Global co-expression network for key factor selection on environmental stress RNA-seq dataset in Capsicum annuum.
Global co-expression network for key factor selection on environmental stress RNA-seq dataset in Capsicum annuum.
复制标题
DOI：
10.1038/s41597-023-02592-3
复制
发表时间：
2023-10-12
期刊：
影响因子：
9.8
通讯作者：
Yeom, Seon-In
中科院分区：
文献类型：
--
作者：
Lee, Junesung;Yeom, Seon-In
环境胁迫显著影响植物的生长、发育和生产力。因此，需要在分子水平上更深入地了解潜在的应激反应。在这项研究中，为了确定与环境胁迫反应相关的关键遗传因素，整个737.3 Gb干净的RNA-seq数据集跨越非生物，生物胁迫和辣椒中的植物激素条件，用于进行个体差异表达基因分析，并构建每种胁迫条件下的基因共表达网络。随后，围绕转录因子重建基因网络，以确定参与胁迫反应的关键因子，包括先前与抗性有关的NLR基因家族。非生物和生物压力网络分别由233个和597个中心组成，分别有10个和89个NLR。网络中NLR组内的每个基因对特定胁迫表现出实质性表达。转录组网络的综合分析策略揭示了复杂环境条件下的潜在关键基因。总之，这可以提供重要的线索，发现新的关键因素，使用高通量转录组数据在其他物种以及植物。
Environmental stresses significantly affect plant growth, development, and productivity. Therefore, a deeper understanding of the underlying stress responses at the molecular level is needed. In this study, to identify critical genetic factors associated with environmental stress responses, the entire 737.3 Gb clean RNA-seq dataset across abiotic, biotic stress, and phytohormone conditions in Capsicum annuum was used to perform individual differentially expressed gene analysis and to construct gene co-expression networks for each stress condition. Subsequently, gene networks were reconstructed around transcription factors to identify critical factors involved in the stress responses, including the NLR gene family, previously implicated in resistance. The abiotic and biotic stress networks comprise 233 and 597 hubs respectively, with 10 and 89 NLRs. Each gene within the NLR groups in the network exhibited substantial expression to particular stresses. The integrated analysis strategy of the transcriptome network revealed potential key genes for complex environmental conditions. Together, this could provide important clues to uncover novel key factors using high-throughput transcriptome data in other species as well as plants.
登录
查看更多内容
影响因子：
5.8
作者：
Gu, Zuguang;Eils, Roland;Schlesner, Matthias
通讯作者：
Schlesner, Matthias
影响因子：
12.3
作者：
Kim S;Park J;Yeom SI;Kim YM;Seo E;Kim KT;Kim MS;Lee JM;Cheong K;Shin HS;Kim SB;Han K;Lee J;Park M;Lee HA;Lee HY;Lee Y;Oh S;Lee JH;Choi E;Choi E;Lee SE;Jeon J;Kim H;Choi G;Song H;Lee J;Lee SC;Kwon JK;Lee HY;Koo N;Hong Y;Kim RW;Kang WH;Huh JH;Kang BC;Yang TJ;Lee YH;Bennetzen JL;Choi D
通讯作者：
Choi D
影响因子：
7.4
作者：
Rasmussen, Simon;Barah, Pankaj;Mundy, John
通讯作者：
Mundy, John
影响因子：
9.8
作者：
Kim, Myung-Shin;Kim, Seungill;Choi, Doil
通讯作者：
Choi, Doil
影响因子：
--
作者：
McKenzie AT;Katsyv I;Song WM;Wang M;Zhang B
通讯作者：
Zhang B