盐胁迫下柳树交替剪接的全基因组图谱分析

IF 2.4 2区 农林科学 Q1 FORESTRY Forests Pub Date : 2023-12-22 DOI:10.3390/f15010030
Xue Wang, Longfeng Gong, Junkang Zhang, Lei Wang, Di Wu, Jichen Xu
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引用次数: 0

摘要

替代剪接(AS)是一种重要的转录后调控模式,可改变正常的转录本表达水平,并可能导致蛋白质的多样性。本研究利用 PromethION 平台对盐处理条件下的 Salix matsudana Koidz 9901 叶片进行了全长转录本测序。共测定了 4786 个 AS 基因(9307 个 AS 事件),占所有转录基因的 7.45%。其中,内含子保留(IR)事件占AS事件的大多数(46.05%),其次是替代3′剪接位点(A3SS)。在盐胁迫期间,IR事件的比例下降,其他事件的比例上升。统计结果表明,在AS事件中,5′GG是内含子5′端最常见的基序,GG3′是3′端最常见的基序。5′GG-AG3′是AS事件中最常见的剪接模式。AS事件的发生与基因的外显子数、外显子长度、内含子长度、GC含量和表达丰度有明显关系。在盐胁迫期间,AS基因的数量逐渐增加,它们主要参与嘌呤和叶绿素代谢、RNA转运和自噬。同时,盐胁迫期间基因的AS位点增加,表明盐胁迫引起的AS事件的复杂性。通过比较盐胁迫期间差异表达基因(DEGs)和差异替代剪接基因(DAS),发现它们在盐胁迫下具有不同的基因表达调控机制。这些结果拓展了我们对AS事件的认识,阐明并加深了我们对柳树植物耐盐性的理解。
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The Genome-Wide Profiling of Alternative Splicing in Willow under Salt Stress
Alternative splicing (AS) is an important post-transcriptional regulatory model that can change the normal transcript expression level and possibly result in protein diversity. In this study, we conducted the full-length transcript sequencing of Salix matsudana Koidz 9901 leaves under salt treatment using the PromethION platform. A total of 4786 AS genes (9307 AS events) were determined, accounting for 7.45% of all the transcribed genes. Of them, intron retention (IR) events accounted for the most AS events (46.05%), followed by alternative 3′ splice sites (A3SS). During salt stress, the percentage of IR events decreased, and the percentage of the others increased. Statistical results showed that 5′GG was the most common motif at the 5′ end of the intron in the AS events, and GG3′ was the most common motif at the 3′ end. 5′GG-AG3′ was the most common splice mode in the AS events. The occurrence of AS events was significantly related to the exon number, exon length, intron length, GC content, and expression abundance of the genes. During salt stress, the number of AS genes gradually increased, and they mainly participated in purine and chlorophyll metabolism, RNA transport, and autophagy. Meanwhile, the AS sites of the gene increased during salt treatment, indicating the complexity of the AS events by salt stress. A comparison of differentially expressed genes (DEGs) and differentially alternative splicing (DAS) genes during salt stress revealed that they had a different mechanism of gene expression regulation when subjected to salt stress. These results expand our knowledge of AS events and shed light on and improve our understanding of plant resistance to salt tolerance in willow.
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来源期刊
Forests
Forests FORESTRY-
CiteScore
4.40
自引率
17.20%
发文量
1823
审稿时长
19.02 days
期刊介绍: Forests (ISSN 1999-4907) is an international and cross-disciplinary scholarly journal of forestry and forest ecology. It publishes research papers, short communications and review papers. There is no restriction on the length of the papers. Our aim is to encourage scientists to publish their experimental and theoretical research in as much detail as possible. Full experimental and/or methodical details must be provided for research articles.
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