东方蜜蜂微孢子虫基因的可变剪接及可变腺苷酸化解析

Analysis of alternative splicing and alternative polyadenylation of Nosema ceranae genes

本研究旨在基于已获得的第三代纳米孔全长转录组数据对东方蜜蜂微孢子虫Nosema ceranae基因的可变剪接(alternative splicing,AS)和可变多聚腺苷酸化(alternative polyadenylation,APA)进行分析。通过Astalavista软件鉴定东方蜜蜂微孢子虫基因的AS事件类型。采用TAPISpipeline对东方蜜蜂微孢子虫基因的APA位点进行鉴定。利用MEME软件分析所有全长转录本的poly (A)剪接位点上游50bp的序列特征并鉴定motif。共鉴定出发生于5个基因的5次AS事件,包括1次可变供体位点(alternative donor site,ADS)和4次内含子保留(intron retention,IR)。鉴定出233个基因发生APA,其中含有1个poly (A)剪接位点的基因数量最多(143,61.37%)。序列特征分析结果显示,东方蜜蜂微孢子虫全长转录本的3’ UTR的上下游表现出明显的碱基倾向性,U在3’ UTR的上游富集,而A在3’ UTR的下游富集。此外,在东方蜜蜂微孢子虫全长转录本的poly (A)剪接位点上游鉴定到3个motif(AAUAAA、UGAUGC和GCGACG)。研究结果揭示了东方蜜蜂微孢子虫转录组的复杂性,完善了现有的参考基因组和转录组注释,也为深入探究不同剪接异构体的分子功能提供了基础。此外,本研究为其他真菌的AS和APA研究提供了有益的思路和方法借鉴。

This work aims to analyze alternative splicing(AS)and alternative polyadenylation(APA)of Nosema ceranae genes on the basis of our previously obtained third-generation nanopore full-length transcriptome data.Astalavista software was used to identify the type of AS events of N.ceranae genes.TAPIS pipeline was utilized to explore APA sites of N.ceranae genes.MEME software was employed to investigate statistics of sequences at 50 bp upstream of poly(A)splicing sites followed by motif identification.In this study,five AS events occurred in five genes were identified,including one alternative donor site(ADS)and four intron retention(IR).In addition,a total of 233 genes with APA were discovered,among them those containing one poly(A)splicing site were the most abundant(143,61.37%).Upstream and downstream sequences of 3’UTR within N.ceranae full-length transcripts showed an obvious base bias,and U was enriched in the upstream of 3’UTR,while A was enriched in the downstream of 3’UTR.Three motifs such as AAUAAA,UGAUGC and GCGACG were identified at the upstream of poly(A)splicing site.Taken together,the results reveal the complexity of the transcriptome of N.ceranae,improve the annotation of current genome and transcriptome,and provide a foundation for further investigation of the molecule role of various isoforms.Our work provides a valuable idea and method reference for study on AS and APA in other fungi.