Alternative splicing preferentially increases transcript diversity associated with stress responses in the extremophyte Schrenkiella parvula
Alternative splicing preferentially increases transcript diversity associated with stress responses in the extremophyte Schrenkiella parvula
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DOI：
10.1101/2022.10.13.512046
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发表时间：
2022-10
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影响因子：
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通讯作者：
Chathura Wijesinghege;Kieu-Nga Tran;M. Dassanayake
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作者：
Chathura Wijesinghege;Kieu-Nga Tran;M. Dassanayake
选择性剪接通过从一个基因产生多个异构体来扩展基因组的编码潜力。异构体可以提供转录特异性和多样性，以启动在应激环境中转录组调整期间所需的多种反应。尽管选择性剪接的普遍性被广泛认可，但不同的异构体如何促进在极端环境中茁壮成长的植物的胁迫适应尚未探索。在这里，我们研究如何极端植物模型，小施伦凯氏菌，协调选择性剪接在高盐度相比，盐胁迫敏感的模型，拟南芥。我们使用Iso-Seq生成全长参考转录本，使用RNA-seq量化响应盐度变化的差异同种型使用。我们发现，单拷贝直系同源物，其中S。parvula具有比A. thaliana和S.使用机器学习观察和预测的具有多种同种型的parvula基因在应激相关功能中富集。表现出差异异构体使用的基因在很大程度上与响应于盐而差异表达的基因互斥。S. parvula转录组在盐下转录组重编程期间通过测量表达紊乱来评估保持同种型使用的特异性。我们的研究为研究植物在极端环境中进化的胁迫耐受性增加了新的资源和见解。
Alternative splicing extends the coding potential of genomes by creating multiple isoforms from one gene. Isoforms can render transcript specificity and diversity to initiate multiple responses required during transcriptome adjustments in stressed environments. Although the prevalence of alternative splicing is widely recognized, how diverse isoforms facilitate stress adaptation in plants that thrive in extreme environments are unexplored. Here we examine how an extremophyte model, Schrenkiella parvula, coordinates alternative splicing in response to high salinity compared to a salt-stress sensitive model, Arabidopsis thaliana. We use Iso-Seq to generate full length reference transcripts and RNA-seq to quantify differential isoform usage in response to salinity changes. We find that single-copy orthologs where S. parvula has a higher number of isoforms than A. thaliana as well as S. parvula genes observed and predicted using machine learning to have multiple isoforms are enriched in stress associated functions. Genes that showed differential isoform usage were largely mutually exclusive from genes that were differentially expressed in response to salt. S. parvula transcriptomes maintained specificity in isoform usage assessed via a measure of expression disorderdness during transcriptome reprogramming under salt. Our study adds a novel resource and insight to study plant stress tolerance evolved in extreme environments.