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



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.



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.
Key Laboratory of Integrated Pest Management on Crops in Central China, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China.
Lirong
L
Jin
Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, Hubei, 430075, China.|College of Life Science, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
Guanglin
G
Li
Key Laboratory of Integrated Pest Management on Crops in Central China, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China. dazhaoyu@china.com.
Dazhao
D
Yu
Key Laboratory of Integrated Pest Management on Crops in Central China, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China.
Wei
W
Huang
Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, Hubei, 430075, China.
Chao
C
Cheng
Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, Hubei, 430075, 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, Wuhan, Hubei, 430075, China.
Shengjie
S
Liao
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, Wuhan, Hubei, 430075, China.|Seqhealth Technology Co., Ltd, Wuhan, Hubei, 430075, China.
Qijia
Q
Wu
Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, Hubei, 430075, China. yizhang@ablife.cc.|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, Wuhan, Hubei, 430075, China. yizhang@ablife.cc.
Yi
Y
Zhang
D020413:3' Untranslated Regions / Q000235:genetics; D020121:5' Untranslated Regions / Q000235:genetics; D017398:Alternative Splicing / Q000235:genetics*; D020869:Gene Expression Profiling; D054884:Host-Pathogen Interactions / Q000235:genetics; D007438:Introns / Q000235:genetics; D020172:Verticillium / Q000235:genetics* / Q000502:physiology
D020413:3' Untranslated Regions; D020121:5' Untranslated Regions
Alternative splicing; Fungus; Intron retention; Verticillium dahliae