Transcriptome analysis reveals the complexity of alternative splicing regulation in the fungus Verticillium dahliae

文献类型： 外文期刊

第一作者： Jin, Lirong

作者： Jin, Lirong;Yu, Dazhao;Huang, Wei;Li, Guanglin;Cheng, Chao;Liao, Shengjie;Zhang, Yi;Liao, Shengjie;Wu, Qijia;Zhang, Yi;Li, Guanglin;Wu, Qijia

作者机构：

关键词： Alternative splicing;Fungus;Verticillium dahliae;Intron retention

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2017 年 18 卷

页码：

收录情况： SCI

摘要： Background: Alternative splicing (AS) regulation is extensive and shapes the functional complexity of higher organisms. However, the contribution of alternative splicing to fungal biology is not well studied. Results: This study provides sequences of the transcriptomes of the plant wilt pathogen Verticillium dahliae, using two different strains and multiple methods for cDNA library preparations. We identified alternatively spliced mRNA isoforms in over a half of the multi-exonic fungal genes. Over one-thousand isoforms involve TopHat novel splice junction; multiple types of combinatory alternative splicing patterns were identified. We showed that one Verticillium gene could use four different 5' splice sites and two different 3' donor sites to produce up to five mature mRNAs, representing one of the most sophisticated alternative splicing model in eukaryotes other than animals. Hundreds of novel intron types involving a pair of new splice sites were identified in the V. dahliae genome. All the types of AS events were validated by using RT-PCR. Functional enrichment analysis showed that AS genes are involved in most known biological functions and enriched in ATP biosynthesis, sexual/asexual reproduction, morphogenesis, signal transduction etc., predicting that the AS regulation modulates mRNA isoform output and shapes the V. dahliae proteome plasticity of the pathogen in response to the environmental and developmental changes. Conclusions: These findings demonstrate the comprehensive alternative splicing mechanisms in a fungal plant pathogen, which argues the importance of this fungus in developing complicate genome regulation strategies in eukaryotes.

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