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1. New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing

Author

Catherine Feuillet, Miroslav Valárik, Bernardo J. Clavijo, Ingrid Garbus, Jeroslav Doležel, Maximo Rivarola, G. Tranquilli, Marcelo Helguera, Leonardo Sebastián Vanzetti, Mario Caccamo, Norma Paniego, Mihaela Martis, Viviana Echenique, Klaus F. X. Mayer, Hana Šimková, Phillippe Leroy, Sergio Alberto González, Estación Experimental Agropecuaria Marcos Juáre, Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), The Genome Analysis Centre (TGAC), MIPS/IBIS, Helmholtz-Zentrum München (HZM), Estación Experimental Agropecuaria Marcos Juárez, Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Centro de Recursos Naturales Renovables de la Zona Semiárida [Bahía Blanca] (CERZOS), Universidad Nacional del Sur [Argentina] (UNS)-Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Universidad Nacional del Sur [Argentina] (UNS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Norwich Research Park, (TGAC), Centro de Investigación de Recursos Naturales (CIRN), CONICET (International Cooperation Grant) D456, AEBIO 245001.711.732 902 PNBIO 1131041.43 PNCYO 1127041, Universidad Nacional del Sur (PGI-TIR) CSU-142/14, Agencia Espanola de Cooperacion Internacional y Desarrollo AECID-A1/041041/11, Czech Science Foundation P501/12/G090, National Program of Sustainability I LO1204, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Helmholtz Zentrum München = German Research Center for Environmental Health, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Sur [Argentina] (UNS), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Cromosoma 4 D, Gene annotation, Virtual gene order, Plant Science, 01 natural sciences, Genome, Chromosome 4d Survey Sequence, Gene Annotation, Gene Content, Synteny, Triticum Aestivum, Virtual Gene Order, Gene Order, Triticum, Expressed Sequence Tags, 2. Zero hunger, Genetics, 0303 health sciences, Expressed sequence tag, virtual gene order, biology, Contig, synteny, Chromosome Mapping, High-Throughput Nucleotide Sequencing, food and beverages, General Medicine, Gene content, SNP, single nucleotide polymorphism, dN/dS, non-synonymous-to-synonymous substitutions, EST, expressed sequence tag, ISBP, insertion site-based polymorphism, Biotecnología Agrícola y Biotecnología Alimentaria, Os, Oryza sativa – rice, Orthologous Gene, Chromosome 4D survey sequence, LMP, long mate pair, Molecular Sequence Data, gene content, Biotecnología Agropecuaria, Triticum aestivum, CDS, coding DNA sequences, Trigo, IWGSC, International Wheat Genome Sequencing Consortium, Bd, Brachypodium distachyon, Chromosomes, Chromosomes, Plant, Article, 03 medical and health sciences, chromosome 4D survey sequence, SE, single end, Aegilops tauschii, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, Sb, Sorghum bicolor – sorghum, Cromosomas, NGS, next generation sequencing, Sequence Analysis, DNA, biology.organism_classification, gene annotation, Chromosome 4, Genes, CIENCIAS AGRÍCOLAS, MDA, multiple displacement amplification, SSR, single sequence repeat, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

Highlights • Survey sequence of T. aestivum chromosome 4D was obtained by pyrosequencing. • Near 5700 genes were predicted on 4D chromosome, ∼2200 on 4DS and ∼3500 on 4DL. • A 4D virtual gene order based on synteny with orthologous gene loci is proposed. • Among group 4, higher collinearity exists between 4D and 4B as compared to 4A. • Complementary data to that provided by IWGSC is presented, available at NCBI., Survey sequencing of the bread wheat (Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) reads were assembled into contigs (223 Mb) and scaffolds (65 Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34 Mb to chromosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheat orthologous gene loci and 381 wheat gene models was built. This order was largely consistent with the scaffold order determined based on a published high density map from the Ae. tauschii chromosome 4, using bin-mapped 4D ESTs as a common reference. The virtual order showed a higher collinearity with homeologous 4B compared to 4A. Additionally, a virtual map was constructed and ∼5700 genes (∼2200 on 4DS and ∼3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information.

