and ORco) were identified that could be involved in the domiciliation process. A better understanding of the mechanisms of adaptation of these bugs to their environment could be a key factor in vector control efforts.; Les Triatominae sont des punaises hématophages vectrices de Trypanosoma cruzi, agent responsable de la maladie de Chagas, endémique en Amérique Latine. En milieu naturel, les punaises hématophages du genre Rhodnius infestent principalement les palmiers et se nourrissent sur une large gamme d'hôtes vertébrés qui trouvent refuge dans cet habitat. Cependant, certaines espèces de Rhodnius sont domiciliaires, c'est-à-dire qu'elles ont quitté leur habitat naturel (milieu sylvatique) et sont venues en contact étroit avec les populations humaines en colonisant leurs habitations. Les liens de parenté entre les différentes espèces du genre Rhodnius ont été retracés par une approche phylogénomique reposant sur l'étude des mitogénomes et d'un set de 51 gènes nucléaires et incluant 16 espèces sur les 24 espèces décrites via l'étude de 36 échantillons. Cette approche phylogénomique a permis de statuer sur les affinités évolutives des 3 groupes d'espèces décrits (pallescens, pictipes et prolixus), de classer les espèces du genre Psammolestes au sein du genre Rhodnius et de montrer des événements d'introgression multiples entre espèces. Cette étude phylogénétique a été complétée par une approche de génomique comparative entre espèces adaptées à différents habitats. La taille des génomes a été estimée par deux méthodes, la cytométrie de flux et l'analyse des données moléculaires à haut débit. Pour étudier la dynamique des génomes une phylogénie calibrée à l'aide de données fossiles a été réalisée. Onze génomes de Rhodnius (dont 4 domiciliaires) ont été assemblés puis annotés. L'estimation de la vitesse de gains et pertes de gènes par million d'années montre que ces événements se produisent 7.5 fois plus rapidement chez les espèces domiciliaires en comparaison des espèces sylvatiques. Cette étude a permis de proposer des gènes candidats dont des récepteurs chimiosensoriels impliqués dans la domiciliation des espèces du genre Rhodnius. Les gènes chimiosensoriels appartiennent à des familles multigéniques dont la dynamique évolutive est rapide et à l'origine de changements dans la sensibilité sensorielle. Ils sont donc des objets d'étude de choix dans la recherche de gènes impliqués dans la reconnaissance d'un nouvel environnement. L'annotation spécifique de ces récepteurs chimiosensoriels (de 49 à 135 ORs, de 21 à 32 GRs, selon les espèces) suivie de la recherche de gènes sous sélection a permis de mettre en évidence 4 gènes candidats en lien avec la domiciliation (OR1, OR38, OR102 et ORco). Une meilleure compréhension des mécanismes d'adaptation des punaises hématophages à leur environnement pourrait être un facteur clé dans l'effort de lutte antivectorielle.
- Published
- 2023
21. Genome characterization and complete sequence of a new badnavirus from Pandanus amaryllifolius
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Robert A. Alvarez-Quinto, Samuel Grinstead, Philippe Rott, and Dimitre Mollov
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Séquence nucléotidique ,Ribonuclease H ,Genome, Viral ,Séquence d'ARN ,génomique ,Open Reading Frames ,Maladie des plantes ,Virology ,Badnavirus ,Pandanaceae ,Phylogeny ,H20 - Maladies des plantes ,Plant Diseases ,Anemia, Hypochromic ,Génome ,Chlorose ,Virus des végétaux ,General Medicine - Abstract
A new badnavirus was sequenced from fragrant pandan grass (Pandanus amaryllifolius) displaying mosaic and chlorosis on the leaves. The complete genome sequence was determined by high-throughput sequencing. The new badnavirus was tentatively named "pandanus mosaic associated virus" (PMaV). Similar to those of other members of the genus Badnavirus, the genome of PMaV consists of a circular DNA molecule of 7,481 bp with three open reading frames (ORF) potentially coding for three proteins. ORF3 encodes a polyprotein with conserved protein domains including zinc finger, trimeric dUTPase, aspartic protease, reverse transcriptase (RT), and RNase H domains. Pairwise comparisons of the highly conserved RT + RNase H region revealed the highest nucleotide (nt) sequence identity (70.71%) to taro bacilliform CH virus-Et17 (MG017324). In addition to PMaV, viral sequences corresponding to orchid fleck dichorhavirus (OFV) were detected in the same plant sample. The complete sequence of the OFV coding region shared >98% nt sequence identity with other isolates of OFV available in the GenBank database. Disease symptoms could not be attributed exclusively to PMaV or OFV, as both viruses were present in the pandan grass exhibiting mosaic and chlorosis.
- Published
- 2022
22. Intérêt et contribution de l’ADN tumoral circulant : une révolution dans la prise en charge du cancer du pancréas ou un outil supplémentaire dansl’arsenal actuel ?
- Author
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Rougerie, Tristan, Aix-Marseille Université - Faculté de pharmacie (AMU PHARM), Aix Marseille Université (AMU), and Romaric Lacroix
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Génomique ,ADN tumoral circulant ,Biomarqueur ,Cancer du pancréas ,[SDV]Life Sciences [q-bio] ,Séquençage ,Dépistage ,Diagnostic ,[SDV.SP]Life Sciences [q-bio]/Pharmaceutical sciences ,Profilage moléculaire - Abstract
Le cancer du pancréas est une maladie agressive associée à un mauvais pronostic clinique, à des options thérapeutiques peu efficaces et à un manque de méthodes de détection précoce. Les raisons de son mauvais pronostic sont principalement liées au diagnostic tardif de ce cancer. Les patients ne présentent généralement pas de symptôme spécifique et il n’y a pas d’outils ou de biomarqueurs précoces permettant un dépistage de la population générale. D’autre part, le profilage moléculaire du cancer du pancréas est insuffisant pour développer des thérapies ciblées et personnalisées efficaces. Aujourd'hui, pour essayer de faire face à ces défis, la recherche se tourne vers les biopsies liquides qui sont peu invasives et permettent de suivre en temps réel l’évolution et l'hétérogénéité des tumeurs. Grâce au progrès de la recherche génomique et au développement de nouvelles technologies de séquençage (dPCR et le NGS) plus sensibles et plus spécifiques, les biopsies liquides offrent de nombreuses applications cliniques potentielles. L’analyse de l’ADNtc dans le sang semble être une méthode très prometteuse pour améliorer la prise en charge de ce cancer. L’ADNtc muté KRAS seul ou associé avec d’autres biomarqueurs, la quantité d’ADNlc ou encore les variations de la méthylation de l’ADNlc sont des biomarqueurs présentant une valeur pronostique et prédictive intéressante mais encore insuffisante pour le dépistage. Les résultats des études sur l’application clinique de l'ADNtc pour le dépistage, le diagnostic, le profilage moléculaire, le pronostic et la surveillance de la réponse thérapeutique doit être évaluée par de nouvelles études prospectives sur un plus grand nombre de patients afin de confirmer que les informations fournies contribuent de manière significative à l'amélioration de la prise en charge des patients. D’autre part, pour une application clinique de routine, il est nécessaire de réduire les coûts et de standardiser les protocoles.
