title: Comprehensive analysis of alternative splicing in Digitalis purpurea by strand-specific RNA-Seq.
abstract: Digitalis purpurea (D. purpurea) is one of the most important medicinal plants and is well known in the treatment of heart failure because of the cardiac glycosides that are its main active compounds. However, in the absence of strand specific sequencing information, the post-transcriptional mechanism of gene regulation in D. purpurea thus far remains unknown. In this study, a strand-specific RNA-Seq library was constructed and sequenced using Illumina HiSeq platforms to characterize the transcriptome of D. purpurea with a focus on alternative splicing (AS) events and the effect of AS on protein domains. De novo RNA-Seq assembly resulted in 48,475 genes. Based on the assembled transcripts, we reported a list of 3,265 AS genes, including 5,408 AS events in D. purpurea. Interestingly, both glycosyltransferases and monooxygenase, which were involved in the biosynthesis of cardiac glycosides, are regulated by AS. A total of 2,422 AS events occurred in coding regions, and 959 AS events were located in the regions of 882 unique protein domains, which could affect protein function. This D. purpurea transcriptome study substantially increased the expressed sequence resource and presented a better understanding of post-transcriptional regulation to further facilitate the medicinal applications of D. purpurea for human health.
authors.affiliation: Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China.
authors.forename: Bin
authors.initials: B
authors.lastname: Wu
authors.affiliation: Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China.
authors.forename: Fengmei
authors.initials: F
authors.lastname: Suo
authors.affiliation: College of Life Science, Shanxi Agricultural University, Taigu, P. R. China.
authors.forename: Wanjun
authors.initials: W
authors.lastname: Lei
authors.affiliation: Institute of Integrative Genome Biology, Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, United States of America.
authors.forename: Lianfeng
authors.initials: L
authors.lastname: Gu
mesh_terms: D017398:Alternative Splicing; D004070:Digitalis / Q000145:classification / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D016695:Glycosyltransferases / Q000235:genetics; D006899:Mixed Function Oxygenases / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D010940:Plant Proteins; D012333:RNA, Messenger; D018749:RNA, Plant; D006899:Mixed Function Oxygenases; D016695:Glycosyltransferases