Published
2015
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2. Genome interplay in the grain transcriptome of hexaploid bread wheat

Author

Pfeifer, Matthias, Kugler, Karl, Sandve, Simen, Zhan, Bujie, Rudi, Heidi, Hvidsten, Torgeir, Mayer, Klaus, Rogers, Jane, Doležel, Jaroslav, Pozniak, Curtis, Eversole, Kellye, Feuillet, Catherine, Gill, Bikram, Friebe, Bernd, Lukaszewski, Adam, Sourdille, Pierre, Endo, Takashi, Kubaláková, Marie, Číhalíková, Jarmila, Dubská, Zdeňka, Vrána, Jan, Šperková, Romana, Šimková, Hana, Febrer, Melanie, Clissold, Leah, Mclay, Kirsten, Singh, Kuldeep, Chhuneja, Parveen, Singh, Nagendra K, Khurana, Jitendra, Akhunov, Eduard, Choulet, Frédéric, Alberti, Adriana, Barbe, Valérie, Wincker, Patrick, Kanamori, Hiroyuki, Kobayashi, Fuminori, Itoh, Takeshi, Matsumoto, Takashi, Sakai, Hiroaki, Tanaka, Tsuyoshi, Wu, Jianzhong, Ogihara, Yasunari, Handa, Hirokazu, Maclachlan, P Ron, Sharpe, Andrew, Klassen, Darrin, Edwards, David, Batley, Jacqueline, Olsen, Odd-Arne, Lien, Sigbjørn, Steuernagel, Burkhard, Wulff, Brande, Caccamo, Mario, Ayling, Sarah, Ramirez-Gonzalez, Ricardo H, Clavijo, Bernardo J, Wright, Jonathan, Spannagl, Manuel, Martis, Mihaela M, Mascher, Martin, Chapman, Jarrod, Poland, Jesse A, Scholz, Uwe, Barry, Kerrie, Waugh, Robbie, Rokhsar, Daniel S, Muehlbauer, Gary J, Stein, Nils, Gundlach, Heidrun, Zytnicki, Matthias, Jamilloux, Véronique, Quesneville, Hadi, Wicker, Thomas, Faccioli, Primetta, Colaiacovo, Moreno, Stanca, Antonio Michele, Budak, Hikmet, Cattivelli, Luigi, Glover, Natasha, Pingault, Lise, Paux, Etienne, Sharma, Sapna, Appels, Rudi, Bellgard, Matthew, Chapman, Brett, Nussbaumer, Thomas, Bader, Kai Christian, Rimbert, Hélène, Wang, Shichen, Knox, Ron, Kilian, Andrzej, Alaux, Michael, Alfama, Françoise, Couderc, Loïc, Guilhot, Nicolas, Viseux, Claire, Loaec, Mikael, Keller, Beat, Praud, Sébastien, Plant Genome and Systems Biology, Helmholtz Diabetes Center at Helmholtz Zentrum, Norwegian University of Life Sciences (NMBU), University of Norway, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Norwegian Research Council 199387, Deutsche Forschungsgemeinschaft (DFG) SFB924, German Federal Ministry of Education and Research (BMBF), European Commission's 7th Framework Program, Plant Genome and Systems Biology (PGSB), Helmholtz Zentrum München = German Research Center for Environmental Health, Centre for Integrative Genetics, Department of Chemistry, Biotechnology and Food Science, Eversole Associates, Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), University of Saskatchewan [Saskatoon] (U of S), Bayer Crop Science, Kansas State Univ, Dept Plant Pathol, Manhattan, KS 66506 USA, Partenaires INRAE, Department of Botany and Plant Sciences [Riverside], University of California [Riverside] (UC Riverside), University of California (UC)-University of California (UC), Graduate School of Agriculture, Kyoto University, Kyoto, Japan, Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Centre of the Region Haná for Biotechnological and Agricultural Research, Fraunhofer Institute for Intelligent Analysis and Information Systems (Fraunhofer IAIS), Fraunhofer (Fraunhofer-Gesellschaft), National Research Centre Plant Biotechnology, Dept Plant Pathol, Kansas State University, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Bayer Cropscience, Institute of Crop Sciences of CAAS [Beijing] (ICS CAAS), Chinese Academy of Agricultural Sciences (CAAS), National Institute of Agrobiological Sciences (NIAS), National Institute of Agrobiological Sciences, Natl Inst Agrobiol Sci, JST-CREST, Japan Science and Technology Agency, Global Institute of Food Security, School of Agriculture and Food Sciences, Australian Centre for Plant Functional Genomics, University of Queensland [Brisbane], Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, The Sainsbury Laboratory [Norwich] (TSL), Genome Analysis Centre, John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), European Synchrotron Radiation Facility (ESRF), German Research Center for Environmental Health - Helmholtz Center München (GmbH), MIPS/IBIS, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), DOE Joint Genome Institute [Walnut Creek], United States Department of Energy, The James Hutton Institute, Inst Bioinformat & Syst Biol, Munich Informat Ctr Prot Sequences, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institute of Plant Biology, Universität Zürich [Zürich] = University of Zurich (UZH), Fac Engn & Nat Sci, Sabanci University [Istanbul], Genomics Research Centre, Consiglio per la Ricerca e Sperimentazione in Agricoltura, York University, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Centre for Comparative Genomics, Murdoch University, CUBE Division of Computational Systems Biology, University of Vienna [Vienna], Department of Plant Pathology, Shizuoka University, Diversity Arrays Technology Pty Ltd (DArT P/L), Centre de Recherche de Chappes, BIOGEMMA, Research Council of Norway [199387], German Research Foundation (DFG) [SFB924], German Federal Ministry of Education and Research (BMBF), European Project: 283496,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2011-2,TRANSPLANT(2011), Helmholtz-Zentrum München (HZM), Univ Saskatchewan, Dept Plant Sci, Saskatoon, SK, Canada, University of California [Riverside] (UCR), University of California-University of California, Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, University of Saskatchewan, John Innes Centre, and University of Zurich