- Published
- 2023
23. Caractérisation moléculaire des micro-organismes endophytes de la canneberge (Vaccinium macrocarpon Ait.)
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Salhi, Lila Naouelle and Lang, Franz Bernd
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Transcriptomique ,Stimulation of plant growth ,Ericoid mycorrhizal fungi (ErMF) ,Champignons mycorhiziens éricoïdes (ErMF) ,Protéines effectrices ,Biocontrol ,Effector proteins ,Bacteria-fungi interactions ,Cranberry (Vaccinium macrocarpon Aiton) ,Génomique ,Transcriptomic ,Canneberge (Vaccinium macrocarpon Aiton) ,Stimulation de la croissance des plantes ,Bacillus velezensis EB37 ,Endophytes ,Genomic ,Bio-contrôle ,Interactions bactéries-champignons ,CAZymes ,Lachnum sp. EC5 - Abstract
Il a été établi que la majorité des plantes vasculaires abritent des micro-organismes endophytes bactériens et fongiques, qui peuvent coloniser les tissus végétaux et former des associations allant du mutualisme à la pathogénèse. Les symbioses végétales mutualistes les plus communes impliquent les champignons endo-mycorhiziens arbusculaires (AMF). Ces champignons s’associent aux racines des plantes et leur permettent d’améliorer leur nutrition minérale, tandis qu’ils bénéficient des composés produits par l'hôte. Toutefois, les plantes de la famille Ericaceae s’engagent plutôt dans des associations mutualistes avec les champignons mycorhiziens éricoïdes (ErMF). Ces derniers sont morphologiquement et taxonomiquement mal définis, en apparence distribués aléatoirement parmi les espèces issues des grandes divisions taxonomiques des Ascomycota et Basidiomycota. En raison de cette incohérence taxonomique et de l'absence d'une histoire évolutive explicative, la diversité réelle de ces champignons est mal caractérisée. De ce fait, ce projet vise à étudier le microbiote associé à la plante Ericaceae Vaccinium macrocarpon Aït (canneberge), axant la recherche sur les angles morphologiques, génomiques et transcriptomiques des champignons de type ErMF et autres endophytes capables de contrôler la croissance des agents phytopathogènes et de stimuler la croissance des plantes. Notre première démarche présentée dans le chapitre 2 s’est focalisée sur la caractérisation du microbiote endophyte bactérien et fongique de la canneberge, une plante vivace principalement produite en Amérique du Nord, notamment au Québec. Nous avons isolé et identifié 180 micro-organismes à partir de plantes de cultivars variés, collectées de champs différents, et avons démontré l'existence d'une variabilité dans le microbiote selon les tissus, les cultivars, et même entre les champs d'une même ferme. Parmi les endophytes d’intérêt identifiés, l’isolat fongique Lachnum sp. EC5 a stimulé la croissance des cultivars de canneberge Stevens et Mullica Queen et a formé des structures intracellulaires similaires à celles des ErMF à l’intérieur des cellules racinaires de la canneberge. De plus, l’isolat EB37 identifié Bacillus velezensis s’est révélé être un puissant agent antifongique, montrant cependant une tolérance particulière au champignon Lachnum sp. EC5, lors des tests de confrontation. Ce volet sera détaillé avec plus de précision dans le chapitre 4. Le chapitre 3 a porté sur l’analyse génomique comparative de l’isolat fongique Lachnum sp. EC5 avec plusieurs espèces de champignons Leotiomycetes ErMF, saprophytes et pathogènes. Nous avons analysé le sécrétome protéique prédit de ces champignons et mis en évidence que les gènes codant pour les enzymes de dégradation des parois végétales ne sont pas corrélés au mode de vie fongique (mycorhizien, pathogène ou saprophyte). A l’inverse, 10 protéines effectrices de Lachnum sp. EC5 prédites pour cibler spécifiquement un compartiment intracellulaire chez les cellules végétales ont des similarités avec celles d’espèces mutualistes comme Meliniomyces variabilis et Oidiodendron maius. Aussi, la protéine effectrice putative Zn-MP, prédite pour cibler, potentiellement, les chloroplastes végétaux nous permet de proposer un rôle dans le renforcement de l’immunité végétale. Le chapitre 4 s’est intéressé aux mécanismes de régulation d'expression de gènes induits lors de l’interaction entre le champignon Lachnum sp. EC5 et la bactérie B. velezensis EB37. Ces mécanismes ont été comparés à ceux activés chez la bactérie en présence de champignons pathogènes. Nous avons démontré une physiologique cellulaire bactérienne distincte en présence de Lachnum sp. EC5, dénotée par une faible expression des gènes induits lors du stress nutritif associé aux processus de sporulation, de formation du biofilm, de secretion de CAZymes et de lipopeptides. Nous avons suggéré que la sous-régulation de ces mécanismes serait essentiellement explicable par une disponibilité plus importante en glucose ou en d’autres sources de carbone préférentielles pour la bactérie. En réponse, le champignon Lachnum sp. EC5 a vécu différents changements morphologiques. Il aurait détoxifié ses environnements intra et extra-cellulaires et surexprimé sa voie de production de carbone dépendante du cycle du glyoxylate, générant ainsi des conditions favorisant un contact physique entre les deux micro-organismes. En conclusion, nous avons argumenté et documenté que la définition des ErMF basée uniquement sur des critères morphologiques est mal adaptée à catégoriser ces champignons. Notre approche multidisciplinaire a mis en évidence la diversité du microbiote de la canneberge, a étendu la notion d’ErMF à d'autres champignons jusqu'ici exclus de ce groupe, et a souligné l'importance des associations interspécifiques sur l’interaction ErMF-plantes. Ces avancées permettront d’améliorer nos connaissances sur le microbiote des plantes éricacées contribuant, au développement de solutions environnementales éco-responsables pour l’industrie de la canneberge., It has been established that the majority of vascular plants harbour bacterial and fungal endophytes that colonize plant tissues, and thus form associations that range from mutualism to pathogenesis. Mycorrhizal fungi are a particular class of endophytes that associate with plant roots and enhance plant mineral uptake. The most common type of mutualistic plant symbiosis involves arbuscular mycorrhizal fungi (AMF), whereas plants of the Ericaceae family instead engage in mutualistic associations with ericoid mycorrhizal fungi (ErMF). The ErMF group, in its current definition, includes both ascomycete and basidiomycete species, yet is morphologically, taxonomically and evolutionarily poorly defined, which implies that the group’s true diversity is not well understood. The objective of this project is to complement morphological information with genomic and transcriptomic data to better understand the role of ErMF in 1) controlling the negative effects of pathogenic infections, and 2) the potential plant growth stimulation for the Ericaceous plant Vaccinium macrocarpon Ait. Our first approach presented in Chapter 2 focused on the characterization of the bacterial and fungal endo-symbiotic microbiota of the Ericaceous plant, Vaccinium macrocarpon Ait (cranberry), a perennial plant mainly in North America, particularly in Quebec. We isolated ~180 distinct bacterial and fungal endophytes collected from roots, stems, and leaves of cranberry plants cultivated in Quebec, Canada. We show that the cranberry microbiome varies substantially between tissues, cultivars, and across fields of the same farm. Among the isolated endophytes, the fungus Lachnum sp. EC5 was found to promote the growth of cranberry cultivars Stevens and Mullica Queen, and to form intracellular structures resembling those other ErMF inside the cortical root cells. In addition, the bacterium Bacillus velezensis (EB37) has been found to be a potent antifungal agent. Interestingly, a confrontation test between EB37 and the fungus Lachnum sp. EC5 revealed a mutual tolerance, which we will describe later in chapter 4. In chapter 3, our project focused on the comparative genomic analysis of the fungus Lachnum sp. EC5 with several Leotiomycete ErMF, saprophytes and pathogens. We analyzed fungal secretomes and demonstrated that genes encoding plant cell wall degradation enzymes are conserved between the tested fungi which suggests that such proteins are not indicative of a particular fungal lifestyle. On the other hand, 10 effector proteins identified in Lachnum sp. EC5 were also only found in mutualistic fungi, such as Meliniomyces variabilis, Oidiodendron maius and have been reported to target the plant intracellular compartments. Also, the identification of the putative effector protein Zn-MP, specific to Lachnum sp. EC5 and predicted to target plant chloroplasts, suggest a role in the reinforcement of plant immunity. Chapter 4 focuses on the patterns of gene expression regulation induced in the biocontrol bacterium B. velezensis EB37 in interaction with the potentially mutualistic fungus Lachnum sp. EC5. These mechanisms were then compared to those activated when the bacterium is in the presence of pathogenic/saprophytic fungi. We demonstrated that in co-culture with Lachnum sp. EC5, EB37expresses fewer genes related to stress, and fewer related to the stationary phase which often involves production of bacterial biofilms and lipopeptides, such as mycosubtilin. We suggest that the lessened response to stress is related to an increased availability of glucose or other preferential sources of carbons for the bacterium. Conversely, Lachnum sp. EC5 in the presence of EB37 underwent morphological changes by a higher lateral branching., detoxified its external and internal environment by expressing both a catalase activity and efflux pumps, and overexpressed its glyoxylate cycle-dependent carbon production pathway, and thus promoting favourable conditions for close physical contact with the bacterium. In conclusion, we demonstrated that the morphological-based definitions are poorly adapted to the categorization of ErMF fungi. Our multidisciplinary approach highlighted the diversity of the cranberry microbiota, extended the notion of ErMF to other fungi hitherto excluded from this fungal group and underlined the importance of interspecific associations on the ErMF-plant interaction. These advances enhance our understanding of the Ericaceous plant microbiota and contributes to the development of sustainable solutions for the cranberry industry.
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- 2023
24. Evolution of the cotton genus, Gossypium, and its domestication in the Americas
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Christopher R. Viot and Jonathan F. Wendel
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Gossypium ,Phylogénie ,F40 - Écologie végétale ,Domestication des plantes ,Hybridation ,Gossypium hirsutum ,Évolution ,Plant Science ,F30 - Génétique et amélioration des plantes ,génomique ,Gossypium barbadense ,Histoire ,F01 - Culture des plantes ,Hybridation interspécifique - Abstract
Gossypium, the cotton genus, includes ∼50 species distributed in tropical and sub-tropical regions of all continents except Europe. Here we provide a synopsis of the evolutionary history of Gossypium and domestication of the American allopolyploid species, integrating data from fundamental taxonomic investigations, biogeography, molecular genetics, phylogenetic analysis, and archaeology. These diverse sources of information provide a temporal and phylogenetic perspective on diversification among the diploids and on polyploid formation, uncover multiple previously cryptic interspecific hybridizations, clarify and contribute to the taxonomy of the genus, and offer a firm foundation for understanding parallel domestications in Mesoamerica and South America, which led to the globally important cotton crop species G. barbadense and G. hirsutum. Gossypium thus offers a testimonial example of the importance and utility of fundamental botanical discovery combined with modern technological capabilities to generate genomic insights into evolutionary history. We also review the current state of our knowledge regarding the archaeological history of cotton domestication and diffusion in the Americas, a seemingly unlikely story entailing parallel domestication origins and parallel directional selection tracing to 8,000 (G. barbadense) and 5,500 (G. hirsutum) years ago, transforming two geographically isolated wild short-day perennial shrubs having small capsules and seeds covered by short, tan-colored epidermal trichomes into modern daylength-neutral annuals bearing abundant, fine, strong white fibers. This dual domestication was followed several millennia later by unintentional and more recently intentional interspecific introgression, as the two species came into contact following their initial domestication in different hemispheres. Thus, the cycle of species divergence and biological reunion was reiterated, this time at the allopolyploid level. Understanding this evolutionary history is vitally important to our understanding of the genomic architecture of the world's most important fiber plant and contributes substantially to our understanding of general biological principles.
