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.

Agriculture Victoria Research Department of Economic Development Jobs Transport and Resources AgriBio Bundoora VIC 3083 Australia

Australian Genome Research Facility Suite 219 55 Flemington Road North Melbourne VIC 3051 Australia

Bioinformatics and Genomics Program Centre for Genomic Regulation 88 Dr Aiguader 08003 Barcelona Spain

Center for Organismal Studies University of Heidelberg Im Neuenheimer Feld 345 69120 Heidelberg Germany

CSIRO Plant Industry Black Mountain Canberra ACT 2601 Australia

Global Institute of Food Security University of Saskatchewan 110 Gymnasium Place Saskatoon SK Canada

GYDLE 1135 Grande Allée Ouest Suite 220 Québec QC G1S 1E7 Canada

Henan Agricultural University Zhengzhou China

Henan Institute of Science and Technology Zhengzhou China

INRA UMR1095 Genetics Diversity and Ecophysiology of Cereals 5 chemin de Beaulieu 63039 Clermont Ferrand France

Institute of Evolution University of Haifa Haifa Israel

Institute of Experimental Botany Centre of the Region Haná for Biotechnological and Agricultural Research Slechtitelu 31 CZ 78371 Olomouc Czech Republic

International Wheat Genome Sequencing Consortium 2841 NE Marywood Ct Lee's Summit MO 64086 USA

King Abdullah University of Science and Technology Desert Agriculture Initiative Thuwal Saudi Arabia

Level Five Co Ltd GYB Akihabara Kanda Sudacho 2 25 Chiyoda ku Tokyo 101 0041 Japan

National Research Council of Canada University of Saskatchewan 110 Gymnasium Place Saskatoon SK Canada

Plant Genome and Systems Biology Helmholtz Center Munich 85764 Neuherberg Germany

School of Agriculture Food and Wine University of Adelaide Urrbrae South Australia 5064 Australia

UC Davis Plant Sciences Plant Genetics and Bioinformatics 258A Hunt Hall Davis CA 95616 USA

Veterinary and Agriculture Murdoch University 90 South St Murdoch Western Australia 6150 Australia

Wheat Genetics Resource Center and Department of Plant Pathology Kansas State University Manhattan KS 66506 USA

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Flow Cytometric Analysis and Sorting of Plant Chromosomes

Flow Sorting-Assisted Optical Mapping