Helena Toegelová, Hana Šimková, Andrew G. Sharpe, Benoit Darrier, Adam M. Dimech, Jan Šafář, Nathan S. Watson-Haigh, Pierre Sourdille, Zeev Frenkel, Matthew J. Hayden, Frédéric Choulet, Johan Nyström-Persson, Iwgsc, Dangqun Cui, Gabriel Keeble-Gagnère, Matthias Pfeifer, Sébastien Boisvert, Angéla Juhász, Jaroslav Doležel, Francisco Câmara, Simone Rochfort, Matthew Tinning, Colin Cavanagh, Kerrie Forrest, Paul Eckermann, Delphine Fleury, Ute Baumann, Aurélien Bernard, Ming-Cheng Luo, B. Emma Huang, Jen Taylor, Rudi Appels, Dal-Hoe Koo, Zhengang Ru, David Konkin, Raj K. Pasam, Philippe Rigault, Michael Abrouk, Don Isdale, Abraham B. Korol, Marc-Alexandre Nolin, Josquin Tibbits, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, GYDLE, Center for Organismal Studies, Heidelberg University, Institute of Evolution, University of Haifa [Haifa], CSIRO Plant Industrie, Desert Agriculture Initiati, King Abdullah University of Science and Technology (KAUST), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Global Institute of Food Security, University of Saskatchewan [Saskatoon] (U of S), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), School of Agriculture, Food and Wine, University of Adelaide, Veterinary and Agriculture, Murdoch University, Plant Genetics and Bioinformatics, Department of Plant Sciences [Univ California Davis] (Plant - UC Davis), University of California [Davis] (UC Davis), University of California (UC)-University of California (UC)-University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra [Barcelona] (UPF), Plant Genome and Systems Biology, Helmholtz Diabetes Center at Helmholtz Zentrum, GYB Akihabara, Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Australian Genome Research Facility, National Research Council of Canada, Henan Agricultural University, Australian Government Department of Industry, Innovation, Science, Research and Tertiary Education ACSRF00542, BioPlatforms Australia (BPA), Grains Research Development Corporation UMU00037, CSIRO Plant Industry, Australia, Agriculture Victoria Research, National Science Foundation (NSF) grant 1338897, INB ('Instituto National de Bioinformatica') Project (ISCIII - FEDER) PT13/0001/0021, Czech Ministry of Education Youth and Sports (National Program of Sustainability) LO1204, University of Saskatchewan, UC Davis Plant Sciences, University of Heidelberg, Institute of Experimental Botany (IEB), Czech Academy of Sciences [Prague] (ASCR), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Universitat Pompeu Fabra [Barcelona], and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
GK-G, PR, JT contributed equally to experimental design, data analysis andinterpretation/writing of manuscript;, RP, MH, KF, RA genome analyses andinterpretation; ZF, AK data analysis and physical map construction; EH, CC, JTMAGIC map construction; MA rice-wheat phylogenomic; AS, DK, mate-pairlibraries; PS. BD, FC, PL, Chinese Spring x Renan molecular genetic map andannotation of genome sequence; NW-H, UB, PE, DF, AJ analysis of genespace and QTL, SB, M-AN, development of Bionano alignments and tools; JD,HŠ, JŠ, HT, flow sorting of chromosomes, BAC library construction andBionano maps; M-CL fingerprinting of BAC library; FC, MP gene annotation;DC, ZR, AK58 genome assembly, JN-P, genome assembly; DI in-housesoftware development; IWGSC, genome assembly network, D-HK, CENH3antibody cytology; RA, planning of experiments and writing of manuscript.All authors have read and approved the final manuscript.; Background: Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.Results: Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region.Conclusions: Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.