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Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond
Author(s) -
Mascher Martin,
Richmond Todd A.,
Gerhardt Daniel J.,
Himmelbach Axel,
Clissold Leah,
Sampath Dharanya,
Ayling Sarah,
Steuernagel Burkhard,
Pfeifer Matthias,
D'Ascenzo Mark,
Akhunov Eduard D.,
Hedley Pete E.,
Gonzales Ana M.,
Morrell Peter L.,
Kilian Benjamin,
Blattner Frank R.,
Scholz Uwe,
Mayer Klaus F.X.,
Flavell Andrew J.,
Muehlbauer Gary J.,
Waugh Robbie,
Jeddeloh Jeffrey A.,
Stein Nils
Publication year - 2013
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.12294
Subject(s) - contig , biology , genome , hordeum vulgare , computational biology , sequence assembly , genetics , exome , whole genome sequencing , exome sequencing , shotgun sequencing , sequence tagged site , genomics , reference genome , in silico , gene , gene mapping , chromosome , transcriptome , mutation , ecology , gene expression , poaceae
Summary Advanced resources for genome‐assisted research in barley ( H ordeum vulgare ) including a whole‐genome shotgun assembly and an integrated physical map have recently become available. These have made possible studies that aim to assess genetic diversity or to isolate single genes by whole‐genome resequencing and in silico variant detection. However such an approach remains expensive given the 5 Gb size of the barley genome. Targeted sequencing of the m RNA ‐coding exome reduces barley genomic complexity more than 50‐fold, thus dramatically reducing this heavy sequencing and analysis load. We have developed and employed an in‐solution hybridization‐based sequence capture platform to selectively enrich for a 61.6 megabase coding sequence target that includes predicted genes from the genome assembly of the cultivar M orex as well as publicly available full‐length c DNA s and de novo assembled RNA‐Seq consensus sequence contigs. The platform provides a highly specific capture with substantial and reproducible enrichment of targeted exons, both for cultivated barley and related species. We show that this exome capture platform provides a clear path towards a broader and deeper understanding of the natural variation residing in the m RNA ‐coding part of the barley genome and will thus constitute a valuable resource for applications such as mapping‐by‐sequencing and genetic diversity analyzes.