@article {Mu{\~n}oz-Amatria{\'\i}n018978, author = {Mar{\'\i}a Mu{\~n}oz-Amatria{\'\i}n and S Lonardi and MC Luo and K Madishetty and JT Svensson and MJ Moscou and S Wanamaker and T Jiang and A Kleinhofs and GJ Muehlbauer and RP Wise and N Stein and Y Ma and E Rodriguez and D Kudrna and PR Bhat and S Chao and P Condamine and S Heinen and J Resnik and R Wing and HN Witt and M Alpert and M Beccuti and S Bozdag and F Cordero and H Mirebrahim and R Ounit and Y Wu and F You and J Zheng and H {\v S}imkov{\'a} and J Dole{\v z}el and J Grimwood and J Schmutz and D Duma and L Altschmied and T Blake and P Bregitzer and L Cooper and M Dilbirligi and A Falk and L Feiz and A Graner and P Gustafson and PM Hayes and P Lemaux and J Mammadov and TJ Close}, title = {Sequencing of 15,622 gene-bearing BACs reveals new features of the barley genome}, elocation-id = {018978}, year = {2015}, doi = {10.1101/018978}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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.}, URL = {https://www.biorxiv.org/content/early/2015/05/05/018978}, eprint = {https://www.biorxiv.org/content/early/2015/05/05/018978.full.pdf}, journal = {bioRxiv} }