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

BMC Genomics

Research Article

Chao Cheng¹  Guanglin Li²  Yi Zhang³  Shengjie Liao³  Dazhao Yu⁴  Wei Huang⁴  Lirong Jin⁴  Qijia Wu⁵ 

[1] Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, 430075, Wuhan, Hubei, China;Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, 430075, Wuhan, Hubei, China;College of Life Science, Shaanxi Normal University, 710119, Xi’an, Shaanxi, China;Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, 430075, Wuhan, Hubei, China;Laboratory for Genome Regulation and Human Heath, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, 430075, Wuhan, Hubei, China;Key Laboratory of Integrated Pest Management on Crops in Central China, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, 430064, Wuhan, Hubei, China;Laboratory for Genome Regulation and Human Heath, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, 430075, Wuhan, Hubei, China;Seqhealth Technology Co., Ltd, 430075, Wuhan, Hubei, China;

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

DOI  :  10.1186/s12864-017-3507-y

 received in 2016-09-24, accepted in 2017-01-14,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundAlternative 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.ResultsThis 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.ConclusionsThese 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.

【 授权许可】

CC BY   
© The Author(s). 2017