Comparative transcriptome analysis of two olive cultivars in response to NaCl-stress.
Comparative transcriptome analysis of two olive cultivars in response to NaCl-stress.
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DOI：
10.1371/journal.pone.0042931
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Kalaitzis P
中科院分区：
文献类型：
--
作者：
Bazakos C;Manioudaki ME;Therios I;Voyiatzis D;Kafetzopoulos D;Awada T;Kalaitzis P
橄榄（Olea europaea L.）种植正在迅速扩大，经常使用低质量的盐水进行灌溉。然而，橄榄耐盐性的分子基础尚未在系统水平上进行研究。在这项研究中，比较转录组学方法被用作一种工具，通过尽可能多地模拟田间橄榄生长条件，揭示橄榄树盐度响应背后的基因调控网络。具体来说，我们研究了耐盐和盐敏感两种橄榄品种转录组反应的基因型依赖性差异。以1年树龄树为研究对象，在NaCl胁迫下处理90 d，然后在夏季进行45 d的后胁迫期，进行为期135 d的盐胁迫试验。对橄榄幼苗mrna cDNA文库进行了测序，并构建了橄榄芯片。在nacl处理15、45、90天以及处理后15、45天分别从根样品中提取总RNA，用于微阵列杂交。nacl胁迫和胁迫后时间过程的SAM分析结果显示，耐盐品种和盐敏感品种分别鉴定出209个和36个差异表达转录本。等级聚类显示每个品种有两个主要的、不同的聚类。尽管探针集数量有限，但我们构建了两个品种的转录调控网络，并鉴定了几个层次聚集的相互作用转录因子调控因子，如JERF和bZIP同源物。采用系统生物学方法，鉴定了差异表达的转录本以及调节相互作用。通过比较橄榄树中转录因子与拟南芥中转录因子的相互作用，可以发现在盐度胁迫下，同一树种与拟南芥在转录水平上的响应具有相似性。
Olive (Olea europaea L.) cultivation is rapidly expanding and low quality saline water is often used for irrigation. The molecular basis of salt tolerance in olive, though, has not yet been investigated at a system level. In this study a comparative transcriptomics approach was used as a tool to unravel gene regulatory networks underlying salinity response in olive trees by simulating as much as possible olive growing conditions in the field. Specifically, we investigated the genotype-dependent differences in the transcriptome response of two olive cultivars, a salt-tolerant and a salt-sensitive one. A 135-day long salinity experiment was conducted using one-year old trees exposed to NaCl stress for 90 days followed by 45 days of post-stress period during the summer. A cDNA library made of olive seedling mRNAs was sequenced and an olive microarray was constructed. Total RNA was extracted from root samples after 15, 45 and 90 days of NaCl-treatment as well as after 15 and 45 days of post-treatment period and used for microarray hybridizations. SAM analysis between the NaCl-stress and the post-stress time course resulted in the identification of 209 and 36 differentially expressed transcripts in the salt–tolerant and salt–sensitive cultivar, respectively. Hierarchical clustering revealed two major, distinct clusters for each cultivar. Despite the limited number of probe sets, transcriptional regulatory networks were constructed for both cultivars while several hierarchically-clustered interacting transcription factor regulators such as JERF and bZIP homologues were identified. A systems biology approach was used and differentially expressed transcripts as well as regulatory interactions were identified. The comparison of the interactions among transcription factors in olive with those reported for Arabidopsis might indicate similarities in the response of a tree species with Arabidopsis at the transcriptional level under salinity stress.
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影响因子：
5.3
作者：
Cramer GR;Urano K;Delrot S;Pezzotti M;Shinozaki K
通讯作者：
Shinozaki K
影响因子：
14.9
作者：
Al-Shahrour F;Minguez P;Tárraga J;Medina I;Alloza E;Montaner D;Dopazo J
通讯作者：
Dopazo J
DOI：
10.1093/bioinformatics/btq395
发表时间：
2010-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Bonnet E;Michoel T;Van de Peer Y
通讯作者：
Van de Peer Y
影响因子：
4
作者：
Gucci, R;Lombardini, L;Tattini, M
通讯作者：
Tattini, M
影响因子：
11.6
作者：
Chen, WQ;Provart, NJ;Zhu, T
通讯作者：
Zhu, T