Sequencing of 15,622 gene-bearing BACs reveals new features of the barley genome
María Muñoz-Amatriaín , Stefano Lonardi , MingCheng Luo , Kavitha Madishetty , Jan Svensson , Matthew Moscou , Steve Wanamaker , Tao Jiang , Andris Kleinhofs , Gary Muehlbauer , Roger Wise , Nils Stein , Yaqin Ma , Edmundo Rodriguez , Dave Kudrna , Prasanna R Bhat , Shiaoman Chao , Pascal Condamine , Shane Heinen , Josh Resnik , Rod Wing , Heather N Witt , Matthew Alpert , Marco Beccuti , Serdar Bozdag , Francesca Cordero , Hamid Mirebrahim , Rachid Ounit , Yonghui Wu , Frank You , Jie Zheng , Hana Šimková , Jaroslav Doležel , Jane Grimwood , Jeremy Schmutz , Denisa Duma , Lothar Altschmied , Tom Blake , Phil Bregitzer , Laurel Cooper , Muharrem Dilbirligi , Anders Falk , Leila Feiz , Andreas Graner , Perry Gustafson , Patrick Hayes , Peggy Lemaux , Jafar Mammadov , Timothy Close
doi: http://dx.doi.org/10.1101/018978

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.