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- 2023
25. Séquençage du génome entier des entérobactéries productrices de bêtalactamases à spectre élargi au sein d’un établissement de santé : mise en place en routine et rôle dans le contrôle des transmissions croisées
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Fevre, Margo, Jeanne-Leroyer, Camille, Déquiré, Paul, Gravey, François, and Hello, Simon Le
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Génomique ,Hygiène hospitalière ,Typage ,Épidémie ,Investigations ,Transmission croisée - Abstract
Introduction et objectif. Depuis 2019, le séquençage du génome entier est réalisé en routine pour toutes les entérobactéries productrices de bêtalactamases à spectre élargi (EBLSE) isolées chez les patients hospitalisés en réanimation au centre hospitalier universitaire de Caen. Cette étude évalue un algorithme d’alerte simple afin de détecter les transmissions croisées et les épidémies. Matériel et méthodes. L’alerte de transmission croisée est basée sur l’identification de deux EBLSE de même espèce en réanimation adulte sur une période d’un mois glissant. Les performances de ces alertes étaient calculées pour trois espèces d’EBLSE (Klebsiella pneumoniae, Escherichia coli et Enterobacter cloacae complexe) en les comparant aux données issues du séquençage des souches isolées en 2019 et 2020 puis en prospectif en 2021. Résultats. L’algorithme a été créé à partir des 320 souches d’EBLSE identifiées et séquencées : 138 E. coli, 91 K. pneumoniae et 91 E. cloacae. Le taux global de transmission croisée était de 22% en 2019-2020 (respectivement 1,5%, 42% et 33% pour chaque espèce) et de 21,2% en 2021 (0%, 16,7% et 54,0%). La valeur prédictive positive de notre algorithme est de 14,3% pour E. coli, 92,7% pour K. pneumoniae et 51,8% pour E. cloacae. Conclusion. Par une approche génomique, nous pouvons détecter et alerter toute transmission croisée afin d’adapter les mesures de prévention ainsi que les enquêtes environnementales en cas d’épidémie. L’algorithme donne une orientation précoce des alertes mais peut et doit s’adapter selon les dynamiques de diffusion, qui semblent être différentes entre espèces.
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- 2023
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26. Global transcriptome profiling reveals differential regulatory, metabolic and hormonal networks during somatic embryogenesis in Coffea arabica
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Rayan Awada, Maud Lepelley, David Breton, Aline Charpagne, Claudine Campa, Victoria Berry, Frédéric Georget, Jean-Christophe Breitler, Sophie Léran, Doâa Djerrab, Federico Martinez-Seidel, Patrick Descombes, Dominique Crouzillat, Benoît Bertrand, and Hervé Etienne
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Genetics ,Embryogénèse somatique ,Marqueur génétique ,Coffea arabica ,Biotechnology ,F30 - Génétique et amélioration des plantes ,génomique - Abstract
Background Somatic embryogenesis (SE) is one of the most promising processes for large-scale dissemination of elite varieties. However, for many plant species, optimizing SE protocols still relies on a trial and error approach. We report the first global scale transcriptome profiling performed at all developmental stages of SE in coffee to unravel the mechanisms that regulate cell fate and totipotency. Results RNA-seq of 48 samples (12 developmental stages × 4 biological replicates) generated 90 million high quality reads per sample, approximately 74% of which were uniquely mapped to the Arabica genome. First, the statistical analysis of transcript data clearly grouped SE developmental stages into seven important phases (Leaf, Dedifferentiation, Primary callus, Embryogenic callus, Embryogenic cell clusters, Redifferentiation and Embryo) enabling the identification of six key developmental phase switches, which are strategic for the overall biological efficiency of embryo regeneration. Differential gene expression and functional analysis showed that genes encoding transcription factors, stress-related genes, metabolism-related genes and hormone signaling-related genes were significantly enriched. Second, the standard environmental drivers used to control SE, i.e. light, growth regulators and cell density, were clearly perceived at the molecular level at different developmental stages. Third, expression profiles of auxin-related genes, transcription factor-related genes and secondary metabolism-related genes were analyzed during SE. Gene co-expression networks were also inferred. Auxin-related genes were upregulated during dedifferentiation and redifferentiation while transcription factor-related genes were switched on from the embryogenic callus and onward. Secondary metabolism-related genes were switched off during dedifferentiation and switched back on at the onset of redifferentiation. Secondary metabolites and endogenous IAA content were tightly linked with their respective gene expression. Lastly, comparing Arabica embryogenic and non-embryogenic cell transcriptomes enabled the identification of biological processes involved in the acquisition of embryogenic capacity. Conclusions The present analysis showed that transcript fingerprints are discriminating signatures of cell fate and are under the direct influence of environmental drivers. A total of 23 molecular candidates were successfully identified overall the 12 developmental stages and can be tested in many plant species to optimize SE protocols in a rational way.
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- 2023
27. Virion-associated nucleic acid-based metagenomics: a decade of advances in molecular characterization of plant viruses
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Moubset, Oumaima, François, Sarah, Maclot, François, Palanga, Essowé, Julian, Charlotte, Claude, Lisa, Fernandez, Emmanuel, Rott, Philippe, Daugrois, Jean-Heinrich, Antoine-Lorquin, Aymeric, Bernardo, Pauline, Blouin, Arnaud G., Temple, Coline, Kraberger, Simona, Fontenele, Rafaela S, Harkins, Gordon William, Ma, Yuxin, Marais, Armelle, Candresse, Thierry, Ben Chehida, Sélim, Lefeuvre, Pierre, Lett, Jean-Michel, Varsani, Arvind, Massart, Sébastien, Ogliastro, Mylène, Martin, Darren Patrick, Filloux, Denis, Roumagnac, Philippe, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of Oxford, Gembloux Agro-Bio Tech [Gembloux], Université de Liège, Institut Togolais de Recherche Agronomique (ITRA), Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Enza Zaden, Agroscope, Arizona State University [Tempe] (ASU), University of the Western Cape (UWC), Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Cape Town, European Union (ERDF, contract GURDT I2016-1731-0006632), Conseil Régional de La Réunion, project SEVIPLANT from Federal Public 17 Service, Public Health, Belgium, Grant Agreement no. RT 18/3, ANR-19-CE35-0008,PHYTOVIRUS,Mesure et cartographie de la richesse des virus des plante à l'échelle de l'écosytème(2019), and European Project: 813542,INEXTVIR
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Identification ,Ecology ,viruses ,[SDV]Life Sciences [q-bio] ,Virion ,Virus des végétaux ,[SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC] ,Plants ,génomique ,Plant Viruses ,[SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology ,Nucleic Acids ,Virology ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Metagenomics ,Pathogen Detection ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,Ecosystem ,H20 - Maladies des plantes ,Plant Diseases - Abstract
Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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- 2022
28. Characterizing the impact of the mutational landscape of SARS-CoV-2 on epitope presentation and CTL
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Hamelin, David, Caron, Étienne, and Hussin, Julie
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Immunopeptidomique ,Immune Escape ,T Cells ,SARS-CoV-2 ,Virologie ,Genomics ,SRAS-CoV-2 ,Immunopeptidomics ,Évasion Immunitaire ,Épitopes ,Génomique ,Epitopes ,Virology ,Cellules T - Abstract
La pandémie actuelle de COVID-19, causée par le coronavirus 2 du syndrome respiratoire aigu sévère (SRAS-CoV-2), a entraîné plus de 6 millions de décès et près de 680 millions de cas confirmés dans le monde. Depuis l'émergence du virus en décembre 2019, beaucoup d’efforts de recherche mondiaux ont visé à étudier la relation entre le SRAS-CoV-2 et l'immunité adaptative à médiation cellulaire. La caractérisation des réponses immunitaires à base de lymphocytes T CD4+ et CD8+ contre le SRAS-CoV-2 dans le contexte de mutations virales est d'une pertinence immédiate pour l’approfondissement de nos connaissances concernant l'immunité adaptative envers un virus en évolution, ainsi que l'amélioration de vaccins. Dans cette thèse, je passerai en revue les découvertes actuelles concernant la biologie du SRAS-CoV-2 et sa relation avec le système immunitaire adaptatif humain. Je discuterai ensuite les divers mécanismes par lesquels le SRAS-CoV-2, ainsi que d'autres virus, se sont avérés échapper l’immunité adaptative humoral et cellulaire. Enfin, je présenterai mes contributions à la compréhension du paysage mutationnel global du SRAS-CoV-2 et de sa capacité à échapper à la reconnaissance par les lymphocytes T CD8+. Dans ce travail, j'ai observé que le paysage mutationnel global du SRAS-CoV-2 était régi par des biais de mutation au cours de la première année de la pandémie, le plus répandu d’entre eux conduisant à la suppression de la proline. Il a ensuite été prédit que cette élimination globale de la proline conduirait à la perte d’épitopes reconnues par les cellules T CD8+ d'une manière dépendante sur les super-types HLA, avec la perte d'épitopes survenant préférentiellement dans le contexte du super-type HLA-B7. Le modèle développé dans ce travail propose un lien entre les biais mutationnels globaux du SRAS-CoV-2, les allèles HLA et l'évasion des lymphocytes T. Ce travail crée un cadre pour anticiper l'impact des variantes existantes et émergentes du SRAS-CoV- 2 envers la réponse immunitaire à base de lymphocytes T CD8+., The current COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has led to upwards of 6 million deaths and nearly 680 million confirmed cases worldwide. Since the emergence of the virus in December 2019, astounding global research efforts have been aimed at investigating the relationship between SARS-CoV-2 and cell-mediated adaptive immunity. Characterizing CD4+ and CD8+ T Lymphocyte responses to SARS-CoV-2 in the context of viral mutations is of immediate relevance to understanding the breadth of a population’s adaptive immunity to an evolving virus and is central to the improving existing vaccines. In this thesis, I will review all present findings pertaining to the biology of SARS-CoV-2 and its relationship with the human adaptive immune system. I will then discuss the various mechanisms by which SARS-CoV-2, along with other viruses, have been found to evade the various arms of the adaptive immune system. Finally, I will present my contributions to the understanding of the global mutational landscape of SARS-CoV-2 and its ability to evade recognition by CD8+ T lymphocytes. By investigating over 300,000 SARS-CoV-2 genomic sequences, I observed that the mutational landscape of SARS-CoV-2 was governed by mutation biases during the first year of the pandemic, with the most prevalent bias leading to the removal of proline. The observed global removal of Proline was predicted to lead to the loss of CD8+ T cell epitopes in an HLA-supertype-dependent manner, with the loss of epitopes occurring preferentially in the context of the HLA-B7 supertype. The model developed proposes a link between SARS-CoV-2 global mutational biases, HLA alleles and T cell evasion. This work creates a framework to anticipate the population-specific impact of existing and emerging SARS-CoV-2 variants on CD8+ T cell-based immunity.