Subjects
MESH: Genome, Plant, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, [SDV]Life Sciences [q-bio], Gene Dosage, 01 natural sciences, Genome, MESH: Gene Dosage, Endosperm, Transcriptome, Gene Expression Regulation, Plant, Triticum, Cancer, Plant Proteins, International Wheat Genome Sequencing Consortium, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, MESH: Plant Proteins, food and beverages, alignment, Bread, MESH: Edible Grain, starchy endosperm, reveals, Genome, Plant, Biotechnology, profiles, General Science & Technology, Cereals, MESH: Triticum, Biology, Gene dosage, MESH: Endosperm, Polyploidy, MESH: Bread, 03 medical and health sciences, Polyploid, MESH: Polyploidy, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MD Multidisciplinary, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene family, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Gene Expression Regulation, Plant, Gene, Metabolic and endocrine, 030304 developmental biology, Whole genome sequencing, triticum, MESH: Transcriptome, Human Genome, Plant, Gene Expression Regulation, germination, gene expression, RNA, identification, Edible Grain, protein, 010606 plant biology & botany
Abstract

Allohexaploid bread wheat ( Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type–specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type– and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome.

Published
2014
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3. A physical, genetic and functional sequence assembly of the barley genome

Author

Mayer, Kf, Waugh, R, Langridge, P, Close, Tj, Wise, Rp, Graner, A, Matsumoto, T, Sato, K, Schulman, A, Muehlbauer, Gj, Stein, N, Ariyadasa, R, Schulte, D, Poursarebani, N, Zhou, R, Steuernagel, B, Mascher, M, Scholz, U, Shi, B, Madishetty, K, Svensson, Jt, Bhat, P, Moscou, M, Resnik, J, Hedley, P, Liu, H, Morris, J, Frenkel, Z, Korol, A, Bergès, H, Taudien, S, Felder, M, Groth, M, Platzer, M, Himmelbach, A, Lonardi, S, Duma, D, Alpert, M, Cordero, Francesca, Beccuti, Marco, Ciardo, G, Ma, Y, Wanamaker, S, Cattonaro, F, Vendramin, V, Scalabrin, S, Radovic, S, Wing, R, Morgante, M, Nussbaumer, T, Gundlach, H, Martis, M, Poland, J, Spannagl, M, Pfeifer, M, Moisy, C, Tanskanen, J, Zuccolo, A, Russell, J, Druka, A, Marshall, D, Bayer, M, Swarbreck, D, Sampath, D, Ayling, S, Febrer, M, Caccamo, M, Tanaka, T, Wannamaker, S, Schmutzer, T, Brown, Jw, Fincher, Gb, Stein, N., MIPS/IBIS, Helmholtz-Zentrum München (HZM), The James Hutton Institute, University of Adelaide, Iowa State University (ISU), Leibniz Institute of Plant Genetics and Crop Plant Research, Natl Inst Agrobiol Sci, Partenaires INRAE, Okayama University, University of Helsinki, University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Inst Evolut, University of Haifa [Haifa], German Ministry of Education and Research (BMBF) [0314000], Leibniz Association, European project of the 7th framework programme 'TriticeaeGenome', Austrian Wissenschaftsfond (FWF) [SFB F3705], ERA-NET PG project 'BARCODE', Scottish Government/BBSRC [BB/100663X/1], National Science Foundation [DBI 0321756, DBI-1062301], USDA-CSREES-NRI [2006-55606-16722], Agriculture and Food Research Initiative Plant Genome, Genetics and Breeding Program of USDA-CSREES-NIFA [2009-65300-05645], BRAIN and NBRP-Japan, and Japanese MAFF [TRG1008]

