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

Qian Zhao,Weiyi He,Minsheng You,Yaqing Li,Liette Vasseur,Yiying Li,Weimin Zhong,Tianpu Li

doi:10.1186/s12864-019-5838-3

Qian Zhao, Weiyi He + Show 6 more

Open Access

https://doi.org/10.1186/s12864-019-5838-3

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Abstract

BackgroundThe 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.ResultsHere, 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.ConclusionOverall, 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.

Highlights

The diamondback moth (DBM), Plutella xylostella (L.), is a major pest of cruciferous crops worldwide
We eventually identified 217,535 (76%) and 16, 398 (33%) non-redundant transcripts based on RNA-seq and Single-molecule long-read sequencing techmology (IsoSeq) (Table 1), covering approximately 77% of the
Comparing these two sequencing methods, we found that they covered different gene lengths with most of the IsoSeq reads mapping genes of 1500–2000 bp (Fig. 1b) while most of the RNA-seq reads mapping genes of < 500 bp and the number of genes declining with increasing gene length (Fig. 1c)

Summary

Introduction

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. Alternative splicing (AS) is the process by which premRNA transcripts can be spliced differentially depending on which exons or portions of exons in a gene are removed from different protein isoforms [1]. The patterns of AS events constantly change under different physiological conditions, allowing organisms to respond to environmental changes through differential genome expressions [1]. AS events are associated with development of various organs, such as brain, liver and heart [3]. Lef exon 6 splicing is regulated in postnatal mouse brain development and T-cell activation [3].

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