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- 2022
29. Évaluation de l’imputation des données génétiques Canadiennes-Françaises
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Pelletier, Justin and Hussin, Julie
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Genotyping ,French-Canadian ,Bioinformatics ,Founder population ,Génotypage ,Panels de référence ,Canadien français ,Québec ,Génomique ,Génétique des populations ,Population fondatrice ,Genomic ,Bio-informatique ,Population genetic ,Reference panels ,Imputation - Abstract
L'imputation est désormais un outil essentiel dans l'analyse des études d'association à l'échelle du génome, permettant l'estimation de génotypes à des positions variables du génome non génotypées, via des inférences statistiques à partir d'haplotypes contenus dans un panel de référence utilisé pour l'imputation, soit une bibliothèque d’haplotype séquencés phasés en haplotypes. Les données génétiques imputés servent aux études d’associations sur les traits et maladies complexes. La population fondatrice canadienne-française est une population très utile dans les études d'association génétique en raison de sa diversité unique d'haplotypes et de l'excès de variantes rares. Ici, nous décrivons les défis qui accompagnent l'imputation de cette population fondatrice, qui n'est pas représentée dans les panels de référence disponibles, ainsi que la stratégie optimale pour imputer des ensembles de données génotypés hétérogènes, provenant de plusieurs plateformes de génotypage. Nous avons caractérisé l'imputation de 29,356 individus génotypés sur plusieurs puces de génotypage de la province du Québec constituant la cohorte CARTaGENE (CaG). Nous avons établi que le panel de référence le plus récent et le plus diversifié Trans-Omics for Precision Medecine (TOPMed) a surpassé le panel de référence Haplotype Reference Consortium (HRC) dans l'ensemble de données canadienne-française de CaG. Nous avons évalué la précision de l'imputation avec le un score de qualité (R2) fréquemment utilisé, ainsi que l’exactitude calculée en fonction des génotypes aux variants observés par séquençage, disponibles dans CARTaGENE pour un sous-groupe d’individus. Nous avons déterminé que la stratégie optimale pour augmenter la qualité d'imputation sur des ensembles de données hétérogènes a été atteinte en fusionnant chaque sous-ensemble de données après les avoir imputés individuellement. Ce résultat ouvre la voie à l’intégration de cohortes génotypées hétérogènes dans les études d’associations. Nos résultats soulignent également les défis que représente une population fondatrice pour l'imputation, en comparant la qualité de l'imputation de CaG avec d'autres sous-cohortes canadiennes du projet CanPath, soit l’Ontario, l’Alberta, la Colombie-Britannique et les provinces atlantiques. Ces résultats mettent en évidence l'impact de l’absence de diversité haplotypique spécifique dans les panels de référence sur l'imputation d'une population européenne fondatrice récente, démontrant l'importance de la représentativité de la population étudiée dans ces panels., Imputation is now an essential tool in the analysis of genome-wide association studies, allowing the estimation of genotypes at variable positions of the ungenotyped genome, via statistical inferences from haplotypes contained in a reference panel used for imputation, (a library of sequenced genotypes phased into haplotype). Imputed genetic data is used for association studies of complex traits and diseases. The French-Canadian founder population is a very useful population in genetic association studies due to its unique haplotype’s diversity and excess of rare variants. Here, we describe the challenges that come with imputing this founder population, which is not represented in available reference panels, as well as the optimal strategy for imputing heterogeneous genotyped datasets, from multiple genotyping platforms. We characterized the imputation of 29,356 individuals genotyped on multiple genotyping arrays from the province of Quebec constituting the CARTaGENE (CaG) cohort. We established that the newer and more diverse Trans-Omics for Precision Medicine (TOPMed) reference panel outperformed the Haplotype Reference Consortium (HRC) reference panel in the CaG French-Canadian dataset. We evaluated the precision of the imputation with the frequently used quality score (R2), as well as the accuracy calculated according to the genotypes observed by sequencing, available in CARTaGENE for a subgroup of individuals. We determined that the optimal strategy for increasing imputation quality on heterogeneous datasets was achieved by merging each subset of data after imputing them individually. This result opens the way to the integration of heterogeneous genotyped cohorts in association studies. Our results also highlight the challenges of a founder population for imputation, comparing the quality of CaG imputation with other Canadian sub-cohorts of the CanPath project, namely Ontario, Alberta, British-Columbia, and the Atlantic provinces. These results highlight the impact of the absence of specific haplotypic diversity in the reference panels on the imputation of a recent European founder population, demonstrating the importance of the representativeness of the population studied in these panels.
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- 2022
30. Méthode d'apprentissage profond pour l'analyse génomique des cancers canins comme modèle des cancers humains
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Kergal, Camille, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Rennes, Christophe Hitte, and Thomas Derrien
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Apprentissage profond ,Génomique ,Modèle animal ,Deep learning ,Genomics ,Species model ,Cancers ,[SDV.MHEP]Life Sciences [q-bio]/Human health and pathology - Abstract
Deep learning (DL) methods have recently been shown to be powerful strategies for predicting the regulatory activity of a genomic sequence and thus for ultimately assessing the impact of regulatory mutations on gene expression. The Basenji tool proposes a DL approach using convolutional neural networks to predict the expression level of human genes. We adapted this program to train a dog-specific gene expression model and showed that this model achieved similar performance to that observed in humans, with high correlations between real and predicted expression levels (r=0.66). To predict the ex- pression level of canine genes, we show that the canine prediction model (within-species approach) leads to better performances than the human model (cross-species approach), particularly due to some specific features of canine sequences (GC content, transposable elements and evolutionary conservation). As the dog is a spontaneous model for human cancers, we used these models to predict the impact of non-coding mutations on the expression of genes involved in cancers. We identified 1301 common mutations to both humans and dogs, suggesting a functional role in the regulation of the expression of genes involved in cancer. Finally, models and tools to exploit them are available on GitHub: https://github.com/ckergal/BLIMP.; Les méthodes d’apprentissage profond (DL) se sont récemment révélées être de puissantes stratégies pour prédire l’activité régulatrice d’une séquence génomique et donc pour, in fine, évaluer l’impact des mutations régulatrices sur l’expression des gènes. L’outil Basenji propose une approche DL utilisant des réseaux de neurones convolutifs pour prédire le niveau d’expression de gènes humains. Nous avons adapté ce programme pour entraîner un modèle d’expression génique spécifique au chien et montré que ce modèle de prédiction atteignait des performances similaires à celles observées chez l’homme, avec des corrélations élevées entre les niveaux d’expression réels et ceux pré- dits (r=0,66). Pour prédire le niveau d’expression de gènes canins, nous démontrons également que l’utilisation du modèle de prédiction canin (approche intra-espèce) aboutit à de meilleures performances que le modèle humain (approche inter-espèce), notamment en lien avec certaines caractéristiques spécifiques aux séquences canines (niveau de GC, d’éléments transposable et conservation évolutive). Le chien étant un modèle naturel pour l’étude des cancers humains, nous avons également exploité ces modèles pour prédire l’impact de mutations non-codantes sur l’expression de gènes impliqués dans les cancers. Nous avons ainsi localisé 1301 mutations communes entre l’homme et le chien, suggérant un rôle fonctionnel dans la régulation de l’expression de gènes impliqués dans les cancers. Finalement, nos modèles et les outils pour les exploiter sont disponibles sur GitHub : https://github.com/ckergal/BLIMP.
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- 2022
31. Virion-associated nucleic acid-based metagenomics: A decade of advances in molecular characterization of plant viruses
- Abstract
Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided.
