PlaASDB: a comprehensive database of plant alternative splicing events in response to stress.
PlaASDB: a comprehensive database of plant alternative splicing events in response to stress.
复制标题
PlaASDB：植物响应应激的选择性剪接事件的综合数据库。
DOI：
10.1186/s12870-023-04234-7
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发表时间：
2023-04-27
影响因子：
5.3
通讯作者：
Zhang, Ziding
中科院分区：
文献类型：
--
作者：
Guo, Xiaokun;Wang, Tianpeng;Jiang, Linyang;Qi, Huan;Zhang, Ziding
选择性剪接(AS)是植物响应环境胁迫的一种共转录调控机制。然而，AS在生物和非生物胁迫反应中的作用在很大程度上仍不清楚。为了加快我们对植物在不同逆境反应下的模式的理解，迫切需要开发信息丰富的、全面的植物数据库。在这项研究中，我们首先收集了两种重要的模式植物(拟南芥和水稻)在生物和非生物胁迫下的3,255个RNA-seq数据。然后，我们进行了AS事件检测和基因表达分析，并建立了一个用户友好的植物数据库PlaASDB。通过使用来自这个高度集成的数据库资源的代表性样本，我们比较了拟南芥和水稻在非生物和生物胁迫下的AS模式，并进一步研究了AS和基因表达之间的相应差异。具体地说，我们发现差异剪接基因(DGs)和差异表达基因(DEG)在各种胁迫下共享非常有限的重叠，这表明基因表达调控和AS似乎在胁迫响应中发挥着独立的作用。与基因表达相比，拟南芥和水稻在逆境条件下更倾向于保守的AS模式。PlaASDB是一个综合性的植物特异性AS数据库，主要集成了拟南芥和水稻在逆境反应中的AS和基因表达数据。通过大规模的比较分析，观察了拟南芥和水稻AS事件的全球格局。我们相信PlaASDB可以帮助研究人员更方便地了解植物在逆境下AS的调控机制。可在http://zzdlab.com/PlaASDB/ASDB/index.html.上免费访问PlaASDB在线版本包含可在10.1186/s12870-023-04234-7上查阅的补充材料
Alternative splicing (AS) is a co-transcriptional regulatory mechanism of plants in response to environmental stress. However, the role of AS in biotic and abiotic stress responses remains largely unknown. To speed up our understanding of plant AS patterns under different stress responses, development of informative and comprehensive plant AS databases is highly demanded. In this study, we first collected 3,255 RNA-seq data under biotic and abiotic stresses from two important model plants (Arabidopsis and rice). Then, we conducted AS event detection and gene expression analysis, and established a user-friendly plant AS database termed PlaASDB. By using representative samples from this highly integrated database resource, we compared AS patterns between Arabidopsis and rice under abiotic and biotic stresses, and further investigated the corresponding difference between AS and gene expression. Specifically, we found that differentially spliced genes (DSGs) and differentially expressed genes (DEG) share very limited overlapping under all kinds of stresses, suggesting that gene expression regulation and AS seemed to play independent roles in response to stresses. Compared with gene expression, Arabidopsis and rice were more inclined to have conserved AS patterns under stress conditions. PlaASDB is a comprehensive plant-specific AS database that mainly integrates the AS and gene expression data of Arabidopsis and rice in stress response. Through large-scale comparative analyses, the global landscape of AS events in Arabidopsis and rice was observed. We believe that PlaASDB could help researchers understand the regulatory mechanisms of AS in plants under stresses more conveniently. PlaASDB is freely accessible at http://zzdlab.com/PlaASDB/ASDB/index.html. The online version contains supplementary material available at 10.1186/s12870-023-04234-7
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影响因子：
14.9
作者：
Gene Ontology Consortium
通讯作者：
Gene Ontology Consortium
影响因子：
3.5
作者：
Kelemen O;Convertini P;Zhang Z;Wen Y;Shen M;Falaleeva M;Stamm S
通讯作者：
Stamm S
DOI：
10.1016/j.gpb.2018.08.002
发表时间：
2018-08
期刊：
Genomics, proteomics & bioinformatics
影响因子：
--
作者：
Qi H;Jiang Z;Zhang K;Yang S;He F;Zhang Z
通讯作者：
Zhang Z
影响因子：
12.3
作者：
Martín G;Márquez Y;Mantica F;Duque P;Irimia M
通讯作者：
Irimia M
影响因子：
4.9
作者：
Jacobs A;Elmer KR
通讯作者：
Elmer KR