Transcriptomic Analysis of a Tertiary Relict Plant, Extreme Xerophyte Reaumuria soongorica to Identify Genes Related to Drought Adaptation

BackgroundReaumuria 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.Methodology/Principal FindingsA 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.Conclusion/SignificanceThe 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.背景 红砂（Reaumuria soongorica）是一种极端耐旱灌木，广泛分布于中亚地区的沙丘、戈壁及黄土边缘荒漠区域，在维系与修复脆弱的荒漠生态系统中发挥着关键作用。然而由于缺乏基因组序列数据，此前针对红砂的研究多局限于其应对干旱胁迫的生理响应。本研究对红砂开展深度转录组测序，将助力其分子功能研究，同时为理解荒漠植物的干旱适应机制铺平道路。 方法与主要结果 本研究基于Illumina HiSeq™ 2000测序平台，共获取53,193,660条双端清洁读段（clean paired-end reads）。通过Trinity软件进行组装，我们得到173,700条重叠群（contigs）与77,647条单基因（unigenes），其平均长度为677 bp，N50值为1109 bp。通过与公共数据库、Rfam数据库及Pfam数据库进行序列相似性比对，超过55%（43,054条）的unigenes成功获得注释。通过本地BLAST比对与京都基因与基因组百科全书（KEGG）通路分析，我们进一步全面筛查了与干旱适应相关的候选基因，最终鉴定出123个潜在候选基因。此外，尽管红砂被归类为典型的C3植物，但其体内所有C4光合相关基因均完整存在且表达活跃。 结论与意义 本研究组装得到的unigenes为极端耐旱植物红砂的功能注释提供了丰富的基因组信息，将有助于我们在未来解析荒漠植物适应干旱环境的遗传基础。