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- 2022
32. Mapping for males: Sustainable sex control in nile tilapia
- Abstract
Sexual dimorphism of aquaculture traits is common for farmed fish. The Nile tilapia is the second most important farmed species with a production 6 million tons in 2020. Intensive farming relies on the production of all-males due to males' higher growth rate, and as a way to avoid uncontrolled reproductions. Currently the large majority of the all-male productions are obtained through androgen treatments. We aim to use more sustainable procedures to produce all-males such as the use of YY males. Until now, the use of YY males has not been reliable. This is because sex determination in Nile tilapia is complex and controlled by several factors. Although sex determinism follows an XX/XY system, the linkage group (LG) carrying the major sex determinant gene has been assigned to either LG1 or LG23, depending on the domesticated strain. Minor parental factors can also be implicated and in addition, high temperatures can override the genetic determinism. It is not clear to what extent these differences in sex determination are due to natural diversity in the mechanisms of sex determination or due to processes of domestication. It is therefore necessary to better understand the genetic basis of sex determinism in order to use this approach to generate all-males. For this, we decided to work on wild populations in Africa that have not suffered domestic manipulations. We underwent a study of sex determination in several wild populations from West (Lake Volta, Lake Kou) and East Africa (Lake Koka and Lake Hora). We used complementary genomic approaches of ddRAD, whole genome sequencing and long Nanopore reads. We were able to determine that the amh region present on LG23 is the major sex-determining region in most of these populations. Nevertheless, our results also show that there is high polymorphism in this SD region. Furthermore, there are populations that lack the male-specific amh duplication on LG23. Hence, there are no universal Y markers for Nile tilapia. It is necess
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- 2022
33. The Banana Genome Hub: A community database for genomics in the Musaceae
- Abstract
The Banana Genome Hub provides centralized access for genome assemblies, annotations, and the extensive related omics resources available for bananas and banana relatives. A series of tools and unique interfaces are implemented to harness the potential of genomics in bananas, leveraging the power of comparative analysis, while recognizing the differences between datasets. Besides effective genomic tools like BLAST and the JBrowse genome browser, additional interfaces enable advanced gene search and gene family analyses including multiple alignments and phylogenies. A synteny viewer enables the comparison of genome structures between chromosome-scale assemblies. Interfaces for differential expression analyses, metabolic pathways and GO enrichment were also added. A catalogue of variants spanning the banana diversity is made available for exploration, filtering, and export to a wide variety of software. Furthermore, we implemented new ways to graphically explore gene presence-absence in pangenomes as well as genome ancestry mosaics for cultivated bananas. Besides, to guide the community in future sequencing efforts, we provide recommendations for nomenclature of locus tags and a curated list of public genomic resources (assemblies, resequencing, high density genotyping) and upcoming resources—planned, ongoing or not yet public.
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- 2022
34. Towards smart and sustainable development of modern berry cultivars in Europe
- Abstract
Fresh berries are a popular and important component of the human diet. The demand for high-quality berries and sustainable production methods is increasing globally, challenging breeders to develop modern berry cultivars that fulfill all desired characteristics. Since 1994, research projects have characterized genetic resources, developed modern tools for high-throughput screening, and published data in publicly available repositories. However, the key findings of different disciplines are rarely linked together, and only a limited range of traits and genotypes has been investigated. The Horizon2020 project BreedingValue will address these challenges by studying a broader panel of strawberry, raspberry and blueberry genotypes in detail, in order to recover the lost genetic diversity that has limited the aroma and flavor intensity of recent cultivars. We will combine metabolic analysis with sensory panel tests and surveys to identify the key components of taste, flavor and aroma in berries across Europe, leading to a high-resolution map of quality requirements for future berry cultivars. Traits linked to berry yields and the effect of environmental stress will be investigated using modern image analysis methods and modeling. We will also use genetic analysis to determine the genetic basis of complex traits for the development and optimization of modern breeding technologies, such as molecular marker arrays, genomic selection and genome-wide association studies. Finally, the results, raw data and metadata will be made publicly available on the open platform Germinate in order to meet FAIR data principles and provide the basis for sustainable research in the future.
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- 2022
35. Genomic instability in somatic hybridization between Poncirus and Citrus species aiming to create new rootstocks
- Abstract
Rootstocks are an important component for citrus adaptation to increasing biotic and abiotic stresses resulting from global climate change. There is a strong complementarity between Citrus species, which adapt to abiotic stresses, and Poncirus trifoliata and its intergeneric hybrids, which exhibit resistances or tolerances to major diseases and pests. Thus, symmetrical somatic hybridization between complementary diploid rootstocks of these two genera appears to be an efficient way to develop new tetraploid rootstocks in order to address the new challenges of the citrus industry. New intergeneric somatic hybrids were obtained by electrofusion between protoplasts of Citrus and P. trifoliata hybrids. Extensive characterization of the nuclear and cytoplasmic genomes was performed by genotyping-by-sequencing (GBS) analysis. This revealed diploid cybrids and nuclear somatic hybrids. Mitochondrial genomes were mostly inherited from the callus parent, but homologous recombination events were observed for one parental combination. Chloroplasts exhibited random uniparental inheritance. GBS revealed local chromosomal instabilities for all nuclear somatic hybrids and whole chromosome eliminations for two hybrids. However, at the whole genome level, symmetrical addition of the nuclear genomes of both parents was predominant and all somatic hybrids displayed at least one trifoliate orange haplotype throughout the genome.
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- 2022
36. Towards smart and sustainable development of modern berry cultivars in Europe
- Abstract
Fresh berries are a popular and important component of the human diet. The demand for high-quality berries and sustainable production methods is increasing globally, challenging breeders to develop modern berry cultivars that fulfill all desired characteristics. Since 1994, research projects have characterized genetic resources, developed modern tools for high-throughput screening, and published data in publicly available repositories. However, the key findings of different disciplines are rarely linked together, and only a limited range of traits and genotypes has been investigated. The Horizon2020 project BreedingValue will address these challenges by studying a broader panel of strawberry, raspberry and blueberry genotypes in detail, in order to recover the lost genetic diversity that has limited the aroma and flavor intensity of recent cultivars. We will combine metabolic analysis with sensory panel tests and surveys to identify the key components of taste, flavor and aroma in berries across Europe, leading to a high-resolution map of quality requirements for future berry cultivars. Traits linked to berry yields and the effect of environmental stress will be investigated using modern image analysis methods and modeling. We will also use genetic analysis to determine the genetic basis of complex traits for the development and optimization of modern breeding technologies, such as molecular marker arrays, genomic selection and genome-wide association studies. Finally, the results, raw data and metadata will be made publicly available on the open platform Germinate in order to meet FAIR data principles and provide the basis for sustainable research in the future.
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- 2022
37. Genomic instability in somatic hybridization between Poncirus and Citrus species aiming to create new rootstocks
- Abstract
Rootstocks are an important component for citrus adaptation to increasing biotic and abiotic stresses resulting from global climate change. There is a strong complementarity between Citrus species, which adapt to abiotic stresses, and Poncirus trifoliata and its intergeneric hybrids, which exhibit resistances or tolerances to major diseases and pests. Thus, symmetrical somatic hybridization between complementary diploid rootstocks of these two genera appears to be an efficient way to develop new tetraploid rootstocks in order to address the new challenges of the citrus industry. New intergeneric somatic hybrids were obtained by electrofusion between protoplasts of Citrus and P. trifoliata hybrids. Extensive characterization of the nuclear and cytoplasmic genomes was performed by genotyping-by-sequencing (GBS) analysis. This revealed diploid cybrids and nuclear somatic hybrids. Mitochondrial genomes were mostly inherited from the callus parent, but homologous recombination events were observed for one parental combination. Chloroplasts exhibited random uniparental inheritance. GBS revealed local chromosomal instabilities for all nuclear somatic hybrids and whole chromosome eliminations for two hybrids. However, at the whole genome level, symmetrical addition of the nuclear genomes of both parents was predominant and all somatic hybrids displayed at least one trifoliate orange haplotype throughout the genome.
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- 2022
38. Caractérisation de la régulation génétique des microARN plasmatiques en grossesse et leur potentielle implication dans le développement du diabète gestationnel
- Abstract
L'arrivée de nouvelles techniques de séquençage à haut débit a procuré une puissante façon d'étudier le génome humain. Parallèlement, le développement d'outils bio-informatiques adaptés à cette révolution a été essentiel à l'interprétation des quantités titanesques de données générées. Le séquençage de plusieurs génomes complets maintenant accessible ouvre la porte à des découvertes autrefois impensable. Ce mémoire présente deux projets portant sur les variations génétiques chez les individus d'une cohorte de femmes enceintes. Le premier projet porte sur l'étude de la régulation génétique de l'abondance des microARN plasmatiques au premier trimestre de grossesse. La mise en commun de l'abondance des microARN et des variations génétiques à proximité des microARN a permis l'identification de variations génétiques associées aux niveaux de microARN mesurés dans le plasma. Ces associations ont révélé des régions régulatrices permettant une meilleure compréhension des mécanismes de régulation des microARN. L'agglomération des variations génétiques identifiés sous forme de variables instrumentales ont mis en évidence l'importante contribution de la génétique dans la régulation des microARN circulants. Le second projet avait pour objectif d'identifier des microARN plasmatiques en grossesse sécrétés par les tissus fœtaux. Pour ce faire, les variations génétiques contenues dans les séquences des microARN mesurées ont été comparées à celles de l'ADN de la mère et de l'enfant. Toutefois, le haut niveau de conservation de leur séquence ne permet pas d'en faire une distinction claire.
