Global insights into high temperature and drought stress regulated genes by RNA-Seq in economically important oilseed crop Brassica juncea.
Global insights into high temperature and drought stress regulated genes by RNA-Seq in economically important oilseed crop Brassica juncea.
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在经济上重要的油料作物木制juncea中，RNA-seq对高温和干旱胁迫调节基因的全球见解。
DOI：
10.1186/s12870-014-0405-1
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发表时间：
2015-01-21
影响因子：
5.3
通讯作者：
Agarwal M
中科院分区：
文献类型：
--
作者：
Bhardwaj AR;Joshi G;Kukreja B;Malik V;Arora P;Pandey R;Shukla RN;Bankar KG;Katiyar-Agarwal S;Goel S;Jagannath A;Kumar A;Agarwal M
芥菜（Brassica juncea var. Varuna）是芸苔科重要的经济油料作物，在其生命周期的特定阶段易受非生物胁迫。迄今为止，还没有人试图阐明其转录组在高温或干旱胁迫下的全基因组变化。为了全面了解这些胁迫调控的基因、转录因子和激酶，并探索与农艺重要性状相关的编码转录本信息，我们利用下一代测序和从头组装的组合方法发现了与高温和干旱胁迫相关的芥菜转录组。我们构建了Brassica control （BC）、Brassica high temperature stress （BHS）和Brassica drought stress （BDS）三个转录组文库并进行了测序。通过质量参数处理产生1.8亿个以上的纯度过滤reads，并使用SOAPdenovo assembler重新组装高质量的reads。共鉴定出77750个独特转录本，其中69,245个（89%）被高置信度注释。我们建立了一个由19110个转录本组成的子集，这些转录本受到高温和/或干旱胁迫的差异调节。此外，还鉴定出编码转录因子和激酶的转录本分别为886和2834个。其中许多对高温、干旱或两者都有反应。在高温和干旱胁迫下，上调数量最多的转录因子分别属于热休克因子（hsf）家族和脱水响应元件结合（DREB）家族。我们还发现了239条代谢途径，这些途径在高温和干旱处理中受到干扰。与差异调控基因相关的基因本体分析预测了它们参与多种生物过程。本研究首次全面发现了芥菜在高温干旱胁迫条件下的转录组。本研究中产生的转录组资源将有助于我们了解芥菜芽孢杆菌对两种重要的非生物胁迫反应的分子机制。此外，这些信息将有助于设计有效的作物改良策略，以适应高温和缺水的条件。本文的在线版本（doi:10.1186/s12870-014-0405-1）包含补充资料，可供授权用户使用。
Brassica juncea var. Varuna is an economically important oilseed crop of family Brassicaceae which is vulnerable to abiotic stresses at specific stages in its life cycle. Till date no attempts have been made to elucidate genome-wide changes in its transcriptome against high temperature or drought stress. To gain global insights into genes, transcription factors and kinases regulated by these stresses and to explore information on coding transcripts that are associated with traits of agronomic importance, we utilized a combinatorial approach of next generation sequencing and de-novo assembly to discover B. juncea transcriptome associated with high temperature and drought stresses. We constructed and sequenced three transcriptome libraries namely Brassica control (BC), Brassica high temperature stress (BHS) and Brassica drought stress (BDS). More than 180 million purity filtered reads were generated which were processed through quality parameters and high quality reads were assembled de-novo using SOAPdenovo assembler. A total of 77750 unique transcripts were identified out of which 69,245 (89%) were annotated with high confidence. We established a subset of 19110 transcripts, which were differentially regulated by either high temperature and/or drought stress. Furthermore, 886 and 2834 transcripts that code for transcription factors and kinases, respectively, were also identified. Many of these were responsive to high temperature, drought or both stresses. Maximum number of up-regulated transcription factors in high temperature and drought stress belonged to heat shock factors (HSFs) and dehydration responsive element-binding (DREB) families, respectively. We also identified 239 metabolic pathways, which were perturbed during high temperature and drought treatments. Analysis of gene ontologies associated with differentially regulated genes forecasted their involvement in diverse biological processes. Our study provides first comprehensive discovery of B. juncea transcriptome under high temperature and drought stress conditions. Transcriptome resource generated in this study will enhance our understanding on the molecular mechanisms involved in defining the response of B. juncea against two important abiotic stresses. Furthermore this information would benefit designing of efficient crop improvement strategies for tolerance against conditions of high temperature regimes and water scarcity. The online version of this article (doi:10.1186/s12870-014-0405-1) contains supplementary material, which is available to authorized users.
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影响因子：
3.7
作者：
Liu X;Lu Y;Yuan Y;Liu S;Guan C;Chen S;Liu Z
通讯作者：
Liu Z
影响因子：
13.8
作者：
Augustine, Rehna;Mukhopadhyay, Arundhati;Bisht, Naveen C.
通讯作者：
Bisht, Naveen C.
DOI：
10.1093/bfgp/eli005
发表时间：
2006-02-01
期刊：
Briefings in Functional Genomics & Proteomics
影响因子：
--
作者：
Langridge, Peter;Paltridge, Nick;Fincher, Geoff
通讯作者：
Fincher, Geoff
影响因子：
4.1
作者：
Goyal, K;Walton, LJ;Tunnacliffe, A
通讯作者：
Tunnacliffe, A
影响因子：
5.8
作者：
Huang, Ying;Niu, Beifang;Li, Weizhong
通讯作者：
Li, Weizhong