1. A physical, genetic and functional sequence assembly of the barley genome
- Author
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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