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Large-scale analysis of the cassava transcriptome reveals the impact of cold stress on alternative splicing

文献类型： 外文期刊

作者： Li, Shuxia 1 ; Yu, Xiang 2 ; Cheng, Zhihao 3 ; Zeng, Changying 1 ; Li, Wenbin 1 ; Zhang, Liangsheng 4 ; Peng, Ming 1 ;

作者机构： 1.Chinese Acad Trop Agr Sci, Inst Trop Biosci & Biotechnol, Haikou, Hainan, Peoples R China

2.Univ Penn, Dept Biol, Philadelphia, PA 19104 USA

3.Chinese Acad Trop Agr Sci, Haikou Expt Stn, Haikou, Hainan, Peoples R China

4.Fujian Agr & Forestry Univ, Ctr Genom & Biotechnol, Haixia Inst Sci & Technol, Fuzhou, Peoples R China

关键词： Alternative splicing; cassava; cold stress; drought stress; RNA-Seq; splicing factor

期刊名称：JOURNAL OF EXPERIMENTAL BOTANY （ 影响因子：6.992； 五年影响因子：7.86 ）

ISSN： 0022-0957

年卷期： 2020 年 71 卷 1 期

页码：

收录情况： SCI

摘要： Alternative splicing is an essential post-transcriptional regulatory mechanism that can impact mRNA stability and protein diversity of eukaryotic genomes. Although numerous forms of stress-responsive alternative splicing have been identified in model plants, a large-scale study of alternative splicing dynamics under abiotic stress conditions in cassava has not been conducted. Here, we report the parallel employment of isoform-Seq, ssRNA-Seq, and Degradome-Seq to investigate the diversity, abundance, and fate of alternatively spliced isoforms in response to cold and drought stress. We identified 38 164 alternative splicing events, among which 3292 and 1025 events were significantly regulated by cold and drought stress, respectively. Intron retention was the most abundant subtype of alternative splicing. Global analysis of splicing regulators revealed that the number of their alternatively spliced isoforms and the corresponding abundance were specifically modulated by cold stress. We found that 58.5% of cold-regulated alternative splicing events introduced a premature termination codon into the transcripts, and 77.6% of differential alternative splicing events were detected by Degradome-Seq. Our data reveal that cold intensely affects both quantitative and qualitative aspects of gene expression via alternative splicing pathways, and advances our understanding of the high complexity and specificity of gene regulation in response to abiotic stresses.

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