Alternative splicing and trans-splicing events revealed by analysis of Bombyx mori transcriptome

As a developing insect model especially after its genome released, regulation of pre-mRNA splicing in the silkworm Bombyx mori has not been systematically studied. Here, we identified 1927 alternative splicing and dozens of trans-splicing events as well as 320 novel and 1140 modified genes from the analysis of B. mori transcriptome by RNA-Seq. Detailed investigation on three SR proteins indicated that their alternative splicing patterns were conserved across species, and one intron retention isoform of Srsf6 was sex-specific in the silkworm gonads. Trans-splicing of Drosophila mod(mdg4) homolog in B. mori was confirmed, which also had multiple 3’ exons from genes located at both the opposite and same DNA strands. Further analysis revealed that there was one alternative trans-splicing event in B. mori, which had expression specificity at developmental stages. Our analysis also implied that long RNA base-pairing between trans-introns were common and might contribute to most trans-splicing events.