PT - JOURNAL ARTICLE AU - María Muñoz-Amatriaín AU - S Lonardi AU - MC Luo AU - K Madishetty AU - JT Svensson AU - MJ Moscou AU - S Wanamaker AU - T Jiang AU - A Kleinhofs AU - GJ Muehlbauer AU - RP Wise AU - N Stein AU - Y Ma AU - E Rodriguez AU - D Kudrna AU - PR Bhat AU - S Chao AU - P Condamine AU - S Heinen AU - J Resnik AU - R Wing AU - HN Witt AU - M Alpert AU - M Beccuti AU - S Bozdag AU - F Cordero AU - H Mirebrahim AU - R Ounit AU - Y Wu AU - F You AU - J Zheng AU - H Šimková AU - J Doležel AU - J Grimwood AU - J Schmutz AU - D Duma AU - L Altschmied AU - T Blake AU - P Bregitzer AU - L Cooper AU - M Dilbirligi AU - A Falk AU - L Feiz AU - A Graner AU - P Gustafson AU - PM Hayes AU - P Lemaux AU - J Mammadov AU - TJ Close TI - Sequencing of 15,622 gene-bearing BACs reveals new features of the barley genome AID - 10.1101/018978 DP - 2015 Jan 01 TA - bioRxiv PG - 018978 4099 - http://biorxiv.org/content/early/2015/05/05/018978.short 4100 - http://biorxiv.org/content/early/2015/05/05/018978.full AB - Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, since only 6,278 BACs in the physical map were sequenced, detailed fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15,622 BACs representing the minimal tiling path of 72,052 physical mapped gene-bearing BACs. This generated about 1.7 Gb of genomic sequence containing 17,386 annotated barley genes. Exploration of the sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high rates of recombination, there are also gene-dense regions with suppressed recombination. Knowledge of these deviant regions is relevant to trait introgression, genome-wide association studies, genomic selection model development and map-based cloning strategies. Sequences and their gene and SNP annotations can be accessed and exported via http://harvest-web.org/hweb/utilmenu.wc or through the software HarvEST:Barley (download from harvest.ucr.edu). In the latter, we have implemented a synteny viewer between barley and Aegilops tauschii to aid in comparative genome analysis.