title: Global identification of alternative splicing via comparative analysis of SMRT- and Illumina-based RNA-seq in strawberry.
abstract: 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.
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
authors.forename: Yongping
authors.initials: Y
authors.lastname: Li
authors.affiliation: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Dai
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
authors.forename: Chungen
authors.initials: C
authors.lastname: Hu
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.|Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
authors.forename: Zhongchi
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
authors.forename: Chunying
authors.initials: C
authors.lastname: Kang
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D031985:Fragaria / Q000235:genetics* / Q000378:metabolism*; D005638:Fruit / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant
keywords: 
  Fragaria vesca
  ; RNA-seq; SMRT sequencing; alternative splicing; fruit development; strawberry