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Sequence assembly, 01 natural sciences, Genome, Gene Expression Regulation, Plant, 2. Zero hunger, Genetics, 0303 health sciences, MESSENGER-RNA DECAY, Multidisciplinary, food and beverages, Genomics, ARABIDOPSIS, Physical Chromosome Mapping, Molecular Sequence Annotation, Codon, Nonsense, MAP, HORDEUM-VULGARE L, Genome, Plant, EXPRESSION, Crops, Agricultural, Sequence analysis, Computational biology, Biology, MILDEW RESISTANCE LOCUS, Genes, Plant, Polymorphism, Single Nucleotide, Plant sciences, Evolution, Molecular, 03 medical and health sciences, REVEALS, RICE, Gene, 030304 developmental biology, Repetitive Sequences, Nucleic Acid, Comparative genomics, Hordeum, Sequence Analysis, DNA, 15. Life on land, EVOLUTION, Alternative Splicing, NONCODING RNAS, Hordeum vulgare, Transcriptome, 010606 plant biology & botany
Abstract

International audience; Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.

Published
2012
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4. Comparative analysis of chromosome 2A molecular organization in diploid and hexaploid wheat.

Author

Kaur P, Jindal S, Yadav B, Yadav I, Mahato A, Sharma P, Kaur S, Gupta OP, Vrána J, Šimková H, Doležel J, Gill BS, Meyer KFX, Khurana JP, Singh NK, Chhuneja P, and Singh K

Subjects
Diploidy, High-Throughput Nucleotide Sequencing, Microsatellite Repeats, Polymorphism, Single Nucleotide, Polyploidy, Sequence Analysis, DNA, Chromosome Mapping methods, Chromosomes, Plant genetics, Quantitative Trait Loci, Triticum genetics
Abstract

Diploid A genome wheat species harbor immense genetic variability which has been targeted and proven useful in wheat improvement. Development and deployment of sequence-based markers has opened avenues for comparative analysis, gene transfer and marker assisted selection (MAS) using high throughput cost effective genotyping techniques. Chromosome 2A of wheat is known to harbor several economically important genes. The present study aimed at identification of genic sequences corresponding to full length cDNAs and mining of SSRs and ISBPs from 2A draft sequence assembly of hexaploid wheat cv. Chinese Spring for marker development. In total, 1029 primer pairs including 478 gene derived, 501 SSRs and 50 ISBPs were amplified in diploid A genome species Triticum monococcum and T. boeoticum identifying 221 polymorphic loci. Out of these, 119 markers were mapped onto a pre-existing chromosome 2A genetic map consisting of 42 mapped markers. The enriched genetic map constituted 161 mapped markers with final map length of 549.6 cM. Further, 2A genetic map of T. monococcum was anchored to the physical map of 2A of cv. Chinese Spring which revealed several rearrangements between the two species. The present study generated a highly saturated genetic map of 2A and physical anchoring of genetically mapped markers revealed a complex genetic architecture of chromosome 2A that needs to be investigated further.

