RT Journal Article
SR Electronic
T1 Sequencing of 15,622 gene-bearing BACs reveals new features of the barley genome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 018978
DO 10.1101/018978
A1 María Muñoz-Amatriaín
A1 S Lonardi
A1 MC Luo
A1 K Madishetty
A1 JT Svensson
A1 MJ Moscou
A1 S Wanamaker
A1 T Jiang
A1 A Kleinhofs
A1 GJ Muehlbauer
A1 RP Wise
A1 N Stein
A1 Y Ma
A1 E Rodriguez
A1 D Kudrna
A1 PR Bhat
A1 S Chao
A1 P Condamine
A1 S Heinen
A1 J Resnik
A1 R Wing
A1 HN Witt
A1 M Alpert
A1 M Beccuti
A1 S Bozdag
A1 F Cordero
A1 H Mirebrahim
A1 R Ounit
A1 Y Wu
A1 F You
A1 J Zheng
A1 H Šimková
A1 J Doležel
A1 J Grimwood
A1 J Schmutz
A1 D Duma
A1 L Altschmied
A1 T Blake
A1 P Bregitzer
A1 L Cooper
A1 M Dilbirligi
A1 A Falk
A1 L Feiz
A1 A Graner
A1 P Gustafson
A1 PM Hayes
A1 P Lemaux
A1 J Mammadov
A1 TJ Close
YR 2015
UL http://biorxiv.org/content/early/2015/05/05/018978.abstract
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.