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Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines
Author(s) -
Gordon Sean P.,
Priest Henry,
Des Marais David L.,
Schackwitz Wendy,
Figueroa Melania,
Martin Joel,
Bragg Jennifer N.,
Tyler Ludmila,
Lee ChengRuei,
Bryant Doug,
Wang Wenqin,
Messing Joachim,
Manzaneda Antonio J.,
Barry Kerrie,
Garvin David F.,
Budak Hikmet,
Tuna Metin,
MitchellOlds Thomas,
Pfender William F.,
Juenger Thomas E.,
Mockler Todd C.,
Vogel John P.
Publication year - 2014
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.12569
Subject(s) - brachypodium distachyon , biology , genetics , brachypodium , genome , computational biology , gene , reference genome , sequence assembly , germplasm , transcriptome , gene expression , agronomy
Summary Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high‐quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA ‐Seq experiments under control and simulated drought‐stress conditions, identified 300 genes with a genotype‐dependent treatment response. We showed that large‐scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype‐dependent treatment responses. We generated a deep mRNA ‐Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines.