Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines.
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.
Gordon, SP; Priest, H; Des Marais, DL; Schackwitz, W; Figueroa, M; Martin, J; Bragg, JN; Tyler, L; Lee, C-R; Bryant, D; Wang, W; Messing, J; Manzaneda, AJ; Barry, K; Garvin, DF; Budak, H; Tuna, M; Mitchell-Olds, T; Pfender, WF; Juenger, TE; Mockler, TC; Vogel, JP
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