Published
2020
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5. A Genome-Wide Survey of Date Palm Cultivars Supports Two Major Subpopulations in Phoenix dactylifera.

Author

Mathew LS, Seidel MA, George B, Mathew S, Spannagl M, Haberer G, Torres MF, Al-Dous EK, Al-Azwani EK, Diboun I, Krueger RR, Mayer KF, Mohamoud YA, Suhre K, and Malek JA

Subjects
Alleles, Chromosome Mapping, Genetic Variation, Genotype, Phoeniceae classification, Phylogeny, Polymorphism, Single Nucleotide, Principal Component Analysis, Sequence Analysis, DNA, Genome, Plant, Phoeniceae genetics
Abstract

The date palm (Phoenix dactylifera L.) is one of the oldest cultivated trees and is intimately tied to the history of human civilization. There are hundreds of commercial cultivars with distinct fruit shapes, colors, and sizes growing mainly in arid lands from the west of North Africa to India. The origin of date palm domestication is still uncertain, and few studies have attempted to document genetic diversity across multiple regions. We conducted genotyping-by-sequencing on 70 female cultivar samples from across the date palm-growing regions, including four Phoenix species as the outgroup. Here, for the first time, we generate genome-wide genotyping data for 13,000-65,000 SNPs in a diverse set of date palm fruit and leaf samples. Our analysis provides the first genome-wide evidence confirming recent findings that the date palm cultivars segregate into two main regions of shared genetic background from North Africa and the Arabian Gulf. We identify genomic regions with high densities of geographically segregating SNPs and also observe higher levels of allele fixation on the recently described X-chromosome than on the autosomes. Our results fit a model with two centers of earliest cultivation including date palms autochthonous to North Africa. These results adjust our understanding of human agriculture history and will provide the foundation for more directed functional studies and a better understanding of genetic diversity in date palm., (Copyright © 2015 Mathew et al.)

Published
2015
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6. New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing.

Author

Helguera M, Rivarola M, Clavijo B, Martis MM, Vanzetti LS, González S, Garbus I, Leroy P, Šimková H, Valárik M, Caccamo M, Doležel J, Mayer KFX, Feuillet C, Tranquilli G, Paniego N, and Echenique V

Subjects
Chromosome Mapping, Expressed Sequence Tags chemistry, High-Throughput Nucleotide Sequencing, Molecular Sequence Data, Sequence Analysis, DNA, Chromosomes, Plant, Gene Order, Triticum genetics
Abstract

Survey sequencing of the bread wheat (Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) reads were assembled into contigs (223Mb) and scaffolds (65Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34Mb to chromosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheat orthologous gene loci and 381 wheat gene models was built. This order was largely consistent with the scaffold order determined based on a published high density map from the Ae. tauschii chromosome 4, using bin-mapped 4D ESTs as a common reference. The virtual order showed a higher collinearity with homeologous 4B compared to 4A. Additionally, a virtual map was constructed and ∼5700 genes (∼2200 on 4DS and ∼3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information., (Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.)

Published
2015
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7. The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle.