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- 2022
39. Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing
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Eva Hřibová, Angélique D'Hont, Patrick Wincker, Franc-Christophe Baurens, Arnaud Lemainque, Benjamin Noel, Corinne Cruaud, Jean-Marc Aury, Caroline Belser, Guillaume Martin, Jaroslav Doležel, Nabila Yahiaoui, Benjamin Istace, Karine Labadie, 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), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), France GenomiqueANR-10-INBS-09-08, Center de cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), Agropolis Fondation1504-006, ERDF project 'Plants as a tool for sustainable global development'CZ.02.1.01/0.0/0.0/16_019/0000827, Genoscope, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - 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)
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0106 biological sciences ,QH301-705.5 ,[SDV]Life Sciences [q-bio] ,Medicine (miscellaneous) ,Computational biology ,Genome informatics ,Musa acuminata ,01 natural sciences ,Genome ,Chromosomes, Plant ,Article ,General Biochemistry, Genetics and Molecular Biology ,F30 - Génétique et amélioration des plantes ,génomique ,Nanopores ,03 medical and health sciences ,Gapless playback ,Centromere ,Biology (General) ,Gene ,030304 developmental biology ,0303 health sciences ,Génome ,biology ,Contig ,phytogénétique ,food and beverages ,Biotechnologie végétale ,Musa ,Genomics ,Télomères ,Telomere ,biology.organism_classification ,Nanopore Sequencing ,Plant biotechnology ,Nanopore sequencing ,General Agricultural and Biological Sciences ,Genome, Plant ,010606 plant biology & botany - Abstract
Long-read technologies hold the promise to obtain more complete genome assemblies and to make them easier. Coupled with long-range technologies, they can reveal the architecture of complex regions, like centromeres or rDNA clusters. These technologies also make it possible to know the complete organization of chromosomes, which remained complicated before even when using genetic maps. However, generating a gapless and telomere-to-telomere assembly is still not trivial, and requires a combination of several technologies and the choice of suitable software. Here, we report a chromosome-scale assembly of a banana genome (Musa acuminata) generated using Oxford Nanopore long-reads. We generated a genome coverage of 177X from a single PromethION flowcell with near 17X with reads longer than 75 kbp. From the 11 chromosomes, 5 were entirely reconstructed in a single contig from telomere to telomere, revealing for the first time the content of complex regions like centromeres or clusters of paralogous genes., Belser, Baurens et al. report a chromosome-scale assembly of a banana genome (Musa acuminata) with five out of eleven chromosomes entirely reconstructed in a single contig from telomere to telomere. This work sheds light on the content of complex regions like centromeres or clusters of paralogous genes in the banana genome.
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- 2021
40. Genomics applied to the study of campylobacter and helicobacter infections
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Jehanne, Quentin, BoRdeaux Institute in onCology (Inserm U1312 - BRIC), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Bordeaux, Philippe Lehours, and STAR, ABES
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Genomique ,Ngs ,Helicobacter ,Linux ,Campylobacter ,Genomics ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,Python ,[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM] - Abstract
Intestinal and gastric bacterial infections caused by Campylobacter and Helicobacter bacteria are frequent: Campylobacter species can lead to severe gastroenteritis cases through the consumption of contaminated products such as meat and Helicobacter bacteria may be responsible of ulcers or gastric cancers. More than 200,000 campylobacteriosis cases are reported in the European Union each year. It has also been shown that about 50% of the world population is infected with Helicobacter pylori. A large number of Campylobacter strains and gastric biopsies from clinical cases are received daily at the French National Reference Center for Campylobacters and Helicobacter (NRCCH) where analyses such as species identification and antimicrobial resistance determination are performed. Several methods are used to study these pathogens: bacterial cultures, antibiograms, MALDI-TOF mass spectrometry and DNA extraction for real-time PCR. Despite the fact these analyses are cheap and quick, it may also introduce some disadvantages: for example species identification using MALDI-TOF is sometimes non-significant and the determination of molecular resistance mecanisms among resistant isolates can also be challenging. Today, next-gen sequencing is a crucial tool to generate a large amount of data and, combined with bioinformatics, can solve numerous clinical problems encountered in the laboratory. In order to modernize the analysis of French clinical cases performed at the NRCCH, various bioinformatic tools and scripts were set up and developped during this PhD. The main objective was to enrich our knowledge on these bacterial infections by highlighting DNA and protein sequences variations involved in various problematics. Over these three years, we have then identify: SNPs (Single Nucleotide Polymorphisms) within the genome of Campylobacter coli that are able to discriminate three different sources of contamination (chickens, cattle and pigs), new antimicrobial resistance genes that have emerged in France in the past few years but also new Campylobacter and Helicobacter species. These differents data and tools are now routinely used in the NRCCH laboratory. All these analyses were made possible by the use of Linux environment and Bash or Python programming languages allowing the study of thousands of DNA sequences from a variety of clinical isolates that have been sequenced throughout many projects. This «genomic exploration» was here the key to answer the different clinical issues., Les infections bactériennes intestinales et gastriques par les bactéries du genre Campylobacter et Helicobacter sont très fréquentes: l’une pouvant provoquer des gastro-entérites sévères des suites d’une contamination alimentaire (principalement la viande) et l’autre étant liée au développement d’ulcères ou bien de cancers gastriques. Plus de 200 000 cas de campylobacterioses sont recensés dans l’Union Européenne chaque année, avec comme principale espèce Campylobacter jejuni. De plus, environ 50% de la population mondiale est infectée par Helicobacter pylori. De très nombreuses souches de Campylobacter et de biopsies gastriques sont reçues quotidiennement au CNR des Campylobacters et des Hélicobacters (CNRCH) où y sont menées des analyses telles l’identification de l’espèce et de la résistance aux antibiotiques. Plusieurs méthodes sont mises en place pour étudier ces pathogènes : cultures bactériennes, antibiogrammes, spectromètre de masse MALDI-TOF et extraction d’ADN pour des PCR en temps réel. Malgré la rapidité et le moindre coût de ces méthodes, les utiliser en routine présente des désavantages notamment des identifications d’espèces parfois non concluantes avec le MALDI-TOF ou la difficulté de déterminer les mécanismes moléculaires de résistance. Aujourd’hui, le séquençage haut débit couplé à la bio-informatique permet de générer des données cruciales pour résoudre ces nombreuses problématiques rencontrées en laboratoire. C’est en vue de moderniser les analyses de cas cliniques français effectuées au CNRCH que différents outils et scripts bio-informatiques ont été mis en place mais aussi développés durant ce doctorat. Le principal objectif étant d’enrichir nos connaissances sur ces infections bactériennes : de mettre en évidence des variations dans les séquences d’ADN (gène et mutations) mais aussi protéiques impliquées dans diverses problématiques. Ainsi, il a pu être identifié durant ces trois années : des SNPs (Single Nucleotide Polymorphisms) dans le génome de Campylobacter coli spécifiques à trois différentes sources de contamination (la volaille, les bovins et les porcs), des nouveaux gènes de résistance aux antibiotiques qui émergent sur le territoire métropolitain mais aussi des nouvelles espèces du genre Helicobacter ou Campylobacter. Ces outils et données sont d’ores et déjà utilisés en routine au sein du CNRCH. Toutes ces analyses ont pu être possibles via l’utilisation de l’environnement Linux (progammation Bash et Python) permettant d’étudier des milliers de séquences d’ADN provenant d’une variété de souches séquencées au cours des différents projets. Cette «exploration génomique» fût ici la clé pour répondre aux différentes problématiques cliniques.
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- 2022
41. Penguin ectoparasite panmixia suggests extensive host movement within a colony.
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Moon, Katherine L., Dann, Peter, Chown, Steven L., McGaughran, Angela, and Fraser, Ceridwen I.
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LITTLE blue penguin , *ECTOPARASITES , *BIRD parasites - Abstract
Parasite population structure can be used to infer fine-scale movement in host species. Many penguin species form large social colonies, and are highly philopatric, returning to the same nest or burrow, along the same route, after each trip to sea. Within a colony, however, the local abundance, physical similarity, and nocturnal habits of penguins hinder the observation of fine-scale movements. To determine the extent of movement and interaction of penguins within colonies, a genotyping by sequencing (GBS) approach was used to study the fine-scale structure of ticks--which depend on host movements for dispersal--exploiting the largest Little Penguin (Eudyptula novaehollandiae) colony in Australia (Phillip Island, Victoria). No barriers to tick gene flow were identified, and we infer that extensive penguin movement occurs throughout the colony. Our findings support the hypothesis that some penguin species are highly gregarious, socializing widely within colonies despite strong nest-site philopatry. [ABSTRACT FROM AUTHOR]
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- 2018
- Full Text
- View/download PDF
42. Population genomics of sorghum ( Sorghum bicolor) across diverse agroclimatic zones of Niger.
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Maina, Fanna, Bouchet, Sophie, Marla, Sandeep R., Hu, Zhenbin, Wang, Jianan, Mamadou, Aissata, Abdou, Magagi, Saïdou, Abdoul-Aziz, Morris, Geoffrey P., and Ungerer, Mark
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COMMERCIAL products , *SORGHUM , *FOOD security , *PLANT growing media , *SINGLE nucleotide polymorphisms - Abstract
Improving adaptation of staple crops in developing countries is important to ensure food security. In the West African country of Niger, the staple crop sorghum ( Sorghum bicolor) is cultivated across diverse agroclimatic zones, but the genetic basis of local adaptation has not been described. The objectives of this study were to characterize the genomic diversity of sorghum from Niger and to identify genomic regions conferring local adaptation to agroclimatic zones and farmer preferences. We analyzed 516 Nigerien accessions for which local variety name, botanical race, and geographic origin were known. We discovered 144 299 single nucleotide polymorphisms (SNPs) using genotyping-by-sequencing (GBS). We performed discriminant analysis of principal components (DAPC), which identified six genetic groups, and performed a genome scan for loci with high discriminant loadings. The highest discriminant coefficients were on chromosome 9, near the putative ortholog of maize flowering time adaptation gene Vgt1. Next, we characterized differentiation among local varieties and used a genome scan of pairwise FST values to identify SNPs associated with specific local varieties. Comparison of varieties named for light- versus dark-grain identified differentiation near Tannin1, the major gene responsible for grain tannins. These findings could facilitate genomics-assisted breeding of locally adapted and farmer-preferred sorghum varieties for Niger. [ABSTRACT FROM AUTHOR]
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- 2018
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43. Evolution as an ecosystem process: insights from genomics.
