Transcriptomic analysis of a tertiary relict plant, extreme xerophyte Reaumuria soongorica to identify genes related to drought adaptation.
Transcriptomic analysis of a tertiary relict plant, extreme xerophyte Reaumuria soongorica to identify genes related to drought adaptation.
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DOI：
10.1371/journal.pone.0063993
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Ma XF
中科院分区：
文献类型：
--
作者：
Shi Y;Yan X;Zhao P;Yin H;Zhao X;Xiao H;Li X;Chen G;Ma XF
红砂（Reaumuria soongorica）是一种极端旱生灌木，广泛分布于亚洲中部的沙丘、戈壁和边缘黄土等荒漠地区，对维持和恢复脆弱的荒漠生态系统具有重要作用。然而，由于缺乏基因组序列，对R.红果木对干旱胁迫的生理反应主要是有限的。在这里，一个深转录组测序的R。soongorica将促进分子功能研究，并为了解沙漠植物的干旱适应铺平道路。从Illumina HiSeq™ 2000平台生成总共53，193，660个干净的配对末端读段。通过Trinity拼接，得到173,700个重叠群和77,647个单基因，平均长度为677 bp，N50为1109 bp。基于与公共数据库以及Rfam和Pfam数据库的序列相似性，超过55%（43，054）的单基因被成功注释。利用本地BLAST和京都基因和基因组百科全书（KEGG）图谱进一步穷尽搜索与干旱适应相关的候选基因，共鉴定出123个候选基因。此外，所有的C4光合作用基因都在R. soongorica是典型的C3植物。本工作中组装的单基因为极端旱生植物R. Soongorica的研究，并将帮助我们在不久的将来开发沙漠植物如何适应干旱环境的遗传基础。
Reaumuria soongorica is an extreme xerophyte shrub widely distributed in the desert regions including sand dune, Gobi and marginal loess of central Asia which plays a crucial role to sustain and restore fragile desert ecosystems. However, due to the lacking of the genomic sequences, studies on R. soongorica had mainly limited in physiological responses to drought stress. Here, a deep transcriptomic sequencing of R. soongorica will facilitate molecular functional studies and pave the path to understand drought adaptation for a desert plant. A total of 53,193,660 clean paired-end reads was generated from the Illumina HiSeq™ 2000 platform. By assembly with Trinity, we got 173,700 contigs and 77,647 unigenes with mean length of 677 bp and N50 of 1109 bp. Over 55% (43,054) unigenes were successfully annotated based on sequence similarity against public databases as well as Rfam and Pfam database. Local BLAST and Kyoto Encyclopedia of Genes and Genomes (KEGG) maps were used to further exhausting seek for candidate genes related to drought adaptation and a set of 123 putative candidate genes were identified. Moreover, all the C4 photosynthesis genes existed and were active in R. soongorica, which has been regarded as a typical C3 plant. The assembled unigenes in present work provide abundant genomic information for the functional assignments in an extreme xerophyte R. soongorica, and will help us exploit the genetic basis of how desert plants adapt to drought environment in the near future.
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