Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. â € Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).
Bibliographical noteFunding Information:
This work was carried out under the auspices of the International Barley Genome Sequencing Consortium and supported from the following funding sources: German Ministry of Education and Research (BMBF) grant 0314000 'BARLEX' and 0315954 'TRITEX' to M.P., U.S. and N.S and 031A536 'de.NBI' to U.S. Leibniz Association grant ('Pakt f. Forschung und Innovation') 'sequencing barley chromosome 3H' to N.S. and U.S.; Scottish Government/UK Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/100663X/1 to R.W, P.E.H., J.R.; BBSRC grants BB/I008357/1 to M. D.C., M.C. and BB/I008071/1 to P.K.; of Finland grant 266430 and a BioNano grant to A.H.S.; Carlsberg Foundation grant nr. 2012-01-0461 to the Carlsberg Research Laboratory; Grain Research and Development Corporation (GRDC) grant DAW00233 to C.L. and P.L.; Department of Agricultural and Food, Government of Western Australia grant 681 to C.L.; National Natural Science Foundation of China (NSFC) grant 31129005 to C.L. and G.Zhang; NSFC grant 31330055 to G.Zhang.; Czech Ministry of Education, Youth and Sports grant LO1204 to J.D.; National Science Foundation grant DBI 0321756 'Coupling EST and Bacterial Artificial Chromosome Resources to Access the Barley Genome' to T.J.C. and S.L.; United States Department of Agriculture (USDA), Agriculture and Food Research Initiative Plant Genome, Genetics and Breeding Program of USDA-CSREES-NIFA grant 2009-65300-05645 'Advancing the Barley Genome' and 2011-68002-30029 'TriticeaeCAP' to T.J.C., S.L. and G.J.M.; United States National Science Foundation (NSF)-ABI grant DBI-1062301 to T.J.C. and S.L.; University of California grant CA-R-BPS-5306-H to T.J.C and S.L.;National Science Foundation grant DBI 0321756 'Algorithms for Genome Assembly of Ultra-deep Sequencing Data' to S.L. Next-generation sequencing and library construction was delivered via the BBSRC National Capability in Genomics (BB/J010375/1) at Earlham Institute (formerly The Genome Analysis Centre) by members of the Platforms and Pipelines group and BBSRC Institute Strategic Programme funding for Bioinformatics (BB/J004669/1) to M.D.C., S.A. and M.C.