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Matthews, Blake, Best, Rebecca J., Feulner, Philine G.D., Narwani, Anita, Limberger, Romana, and Morgan, Ted
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ECOSYSTEM dynamics , *GENOMES , *BIODIVERSITY , *PHENOTYPES , *ENVIRONMENTAL sciences - Abstract
Evolution is a fundamental ecosystem process. The study of genomic variation of organisms can not only improve our understanding of evolutionary processes, but also of contemporary and future ecosystem dynamics. We argue that integrative research between the fields of genomics and ecosystem ecology could generate new insights. Specifically, studies of biodiversity and ecosystem functioning, evolutionary rescue, and eco-evolutionary dynamics could all benefit from information about variation in genome structure and the genetic architecture of traits, whereas genomic studies could benefit from information about the ecological context of evolutionary dynamics. We propose new ways to help link research on functional genomic diversity with (reciprocal) interactions between phenotypic evolution and ecosystem change. Despite numerous challenges, we anticipate that the wealth of genomic data being collected on natural populations will improve our understanding of ecosystems. [ABSTRACT FROM AUTHOR]
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- 2018
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44. Les big data, généralités et intégration en radiothérapie.
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Le Fèvre, C., Poty, L., and Noël, G.
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Résumé Les nombreuses avancées dans les systèmes informatiques (collection de données, bases de données, stockage), les possibilités diagnostiques et thérapeutiques sont responsables d’une augmentation et d’une diversification des données disponibles. Les big data offrent les capacités, dans le domaine de la santé, d’accélérer les découvertes et d’optimiser la prise en charge des patients en combinant un nombre de données presque infini par la création de modèles thérapeutiques. En radiothérapie, le développement des big data est attrayant car les données à traiter sont très nombreuses et hétérogènes (démographiques, radiomiques, génomiques, radiogénomiques, etc.). La prédiction de l’efficacité et de la tolérance du traitement par irradiation serait alors optimisée. Avec ces nouveaux concepts, encore au stade préliminaire, il apparaît possible de développer une médecine de haute précision et personnalisée, toujours plus sécurisée et fiable. The many advances in data collection computing systems (data collection, database, storage), diagnostic and therapeutic possibilities are responsible for an increase and a diversification of available data. Big data offers the capacities, in the field of health, to accelerate the discoveries and to optimize the management of patients by combining a large volume of data and the creation of therapeutic models. In radiotherapy, the development of big data is attractive because data are very numerous et heterogeneous (demographics, radiomics, genomics, radiogenomics, etc.). The expectation would be to predict the effectiveness and tolerance of radiation therapy. With these new concepts, still at the preliminary stage, it is possible to create a personalized medicine which is always more secure and reliable. [ABSTRACT FROM AUTHOR]
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- 2018
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45. Genomic tools for traceability: Opportunities, challenges and perspectives for the Canadian forestry sector.
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Godbout, Julie, Bomal, Claude, Farr, Ken, Williamson, Miranda, and Isabel, Nathalie
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FOREST management ,NATURAL resources management ,FOREST conversion ,GOVERNMENT policy - Abstract
Copyright of Forestry Chronicle is the property of Canadian Institute of Forestry and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2018
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46. International Barcode of Life: Focus on big biodiversity in South Africa.
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Adamowicz, Sarah J., Hollingsworth, Peter M., Ratnasingham, Sujeevan, van der Bank, Michelle, and Cristescu, M.E.
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Participants in the 7th International Barcode of Life Conference (Kruger National Park, South Africa, 20-24 November 2017) share the latest findings in DNA barcoding research and its increasingly diversified applications. Here, we review prevailing trends synthesized from among 429 invited and contributed abstracts, which are collated in this open-access special issue of Genome. Hosted for the first time on the African continent, the 7th Conference places special emphasis on the evolutionary origins, biogeography, and conservation of African flora and fauna. Within Africa and elsewhere, DNA barcoding and related techniques are being increasingly used for wildlife forensics and for the validation of commercial products, such as medicinal plants and seafood species. A striking trend of the conference is the dramatic rise of studies on environmental DNA (eDNA) and on diverse uses of high-throughput sequencing techniques. Emerging techniques in these areas are opening new avenues for environmental biomonitoring, managing species-at-risk and invasive species, and revealing species interaction networks in unprecedented detail. Contributors call for the development of validated community standards for high-throughput sequence data generation and analysis, to enable the full potential of these methods to be realized for understanding and managing biodiversity on a global scale. [ABSTRACT FROM AUTHOR]
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- 2017
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47. Identification de gènes impliqués dans les ataxies épisodiques par combinaison de séquençages génomique et transcriptomique
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Audet, Sébastien and Tétreault, Martine
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Transcriptomique ,Génétique clinique ,SpliceAI ,ExpansionHunter ,Bioinformatics ,Integrative analysis ,Ataxies ,Génomique ,Transcriptomic ,Analyse intégrative ,Genomic ,Bio-informatique ,Ataxia ,Clinical genetics ,RNA-seq ,WGS - Abstract
Cette étude pilote vise à développer une méthode d'analyse intégrative qui permet d'augmenter le taux de réussite du diagnostic clinique des mutations génétiques rares. De plus, l'identification de nouveaux gènes associés à l'ataxie épisodique (EA) et l'évaluation de nouveaux algorithmes de prédiction, pour un examen de variants plus robuste, découleront de l'enquête. Caractérisé par une perte sporadique de la coordination des mouvements volontaires, l'EA se manifeste généralement tardivement, avec une hétérogénéité clinique et génétique élevée, compliquant largement l’obtention d’un diagnostic précis. Alors que quatre gènes ont été liés aux huit sous-types d'EA, de nombreux patients demeurent sans diagnostic moléculaire dû aux limites des méthodes de séquençage d’ADN. Ces lacunes accentuent l’intérêt d’implanter le séquençage de l’ARN en milieu clinique, afin d’obtenir l’information fonctionnelle offerte par l’approche. Des patients atteints d’EA, sans diagnostic moléculaire malgré un examen approfondi, ont été recrutés à Montréal. Le séquençage du génome entier (WGS) et de l'ARN a été effectué sur des échantillons de sang pour identifier les variants nucléotidiques, l'expression différentielle, les événements d'épissage ainsi que les expansions de microsatellites. Plusieurs algorithmes de prédiction de la pathogénicité récents ont été choisis pour être testés parallèlement aux algorithmes standard. Des données WGS provenant d’un trio familial atteint de pathologies neurologiques ont également été soumises au pipeline génomique développé pour la cohorte EA. Des variants candidats ont été identifiés pour chaque patient en fonction des scores de pathogénicité, de la rareté des événements génétiques et des informations fonctionnelles et cliniques connues pour un gène altéré donné. Parmi les découvertes figurent des mutations non-sens, des faux-sens, de l'épissage alternatif ainsi que des expansions nucléotidiques dans des gènes associés aux ataxies spinocérébelleuses ou aux paraplégies spastiques. En plus d'être présents dans les ensembles de données de séquençage disponibles pour chaque patient, les événements génomiques ont été vérifiés par séquençage Sanger de l'ADN et de l'ARN lorsque possible. Les effets fonctionnels potentiels, prédits principalement à partir du RNA-seq et suggérant une expression anormale de l'ARNm, ont également été évalués par amplification PCR et qPCR traditionnelle. À ce jour, quatre des dix patients ont reçu ou sont en voie de recevoir un diagnostic clinique, et quatre autres présentent d’excellents candidats moléculaires pour expliquer une pathologie ataxique. Ce projet devrait permettre un diagnostic mieux défini, conduisant à une meilleure qualité de vie, une meilleure évaluation du pronostic et une meilleure prise en charge des patients. L’identification de modulateurs génétiques chez certains d’entre eux devrait également permettre une meilleure caractérisation clinique des conditions rapportées, bénéficiant les évaluations symptomatiques futures. De plus, la méta-analyse des données RNA-seq offre le potentiel de découvrir des régulateurs de pathogenèse communs à l’EA. Il favorisera également l'approche intégrative pour un plus large éventail de troubles et pourrait éventuellement conduire à de nouvelles stratégies thérapeutiques., This pilot study aims to develop an integrative analysis method that allows for an increased diagnosis success rate of rare genetic mutations. Moreover, identification of novel genes associated with Episodic Ataxia (EA) and evaluation of new AI-generated prediction algorithms, for a more robust variant examination, will ensue from the investigation. Characterized by sporadic loss of voluntary movement coordination, EA typically manifest with a late onset as well as high-clinical and genetic heterogeneity, setting additional hurdles to diagnosis. While four genes have been linked to the eight subtypes of EA, many patients are left without molecular diagnosis due to the limitations of individual DNA-sequencing methods, which can be mitigated by the functional overview that RNA sequencing (RNA-seq) offers. EA patients, lacking molecular diagnosis despite in-depth examination, were recruited in Montreal. Whole-Genome sequencing (WGS) and RNA-seq were performed on blood samples to identify single nucleotide variants, differential expression, splicing events, structural variants and repeat expansions. Multiple recent pathogenicity prediction algorithms were chosen for testing concurrently to standard ones, in order to evaluate their performance and potential for clinical pipelines integration. WGS data of a family trio from France, in which the father and the daughter present neurologic pathologies, were also processed through the genomic pipeline that was developed for the EA cohort in order to identify the cause of their disorder. Candidate variants were identified for each patient according to pathogenicity scores, rarity of genetic events, and known functional as well as clinical information for a given altered gene. Among the findings are truncations, missenses, alternative splicing, and repeat expansions in genes already associated to either spinocerebellar ataxia or spastic paraplegia. In addition to being present in both datasets when available, validation of these interesting genomic events has been performed through Sanger Sequencing of both DNA and RNA when feasible. For strong candidates where the available functional information from RNA-seq suggests abnormal mRNA expression, validation includes PCR amplification as well as a traditional qPCR to support effects on transcripts. To this day, four out of ten patients have received or are on the verge of receiving a diagnosis, and four others are carrying excellent molecular candidates requiring further validation to explain their ataxic pathologies. This project should provide more defined diagnosis, leading to better quality of life, better evaluation of prognosis and better management of care for patients. Identification of genetic modifier in some of them should also allow for a better clinical characterization of the reported conditions, benefiting future patient examinations. A meta-analysis of our patients’ transcriptomic profiles could also uncover commonly affected pathways in EA development. It will also promote the integrative approach for a larger spectrum of disorders and might eventually lead to new therapeutic strategies.
