The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper
The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper
复制标题
辣椒中非生物和生物胁迫响应剪接变异与深度 RNA-seq 数据集的景观
DOI：
10.1038/s41597-024-03239-7
复制
发表时间：
2024
期刊：
影响因子：
9.8
通讯作者：
Won
中科院分区：
文献类型：
--
作者：
Nayoung Kim;Junesung Lee;Seon;Nam;Won
选择性剪接（alternative splicing，AS）是真核生物中广泛存在的一种剪接现象，在生物的发育和应激反应中起着重要作用。在植物中，响应于不同环境胁迫的大量RNA-seq数据集可以为鉴定优选农艺性状的条件特异性和/或常见AS变体提供线索。我们报告了来自辣椒的RNA-seq数据集（350.7 Gb），辣椒接种了三种细菌、一种病毒或一种卵菌中的一种，并获得了额外的现有转录组数据集。在这项研究中，我们调查了景观AS在响应环境应激源，信号分子和组织从425个总样本，包括841.49 Gb。此外，我们确定了在特定和共享的压力条件下进行AS的基因，以获得可能参与增强对压力源的耐受性的潜在基因。我们发现了1，642，007个AS事件，并确定了4，354个与环境应激源，组织和信号分子相关的差异选择性剪接基因。这些信息和方法为提高辣椒对环境胁迫的耐受性或建立育种计划提供了有用的基础研究数据。
Alternative splicing (AS) is a widely observed phenomenon in eukaryotes that plays a critical role in development and stress responses. In plants, the large number of RNA-seq datasets in response to different environmental stressors can provide clues for identification of condition-specific and/or common AS variants for preferred agronomic traits. We report RNA-seq datasets (350.7 Gb) from Capsicum annuum inoculated with one of three bacteria, one virus, or one oomycete and obtained additional existing transcriptome datasets. In this study, we investigated the landscape of AS in response to environmental stressors, signaling molecules, and tissues from 425 total samples comprising 841.49 Gb. In addition, we identified genes that undergo AS under specific and shared stress conditions to obtain potential genes that may be involved in enhancing tolerance to stressors. We uncovered 1,642,007 AS events and identified 4,354 differential alternative splicing genes related to environmental stressors, tissues, and signaling molecules. This information and approach provide useful data for basic-research focused on enhancing tolerance to environmental stressors in hot pepper or establishing breeding programs.