title: Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome.
abstract: Alternative splicing and trans-splicing events have not been systematically studied in the silkworm Bombyx mori. Here, the silkworm transcriptome was analyzed by RNA-seq. We identified 320 novel genes, modified 1140 gene models, and found thousands of alternative splicing and 58 trans-splicing events. Studies of three SR proteins show that both their alternative splicing patterns and mRNA products are conserved from insect to human, and one isoform of Srsf6 with a retained intron is expressed sex-specifically in silkworm gonads. Trans-splicing of mod(mdg4) in silkworm was experimentally confirmed. We identified integrations from a common 5'-gene with 46 newly identified alternative 3'-exons that are located on both DNA strands over a 500-kb region. Other trans-splicing events in B. mori were predicted by bioinformatic analysis, in which 12 events were confirmed by RT-PCR, six events were further validated by chimeric SNPs, and two events were confirmed by allele-specific RT-PCR in F(1) hybrids from distinct silkworm lines of JS and L10, indicating that trans-splicing is more widespread in insects than previously thought. Analysis of the B. mori transcriptome by RNA-seq provides valuable information of regulatory alternative splicing events. The conservation of splicing events across species and newly identified trans-splicing events suggest that B. mori is a good model for future studies.
authors.affiliation: Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Shao
authors.forename: Qiong-Yi
authors.initials: QY
authors.lastname: Zhao
authors.forename: Xiu-Ye
authors.initials: XY
authors.lastname: Wang
authors.forename: Xin-Yan
authors.initials: XY
authors.lastname: Xu
authors.forename: Qing
authors.initials: Q
authors.lastname: Tang
authors.forename: Muwang
authors.initials: M
authors.lastname: Li
authors.forename: Xuan
authors.initials: X
authors.lastname: Li
authors.forename: Yong-Zhen
authors.initials: YZ
authors.lastname: Xu
mesh_terms: D017398:Alternative Splicing; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D012831:Bombyx / Q000235:genetics*; D005091:Exons; D005260:Female; D007438:Introns; D008297:Male; D008957:Models, Genetic; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D017386:Sequence Homology, Amino Acid; D020040:Trans-Splicing; D059467:Transcriptome