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- 2022
48. Towards smart and sustainable development of modern berry cultivars in Europe
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Elisa Senger, Sonia Osorio, Klaus Olbricht, Paul Shaw, Béatrice Denoyes, Jahn Davik, Stefano Predieri, Saila Karhu, Sebastian Raubach, Nico Lippi, Monika Höfer, Helen Cockerton, Christophe Pradal, Ebru Kafkas, Suzanne Litthauer, Iraida Amaya, Björn Usadel, Bruno Mezzetti, Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, Instituto de Hortofruticultura Subtropical y Mediterranea 'La Mayora' (IHSM), Universidad de Málaga [Málaga] = University of Málaga [Málaga]-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Hansabred [Dresden], The James Hutton Institute, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Norsk institutt for bioøkonomi=Norwegian Institute of Bioeconomy Research (NIBIO), Institute for BioEconomy [Sesto Fiorentino] (IBE | CNR), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Natural Resources Institute Finland (LUKE), Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), National Institute of Agricultural Botany (NIAB), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Scientific Data Management (ZENITH), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Cukurova University, Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Università Politecnica delle Marche [Ancona] (UNIVPM), and The authors acknowledge support from the European Union’s Horizon 2020 research and innovation program (grant agreement ID: 101000747)
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consumer preference ,[SDV]Life Sciences [q-bio] ,métadonnées ,plant genetic resources ,Plant Science ,Fragaria ,F30 - Génétique et amélioration des plantes ,génomique ,Ressource génétique végétale ,image analysis ,Genetics ,genomics ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Humans ,amélioration génétique ,QK ,BreedingValue project ,trait/genotype association ,Cell Biology ,Sustainable Development ,metabolomics ,Amélioration des plantes ,Petits fruits ,Propriété organoleptique ,[SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding ,Valeur génétique ,Plant Breeding ,ddc:580 ,berry breeding ,Fruit ,Rubus ,Vaccinium ,Génotype ,Genome-Wide Association Study - Abstract
International audience; Fresh berries are a popular and important component of the human diet. The demand for high-quality berries and sustainable production methods is increasing globally, challenging breeders to develop modern berry cultivars that fulfill all desired characteristics. Since 1994, research projects have characterized genetic resources, developed modern tools for high-throughput screening, and published data in publicly available repositories. However, the key findings of different disciplines are rarely linked together and only a limited range of traits and genotypes has been investigated. The Horizon2020 project BreedingValue will address these challenges by studying a broader panel of strawberry, raspberry and blueberry genotypes in detail, in order to recover the lost genetic diversity that has limited the aroma and flavor intensity of recent cultivars. We will combine metabolic analysis with sensory panel tests and surveys to identify the key components of taste, flavor and aroma in berries across Europe, leading to a high-resolution map of quality requirements for future berry cultivars. Traits linked to berry yields and the effect of environmental stress will be investigated using modern image analysis methods and modeling. We will also use genetic analysis to determine the genetic basis of complex traits for the development and optimization of modern breeding technologies such as molecular marker arrays, genomic selection and genome wide association studies. Finally, the results, raw data and metadata will be made publicly available on the open platform Germinate in order to meet FAIR data principles and provide the basis for sustainable research in the future.
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- 2022
49. Inférences démographiques à partir de données génomiques sous des modèles spatialisés
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Virgoulay, Thimothée, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Montpellier, and François Rousset
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[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,Génomique ,Modèle d'isolement par la distance ,Génétique des populations ,Population genetics ,Isolation by distance models ,Dispersal ,Genomics ,Dispersion ,Méthode d'inférence par simulation ,Inference by simulation method - Abstract
This thesis aims at presenting a set of concepts and inferential tools adapted to the analysis of neutral genetic polymorphism in a specific class of stochastic population genetics models : spatialized demographic models of populations where the dispersal of individuals between generations is limited in space (isolation by distance models). Such analysis is based on the combination of stochastic models of population evolution (generation by generation coalescence) and statistical inference method by simulation (“the summary-likelihood method”). In a first step various tools were developed and tested independently before being integrated together to create an inferential framework adapted to our models. In a second step, we used this framework to study the performances and benefits of these new inference methods and the influence of considering linkage disequilibrium patterns on parameter inference under distance isolation models.; Cette thèse a pour but de développer un ensemble de concepts et d’outils inférentiels adaptés à l’analyse du polymorphisme génétique neutre dans une classe bien spécifique de modèles stochastiques de génétique des populations : les modèles démographiques spatialisés de populations où la dispersion des individus entre générations est limitée dans l’espace (modèles d’isolement par la distance). Cette analyse repose sur la combinaison de modèles stochastiques de l’évolution des populations (la coalescence en génération par génération) et d’une méthode d’inférence statistique par simulation (“the summary-likelihood method”). Dans un premier temps, les divers outils furent mis au point et testés indépendamment avant d’être intégré ensemble afin de créer un canevas d’inférence reliant des outils adaptés à nos modèles. Dans un second temps nous avons utilisé ce canevas afin d’étudier les performances et les bénéfices de ces nouvelles méthodes d’inférences par simulation dans ce contexte d’isolement par la distance, notamment l’influence de la prise en compte des patrons de déséquilibre de liaison sur l’inférence des paramètres de densité et de dispersion.
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- 2022
50. Genomic Instability in Somatic Hybridization between Poncirus and Citrus Species Aiming to Create New Rootstocks
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Dominique Dambier, Pascal Barantin, Gabriel Boulard, Gilles Costantino, Pierre Mournet, Aude Perdereau, Raphaël Morillon, Patrick Ollitrault, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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)-Université de Montpellier (UM), 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), Amélioration Génétique et Adaptation des Plantes méditerranéennes et Tropicales Corse - Antenne Corse (AGAP-Corse), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), and European Project: LIFE18 CCA/ES/001109,LIFE Vida for Citrus
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H01 - Protection des végétaux - Considérations générales ,Citrus ,Stress abiotique ,citrumelo ,Plant Science ,protoplast fusion ,somatic embryogenesis ,genotyping by sequencing ,somaclonal variation ,Citrus sinensis ,Citrus reticulata ,Poncirus trifoliata ,citrange ,citrandarin ,F30 - Génétique et amélioration des plantes ,génomique ,Résistance aux facteurs nuisibles ,Hybridation somatique ,Résistance physiologique au stress ,Porte greffe ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,food and beverages ,Amélioration des plantes ,Stress biotique ,Agronomy and Crop Science ,Food Science - Abstract
International audience; Rootstocks are an important component for citrus adaptation to increasing biotic and abiotic stresses resulting from global climate change. There is a strong complementarity between Citrus species, which adapt to abiotic stresses, and Poncirus trifoliata and its intergeneric hybrids, which exhibit resistances or tolerances to major diseases and pests. Thus, symmetrical somatic hybridization between complementary diploid rootstocks of these two genera appears to be an efficient way to develop new tetraploid rootstocks in order to address the new challenges of the citrus industry. New intergeneric somatic hybrids were obtained by electrofusion between protoplasts of Citrus and P. trifoliata hybrids. Extensive characterization of the nuclear and cytoplasmic genomes was performed by genotyping-by-sequencing (GBS) analysis. This revealed diploid cybrids and nuclear somatic hybrids. Mitochondrial genomes were mostly inherited from the callus parent, but homologous recombination events were observed for one parental combination. Chloroplasts exhibited random uniparental inheritance. GBS revealed local chromosomal instabilities for all nuclear somatic hybrids and whole chromosome eliminations for two hybrids. However, at the whole genome level, symmetrical addition of the nuclear genomes of both parents was predominant and all somatic hybrids displayed at least one trifoliate orange haplotype throughout the genome.
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- 2022
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