Deep-sequencing transcriptome analysis of low temperature perception in a desert tree, Populus euphratica.
Deep-sequencing transcriptome analysis of low temperature perception in a desert tree, Populus euphratica.
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沙漠树胡杨低温感知的深度测序转录组分析
DOI：
10.1186/1471-2164-15-326
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发表时间：
2014-05-01
期刊：
影响因子：
4.4
通讯作者：
Yin W
中科院分区：
文献类型：
--
作者：
Chen J;Tian Q;Pang T;Jiang L;Wu R;Xia X;Yin W
研究背景胡杨（Populus euphratica Oliv.）对非生物胁迫表现出更好的耐受性，特别是那些涉及极端温度的胁迫。然而，很少有人知道在这个物种的低温胁迫反应的基因调控和信号通路。基于Illumina/Solexa的深度测序技术的最新发展加速了特定条件下全局转录谱的研究。了解控制低温感知的基因网络。胡杨，我们进行了转录组测序使用Solexa序列分析，以产生一个叶转录组在10千兆碱基的深度为each sample.ResultsUsing的Trinity方法，52,081,238高质量的修剪读取组装成一个非冗余集和108,502 unigenes，平均长度为1,047 bp的产生。在通过将所有unigenes与公共蛋白质数据库比对进行功能注释后，注释了85，584个unigenes。通过应用Benjamini和Hochberg校正，使用FPKM方法研究差异表达的基因。总体而言，2，858个转录物在至少两个样品中被鉴定为差异表达的unigenes，并且131个转录物在所有三个样品中被指定为差异表达的unigenes。在4° C处理的样品和-4° C处理的样品中，分别检测到1，661和866个不同表达的单一基因，估计绝对log 2-倍数变化> 1。其中，C4和F4样品中上调的单基因数量分别为1，113和630，而下调的非基因数量分别为548和236。为了增加我们对这些差异表达基因的理解，我们进行了基因本体富集和代谢途径富集分析。大量的早期冷（低于或高于冻结温度）响应基因被确定，这表明大量的转录级联在冷感知中起作用。对多个低温响应基因、转录因子和一些参与阿坝和钙信号转导的关键元件的分析揭示了它们在低温响应中的潜在功能。结论我们的结果提供了一个全球转录组图片P。低温胁迫下的胡杨。本研究中发现的与低温胁迫相关的转录本为进一步了解低温感知的分子机制提供了有价值的信息。胡杨
BackgroundCompared with otherPopulusspecies,Populus euphraticaOliv. exhibits better tolerance to abiotic stress, especially those involving extreme temperatures. However, little is known about gene regulation and signaling pathways involved in low temperature stress responses in this species. Recent development of Illumina/Solexa-based deep-sequencing technologies has accelerated the study of global transcription profiling under specific conditions. To understand the gene network controlling low temperature perception inP. euphratica, we performed transcriptome sequencing using Solexa sequence analysis to generate a leaf transcriptome at a depth of 10 gigabases for each sample.ResultsUsing the Trinity method, 52,081,238 high-quality trimmed reads were assembled into a non-redundant set and 108,502 unigenes with an average length of 1,047 bp were generated. After performing functional annotations by aligning all-unigenes with public protein databases, 85,584 unigenes were annotated. Differentially expressed genes were investigated using the FPKM method by applying the Benjamini and Hochberg corrections. Overall, 2,858 transcripts were identified as differentially expressed unigenes in at least two samples and 131 were assigned as unigenes expressed differently in all three samples. In 4°C-treated sample and -4°C-treated sample, 1,661 and 866 differently expressed unigenes were detected at an estimated absolute log2-fold change of > 1, respectively. Among them, the respective number of up-regulated unigenes in C4 and F4 sample was 1,113 and 630, while the respective number of down-regulated ungenes is 548 and 236. To increase our understanding of these differentially expressed genes, we performed gene ontology enrichment and metabolic pathway enrichment analyses. A large number of early cold (below or above freezing temperature)-responsive genes were identified, suggesting that a multitude of transcriptional cascades function in cold perception. Analyses of multiple cold-responsive genes, transcription factors, and some key transduction components involved in ABA and calcium signaling revealed their potential function in low temperature responses inP. euphratica.ConclusionsOur results provide a global transcriptome picture ofP. euphraticaunder low temperature stress. The potential cold stress related transcripts identified in this study provide valuable information for further understanding the molecular mechanisms of low temperature perception inP. euphratica.
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影响因子：
7.4
作者：
FRYER, MJ;OXBOROUGH, K;BAKER, NR
通讯作者：
BAKER, NR
影响因子：
4.4
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Junttila S;Laiho A;Gyenesei A;Rudd S
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Yamanishi Y
影响因子：
4
作者：
Gu, RS;Fonseca, S;Pais, MS
通讯作者：
Pais, MS
影响因子：
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作者：
Aslam, Mohammad;Grover, Atul;Ahmed, Zakwan
通讯作者：
Ahmed, Zakwan