易變山羊草（2n=4x=28, UUSvSv, Ae. variabilis syn. Triticum peregrinum (Hack In J. Fraser) Marie & Hackel）是小麥的近緣物種,，與小麥進行遠源雜交時可產生可育后代,，是小麥育種改良的重要資源,。人們除了從這個屬中發(fā)現了一些抗小麥斑點病（Cochliobolus sativus,，spot blotch）、赤霉病和白粉病的抗性基因,，還發(fā)現其中的品系易變山羊草1號既抗禾谷孢囊線蟲(cereal cyst nematode, CCN, Heterodera avanae）又抗南方根結線蟲（root knot nematode,，RKN，Meloidogyne naasi）,。最近的研究還表明,，該材料對起源于10個國家的14個CCN生理小種具有抗性。因此,，深入了解生物學特性將有利于易變山羊草的在小麥育種改良中的利用和全面闡釋植物抗線蟲機理,。然而，至今尚無關于易變山羊草基因組,、轉錄組和cDNA文庫的報道,。
中科院成都生物所余懋群研究組博士生徐德林等人利用第二代高通量測序技術，對該物種的根部進行了深度的轉錄組測序。等量混合接種禾谷孢囊線蟲L2幼蟲和不接蟲兩種處理在接蟲后30小時,、3天和9天的根部RNA在Illumina HiSeq 2000測序平臺上進行4G深度的轉錄組從頭測序,，運用兩個組裝程序對測序數據進行拼接，最終發(fā)現Trinity method的組裝結果在本研究中優(yōu)于SOAPdenovo軟件,。
通過Trinity method獲得了118,064條unigene,，其平均長度為500 bp、N50為599 bp,、平均測序深度為33.25倍的,。進一步對這些unigene進行注解發(fā)現有7,408條unigene和3個代謝途徑與CCN的拮抗調控相關。該轉錄組數據幾乎涵蓋了主要代謝途徑的已知基因,，這為易變山羊草的研究提供了大量序列信息,，也可以作為易變山羊草中基因表達分析、基因組和功能基因組等領域研究的基礎和公共信息平臺,，同時,，再結合多基因組學工具（multigenomic tools），將有力促進對CCN抗性機理,、根部發(fā)育和小麥進化機制的了解,。
該研究結果近期發(fā)表在BMC Genomics刊物上。(生物谷Bioon.com)
doi:10.1186/1471-2164-13-133
PMC:
PMID:
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.
