Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines
Yükleniyor...
Dosyalar
Tarih
2014
Dergi Başlığı
Dergi ISSN
Cilt Başlığı
Yayıncı
Wiley
Erişim Hakkı
info:eu-repo/semantics/openAccess
Özet
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.
Açıklama
Anahtar Kelimeler
Brachypodium distachyon, natural diversity, genome sequencing, transcriptome, drought, Arabidopsis-Thaliana, Model System, Drought, Stress, Expression, Overexpression, Patterns, Reveals, Rice, Map
Kaynak
Plant Journal
WoS Q Değeri
Q1
Scopus Q Değeri
Q1
Cilt
79
Sayı
3
