Jin Lirong, Li Guanglin, Yu Dazhao, Huang Wei, Cheng Chao, Liao Shengjie, Wu Qijia, Zhang Yi
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.
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.
BMC Genomics. 2017 Feb 6;18(1):130. doi: 10.1186/s12864-017-3507-y.
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.
可变剪接（AS）调控广泛存在，塑造了高等生物的功能复杂性。然而，可变剪接对真菌生物学的贡献尚未得到充分研究。
本研究利用两种不同菌株和多种制备cDNA文库的方法，提供了植物枯萎病病原菌大丽轮枝菌的转录组序列。我们在超过一半的多外显子真菌基因中鉴定出了可变剪接的mRNA异构体。超过一千种异构体涉及TopHat新的剪接位点；鉴定出了多种类型的组合可变剪接模式。我们发现一个大丽轮枝菌基因可以使用四个不同的5'剪接位点和两个不同的3'供体位点来产生多达五种成熟的mRNA，这代表了除动物外真核生物中最复杂的可变剪接模式之一。在大丽轮枝菌基因组中鉴定出了数百种涉及一对新剪接位点的新型内含子类型。所有类型的AS事件均通过RT-PCR进行了验证。功能富集分析表明，AS基因参与了大多数已知的生物学功能，并在ATP生物合成、有性/无性繁殖、形态发生、信号转导等方面富集，预测AS调控调节mRNA异构体输出，并塑造了病原菌大丽轮枝菌蛋白质组的可塑性以响应环境和发育变化。
这些发现证明了一种真菌植物病原菌中存在全面的可变剪接机制，这表明这种真菌在真核生物中发展复杂的基因组调控策略方面具有重要意义。
