Genome-wide profiling of the alternative splicing provides insights into development in Plutella xylostella

Abstract

Abstract Background The diamondback moth (DBM), Plutella xylostella (L.), is a major pest of cruciferous crops worldwide. While the species has become a model for genomics, post-transcriptional mechanisms associated with development and sex determination have not been comprehensively studied and the lack of complete structure of mRNA transcripts limits further research. Results Here, we combined the methods of single-molecule long-read sequencing technology (IsoSeq) and RNA-seq to re-annotate the published DBM genome and present the genome-wide identification of alternative splicing (AS) associated with development and sex determination of DBM. In total, we identified ~ 13,900 genes (~ 77%) annotated in the DBM genome (version-2), resulting in the correction of 1586 wrongly annotated genes and identification of 78,000 previously unannotated transcripts. We also identified 1804 genes showing alternative splicing (AS) in each of the developmental stages and sexes, suggesting that AS events are ubiquitous in DBM. Comparative analyses showed that these AS events were rarely shared among developmental stages, indicating that they may play key specific roles in regulation of insect development. Further, we found 156 genes showing different AS events and expression patterns between males and females, linking them to potential functions in sex determination. Conclusion Overall, the P. xylostella transcriptome provides the significant information about regulatory alternative splicing events, which are shown to be involved in development and sex determination. Our work presents a solid foundation to better understand the mechanism of post-transcriptional regulation, and offers wider insights into insect development and sex determination.

Keywords

• IsoSeq
• RNA-seq
• Diamondback moth (DBM)
• Alternative splicing
• Development
• Sex-determination