Author

Wang W, Haberer G, Gundlach H, Gläßer C, Nussbaumer T, Luo MC, Lomsadze A, Borodovsky M, Kerstetter RA, Shanklin J, Byrant DW, Mockler TC, Appenroth KJ, Grimwood J, Jenkins J, Chow J, Choi C, Adam C, Cao XH, Fuchs J, Schubert I, Rokhsar D, Schmutz J, Michael TP, Mayer KF, and Messing J

Subjects
Fresh Water, Molecular Sequence Data, Araceae genetics, Araceae growth & development, Genome, Plant genetics
Abstract

The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. Here we select Spirodela polyrhiza for whole-genome sequencing. We show that Spirodela has a genome with no signs of recent retrotranspositions but signatures of two ancient whole-genome duplications, possibly 95 million years ago (mya), older than those in Arabidopsis and rice. Its genome has only 19,623 predicted protein-coding genes, which is 28% less than the dicotyledonous Arabidopsis thaliana and 50% less than monocotyledonous rice. We propose that at least in part, the neotenous reduction of these aquatic plants is based on readjusted copy numbers of promoters and repressors of the juvenile-to-adult transition. The Spirodela genome, along with its unique biology and physiology, will stimulate new insights into environmental adaptation, ecology, evolution and plant development, and will be instrumental for future bioenergy applications.

Published
2014
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8. Analysing complex Triticeae genomes - concepts and strategies.

Author

Spannagl M, Martis MM, Pfeifer M, Nussbaumer T, and Mayer KF

Abstract

The genomic sequences of many important Triticeae crop species are hard to assemble and analyse due to their large genome sizes, (in part) polyploid genomes and high repeat content. Recently, the draft genomes of barley and bread wheat were reported thanks to cost-efficient and fast NGS technologies. The genome of barley is estimated to be 5 Gb in size whereas the genome of bread wheat accounts for 17 Gb and harbours an allo-hexaploid genome. Direct assembly of the sequence reads and access to the gene content is hampered by the repeat content. As a consequence, novel strategies and data analysis concepts had to be developed to provide much-needed whole genome sequence surveys and access to the gene repertoires. Here we describe some analytical strategies that now enable structuring of massive NGS data generated and pave the way towards structured and ordered sequence data and gene order. Specifically we report on the GenomeZipper, a synteny driven approach to order and structure NGS survey sequences of grass genomes that lack a physical map. In addition, to access and analyse the gene repertoire of allo-hexaploid bread wheat from the raw sequence reads, a reference-guided approach was developed utilizing representative genes from rice, Brachypodium distachyon, sorghum and barley. Stringent sub-assembly on the reference genes prevented collapsing of homeologous wheat genes and allowed to estimate gene retention rate and determine gene family sizes. Genomic sequences from the wheat sub-genome progenitors enabled to discriminate a large number of sub-assemblies between the wheat A, B or D sub-genome using machine learning algorithms. Many of the concepts outlined here can readily be applied to other complex plant and non-plant genomes.

Published
2013
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9. Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation.

Author

Wang X, Haberer G, and Mayer KF

Subjects
Base Sequence, Computational Biology, DNA, Plant genetics, Gene Expression Profiling, Gene Expression Regulation, Plant, Genes, Plant, Molecular Sequence Data, Phylogeny, Promoter Regions, Genetic, Sequence Analysis, DNA, Sorghum genetics, Conserved Sequence genetics, Evolution, Molecular, Genome, Plant, Oryza genetics
Abstract

Background: The spatiotemporal regulation of gene expression largely depends on the presence and absence of cis-regulatory sites in the promoter. In the economically highly important grass family, our knowledge of transcription factor binding sites and transcriptional networks is still very limited. With the completion of the sorghum genome and the available rice genome sequence, comparative promoter analyses now allow genome-scale detection of conserved cis-elements., Results: In this study, we identified thousands of phylogenetic footprints conserved between orthologous rice and sorghum upstream regions that are supported by co-expression information derived from three different rice expression data sets. In a complementary approach, cis-motifs were discovered by their highly conserved co-occurrence in syntenic promoter pairs. Sequence conservation and matches to known plant motifs support our findings. Expression similarities of gene pairs positively correlate with the number of motifs that are shared by gene pairs and corroborate the importance of similar promoter architectures for concerted regulation. This strongly suggests that these motifs function in the regulation of transcript levels in rice and, presumably also in sorghum., Conclusion: Our work provides the first large-scale collection of cis-elements for rice and sorghum and can serve as a paradigm for cis-element analysis through comparative genomics in grasses in general.

Published
2009
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