1. Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome
- Author
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Muñoz-Amatriaín, María, Lonardi, Stefano, Luo, MingCheng, Madishetty, Kavitha, Svensson, Jan T, Moscou, Matthew J, Wanamaker, Steve, Jiang, Tao, Kleinhofs, Andris, Muehlbauer, Gary J, Wise, Roger P, Stein, Nils, Ma, Yaqin, Rodriguez, Edmundo, Kudrna, Dave, Bhat, Prasanna R, Chao, Shiaoman, Condamine, Pascal, Heinen, Shane, Resnik, Josh, Wing, Rod, Witt, Heather N, Alpert, Matthew, Beccuti, Marco, Bozdag, Serdar, Cordero, Francesca, Mirebrahim, Hamid, Ounit, Rachid, Wu, Yonghui, You, Frank, Zheng, Jie, Simková, Hana, Dolezel, Jaroslav, Grimwood, Jane, Schmutz, Jeremy, Duma, Denisa, Altschmied, Lothar, Blake, Tom, Bregitzer, Phil, Cooper, Laurel, Dilbirligi, Muharrem, Falk, Anders, Feiz, Leila, Graner, Andreas, Gustafson, Perry, Hayes, Patrick M, Lemaux, Peggy, Mammadov, Jafar, and Close, Timothy J
- Subjects
Hordeum vulgare L ,Genome ,gene distribution ,Human Genome ,Molecular Sequence Data ,synteny ,Plant Biology & Botany ,Bacterial ,food and beverages ,Plant Biology ,Hordeum ,Aegilops tauschii ,BAC sequencing ,Plant ,Barley [HarvEST] ,Chromosomes ,Vaccine Related ,recombination frequency ,Barley ,Artificial ,Genetics ,centromere BACs ,Biochemistry and Cell Biology ,Biotechnology - Abstract
Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1Gb 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, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15622 BACs representing the minimal tiling path of 72052 physical-mapped gene-bearing BACs. This generated ~1.7Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae.tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.
- Published
- 2015