Genome-scale transcriptome analysis of the desert poplar, Populus euphratica
Genome-scale transcriptome analysis of the desert poplar, Populus euphratica
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DOI：
10.1093/treephys/tpr015
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发表时间：
2011-04-01
期刊：
影响因子：
4
通讯作者：
Liu, Jianquan
中科院分区：
文献类型：
--
作者：
Qiu, Qiang;Ma, Tao;Liu, Jianquan
胡杨对极端沙漠环境具有良好的适应能力，是研究非生物胁迫对树木影响的重要模式树种。在这里，我们提出了该物种的第一个深度转录组学分析。为了最大限度地表达条件转录本，从沙漠生长树木的活组织和两种类型的愈伤组织（盐胁迫和非盐胁迫）中获得mRNA。De novo组装使用Solexa序列数据生成86,777个Unigenes。这些序列覆盖了先前报道的胡杨表达序列标签（est）的92%和TIGR杨树est的90%，通过BLAST相似度检索在公共数据库中标注了58,499条高质量的独特序列。研究发现，胡杨愈伤组织中有27%的Unigenes在盐胁迫下发生差异表达（上调或下调）。这些差异表达基因主要参与转运、转录、细胞通讯和代谢。此外，我们发现许多被认为参与ABA调控和生物合成的基因也受到差异调控。这项研究是迄今为止对胡杨进行的最深入的转录组学和基因注释分析。所获得的遗传知识将为进一步研究该树种对非生物胁迫的分子适应性以及促进其他杨树物种的遗传操作提供有用的信息。
Populus euphratica is well-adapted to extreme desert environments and is an important model species for studying the effects of abiotic stresses on trees. Here we present the first deep transcriptomic analysis of this species. To maximize representation of conditional transcripts, mRNA was obtained from living tissues of desert-grown trees and two types of callus (salt-stressed and unstressed). De novo assembly generated 86,777 Unigenes using Solexa sequence data. These sequences covered 92% of previously reported P. euphratica expressed sequence tags (ESTs) and 90% of the TIGR poplar ESTs, and a total of 58,499 high-quality unique sequences were annotated by BLAST similarity searches against public databases. We found that 27% of the total Unigenes were differentially expressed (up- or down-regulated) in response to salt stress in P. euphratica callus. These differentially expressed genes are mainly involved in transport, transcription, cellular communication and metabolism. In addition, we found that numerous putative genes involved in ABA regulation and biosynthesis were also differentially regulated. This study represents the deepest transcriptomic and gene-annotation analysis of P. euphratica to date. The genetic knowledge acquired should be very useful for future studies of the molecular adaptation of this tree species to abiotic stress and facilitate genetic manipulation of other poplar species.