Global identification of alternative splicing via comparative analysis of SMRT‐ and Illumina‐based RNA‐seq in strawberry

• DOI: 10.1111/tpj.13462
• Publication Date: 2016-12-20T19:56:47Z
• Authors: Yongping Li; Cheng Dai; Chungen Hu; Zhongchi Liu; Chunying Kang
• Keywords: RNA-Seq; Illumina dye sequencing

Alternative splicing (AS) is a key post-transcriptional regulatory mechanism, yet little information known about its roles in fruit crops. Here, AS was globally analyzed the wild strawberry Fragaria vesca genome with RNA-seq data derived from different stages of development. The landscape characterized and compared between single-molecule, real-time (SMRT) Illumina platform. While SMRT has lower sequencing depth, it identifies more genes undergoing (57.67% detected multiexon genes) when (33.48%), illustrating efficacy identification. We investigated modes context development; percentage intron retention (IR) markedly reduced whereas that alternative acceptor sites (AA) significantly increased post-fertilization pre-fertilization. When all identified transcripts were combined, total 66.43% undergo AS, some which lead to gain or loss conserved domains gene products. work demonstrates highly powerful discovery provides rich resource for later functional studies isoforms. Further, shifting may contribute rapid changes expression during set.