易变山羊草（2n=4x=28, UUSvSv, Ae. variabilis syn. Triticum peregrinum (Hack In J. Fraser) Marie & Hackel）是小麦的近缘物种，与小麦进行远源杂交时可产生可育后代，是小麦育种改良的重要资源。人们除了从这个属中发现了一些抗小麦斑点病（Cochliobolus sativus，spot blotch）、赤霉病和白粉病的抗性基因，还发现其中的品系易变山羊草1号既抗禾谷孢囊线虫(cereal cyst nematode, CCN, Heterodera avanae）又抗南方根结线虫（root knot nematode，RKN，Meloidogyne naasi）。最近的研究还表明，该材料对起源于10个国家的14个CCN生理小种具有抗性。因此，深入了解生物学特性将有利于易变山羊草的在小麦育种改良中的利用和全面阐释植物抗线虫机理。然而，至今尚无关于易变山羊草基因组、转录组和cDNA文库的报道。
中科院成都生物所余懋群研究组博士生徐德林等人利用第二代高通量测序技术，对该物种的根部进行了深度的转录组测序。等量混合接种禾谷孢囊线虫L2幼虫和不接虫两种处理在接虫后30小时、3天和9天的根部RNA在Illumina HiSeq 2000测序平台上进行4G深度的转录组从头测序，运用两个组装程序对测序数据进行拼接，最终发现Trinity method的组装结果在本研究中优于SOAPdenovo软件。
通过Trinity method获得了118,064条unigene，其平均长度为500 bp、N50为599 bp、平均测序深度为33.25倍的。进一步对这些unigene进行注解发现有7,408条unigene和3个代谢途径与CCN的拮抗调控相关。该转录组数据几乎涵盖了主要代谢途径的已知基因，这为易变山羊草的研究提供了大量序列信息，也可以作为易变山羊草中基因表达分析、基因组和功能基因组等领域研究的基础和公共信息平台，同时，再结合多基因组学工具（multigenomic tools），将有力促进对CCN抗性机理、根部发育和小麦进化机制的了解。
该研究结果近期发表在BMC Genomics刊物上。(生物谷Bioon.com)
doi:10.1186/1471-2164-13-133
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De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode
De-Lin Xu1,2, Hai Long1*, Jun-Jun Liang1,2, Jie Zhang1,2, Xin Chen1,2, Jing-Liang Li1,2, Zhi-Fen Pan1, Guang-Bing Deng1 and Mao-Qun Yu1*
Background Aegilops variabilis No.1 is highly resistant to cereal cyst nematode (CCN). However, a lack of genomic information has restricted studies on CCN resistance genes in Ae. variabilis and has limited genetic applications in wheat breeding. Results Using RNA-Seq technology, we generated a root transcriptome at a sequencing depth of 4.69 gigabases of Ae. variabilis No. 1 from a pooled RNA sample. The sample contained equal amounts of RNA extracted from CCN-infected and untreated control plants at three time-points. Using the Trinity method, nearly 52,081,238 high-quality trimmed reads were assembled into a non-redundant set of 118,064 unigenes with an average length of 500 bp and an N50 of 599 bp. The total assembly was 59.09 Mb of unique transcriptome sequences with average read-depth coverage of 33.25×. In BLAST searches of our database against public databases, 66.46% (78,467) of the unigenes were annotated with gene descriptions, conserved protein domains, or gene ontology terms. Functional categorization further revealed 7,408 individual unigenes and three pathways related to plant stress resistance. Conclusions We conducted high-resolution transcriptome profiling related to root development and the response to CCN infection in Ae. variabilis No.1. This research facilitates further studies on gene discovery and on the molecular mechanisms related to CCN resistance.
