Deep sequencing-based characterization of transcriptome of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress.
Deep sequencing-based characterization of transcriptome of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress.
复制标题
基于深度测序的三叶橙 (Poncirus trifoliata (L.) Raf.) 转录组表征对冷胁迫的响应
DOI：
10.1186/s12864-015-1629-7
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发表时间：
2015-07-29
期刊：
影响因子：
4.4
通讯作者：
Liu JH
中科院分区：
文献类型：
--
作者：
Wang M;Zhang X;Liu JH
背景：三叶橙(PonCirus trifoliata(L.)(英国皇家空军)在完全驯化后是极其寒冷和耐寒的；然而，这种具有经济价值的特征背后的潜在分子机制仍然知之甚少。本研究通过高通量测序，获得了低温(4℃)条件下三叶柑橘在一段时间内的整体转录组图谱。结果：获得了6800多万个高质量的读数，并组装成77,292个非冗余数据，平均长度为1112个核苷酸(N50=1778个核苷酸)。其中23,846个基因与已知基因有显著的序列相似性，这些基因被归入61个基因本体论(GO)类别和25个同源基团(COG)簇，涉及128个KEGG途径。将来自冷处理植物和对照植物的序列映射到组装的转录组，从而鉴定出5549个差异表达基因(DEG)。这些基因分别包括600个(462个上调，138个下调)、2346个(1631个上调，715个下调)和5177个(2702个上调，2475个下调)基因。通过定量聚合酶链式反应分析17个DEGS的表达模式，验证了RNA-seq转录本表达数据的准确性。在DEGS中，植物激素信号转导、植物-病原菌相互作用和次生代谢是GO最显著丰富的类别。共有60个转录因子被证明是冷响应的。此外，一些参与激素分解代谢和信号传递的基因，如脱落酸、乙烯和赤霉素等，也受到低温胁迫的影响。同时，在低温下，腐胺水平逐渐增加，这与精氨酸脱羧酶基因的上调是一致的。结论：该数据集提供了关于柑橘转录组在低温胁迫下变化的有价值的信息，可能有助于指导未来对增强抗寒性至关重要的基因的鉴定和功能分析。
Background:Trifoliate orange (Poncirus trifoliata (L.) Raf.) is extremely cold hardy after a full acclimation; however the underlying molecular mechanisms underlying this economically valuable trait remain poorly understood. In this study, global transcriptome profiles of trifoliate orange under cold conditions (4 °C) over a time course were generated by high-throughput sequencing.Results:More than 68 million high-quality reads were produced and assembled into a non-redundant data of 77,292 unigenes with an average length of 1112 bp (N50 = 1778 bp). Of these, 23,846 had significant sequence similarity to known genes and these were assigned to 61 gene ontology (GO) categories and 25 clusters of orthologous groups (COG) involved in 128 KEGG pathways. Sequences derived from cold-treated and control plants were mapped to the assembled transcriptome, resulting in the identification of 5549 differentially expressed genes (DEGs). These comprised 600 (462 up-regulated, 138 down-regulated), 2346 (1631 up-regulated, 715 down-regulated), and 5177 (2702 up-regulated, 2475 down-regulated) genes from the cold-treated samples at 6, 24 and 72 h, respectively. The accuracy of the RNA-seq derived transcript expression data was validated by analyzing the expression patterns of 17 DEGs by qPCR. Plant hormone signal transduction, plant-pathogen interaction, and secondary metabolism were the most significantly enriched GO categories amongst in the DEGs. A total of 60 transcription factors were shown to be cold responsive. In addition, a number of genes involved in the catabolism and signaling of hormones, such as abscisic acid, ethylene and gibberellin, were affected by the cold stress. Meanwhile, levels of putrescine progressively increased under cold, which was consistent with up-regulation of an arginine decarboxylase gene.Conclusions:This dataset provides valuable information regarding the trifoliate orange transcriptome changes in response to cold stress and may help guide future identification and functional analysis of genes that are importnatn for enhancing cold hardiness.