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Genome diversity in brachypodium distachyon: deep sequencing of highly diverse inbred lines

Gordon, Sean P. and Priest, Henry and Marais, David L. Des and Schackwitz, Wendy and Figueroa, Melania and Martin, Joel and Bragg, Jennifer N. and Tyler, Ludmila and Lee, Cheng-Ruei and Bryant, Doug and Wang, Wenqin and Messing, Joachim and Manzaneda, Antonio J. and Barry, Kerrie and Garvin, David F. and Budak, Hikmet and Tuna, Metin and Mitchell-Olds, Thomas and Pfender, William F. and Juenger, Thomas E. and Mockler, Todd C. and Vogel, John (2014) Genome diversity in brachypodium distachyon: deep sequencing of highly diverse inbred lines. Plant Journal, 79 (3). pp. 361-374. ISSN 0960-7412 (Print) 1365-313X (Online)

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Official URL: http://dx.doi.org/10.1111/tpj.12569

Abstract

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.

Item Type:Article
Uncontrolled Keywords:Brachypodium distachyon; natural diversity; genome sequencing; transcriptome; drought
Subjects:UNSPECIFIED
ID Code:25540
Deposited By:Hikmet Budak
Deposited On:13 Dec 2014 15:33
Last Modified:13 Dec 2014 15:33

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