期刊
PLANT JOURNAL
卷 90, 期 1, 页码 164-176出版社
WILEY
DOI: 10.1111/tpj.13462
关键词
alternative splicing; fruit development; SMRT sequencing; RNA-seq; strawberry; Fragaria vesca
资金
- National Natural Science Foundation of China [31572098, 31301764]
- Scientific and Technological Self-innovation Foundation of Huazhong Agricultural University [2014RC005, 2014RC017]
Alternative splicing (AS) is a key post-transcriptional regulatory mechanism, yet little information is known about its roles in fruit crops. Here, AS was globally analyzed in the wild strawberry Fragaria vesca genome with RNA-seq data derived from different stages of fruit development. The AS landscape was characterized and compared between the single-molecule, real-time (SMRT) and Illumina RNA-seq platform. While SMRT has a lower sequencing depth, it identifies more genes undergoing AS (57.67% of detected multiexon genes) when it is compared with Illumina (33.48%), illustrating the efficacy of SMRT in AS identification. We investigated different modes of AS in the context of fruit development; the percentage of intron retention (IR) is markedly reduced whereas that of alternative acceptor sites (AA) is significantly increased post-fertilization when compared with pre-fertilization. When all the identified transcripts were combined, a total of 66.43% detected multiexon genes in strawberry undergo AS, some of which lead to a gain or loss of conserved domains in the gene products. The work demonstrates that SMRT sequencing is highly powerful in AS discovery and provides a rich data resource for later functional studies of different isoforms. Further, shifting AS modes may contribute to rapid changes of gene expression during fruit set. Significance Statement Alternative splicing is a key post-transcriptional regulatory mechanism, yet little is known about its roles in fruit crops. Here we globally analyzed alternative splicing using transcriptome data from strawberry fruits, and show that single molecule real time (SMRT) RNA-seq data is highly efficient in uncovering alternatively spliced variants.
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