title: Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines.
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.
authors.affiliation: USDA-ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710, USA.
authors.forename: Sean P
authors.initials: SP
authors.lastname: Gordon
authors.forename: Henry
authors.initials: H
authors.lastname: Priest
authors.forename: David L
authors.initials: DL
authors.lastname: Des Marais
authors.forename: Wendy
authors.initials: W
authors.lastname: Schackwitz
authors.forename: Melania
authors.initials: M
authors.lastname: Figueroa
authors.forename: Joel
authors.initials: J
authors.lastname: Martin
authors.forename: Jennifer N
authors.initials: JN
authors.lastname: Bragg
authors.forename: Ludmila
authors.initials: L
authors.lastname: Tyler
authors.forename: Cheng-Ruei
authors.initials: CR
authors.lastname: Lee
authors.forename: Doug
authors.initials: D
authors.lastname: Bryant
authors.forename: Wenqin
authors.initials: W
authors.lastname: Wang
authors.forename: Joachim
authors.initials: J
authors.lastname: Messing
authors.forename: Antonio J
authors.initials: AJ
authors.lastname: Manzaneda
authors.forename: Kerrie
authors.initials: K
authors.lastname: Barry
authors.forename: David F
authors.initials: DF
authors.lastname: Garvin
authors.forename: Hikmet
authors.initials: H
authors.lastname: Budak
authors.forename: Metin
authors.initials: M
authors.lastname: Tuna
authors.forename: Thomas
authors.initials: T
authors.lastname: Mitchell-Olds
authors.forename: William F
authors.initials: WF
authors.lastname: Pfender
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Juenger
authors.forename: Todd C
authors.initials: TC
authors.lastname: Mockler
authors.forename: John P
authors.initials: JP
authors.lastname: Vogel
mesh_terms: D058431:Brachypodium / Q000235:genetics*; D055864:Droughts; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D059467:Transcriptome / Q000235:genetics
keywords: Brachypodium distachyon; drought; genome sequencing; natural diversity; transcriptome