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(jìn)行遠(yuǎn)源雜交時(shí)可產(chǎn)生可育后代,，是小麥育種改良的重要資源。人們除了從這個(gè)屬中發(fā)現(xiàn)了一些抗小麥斑點(diǎn)?。–ochliobolus sativus,，spot blotch）、赤霉病和白粉病的抗性基因,，還發(fā)現(xiàn)其中的品系易變山羊草1號(hào)既抗禾谷孢囊線蟲(chóng)(cereal cyst nematode, CCN, Heterodera avanae）又抗南方根結(jié)線蟲(chóng)（root knot nematode,，RKN，Meloidogyne naasi）,。最近的研究還表明,，該材料對(duì)起源于10個(gè)國(guó)家的14個(gè)CCN生理小種具有抗性。因此,，深入了解生物學(xué)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(chóng)機(jī)理,。然而，至今尚無(wú)關(guān)于易變山羊草基因組,、轉(zhuǎn)錄組和cDNA文庫(kù)的報(bào)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(cè)序技術(shù)，對(duì)該物種的根部進(jìn)行了深度的轉(zhuǎn)錄組測(cè)序,。等量混合接種禾谷孢囊線蟲(chóng)L2幼蟲(chóng)和不接蟲(chóng)兩種處理在接蟲(chóng)后30小時(shí),、3天和9天的根部RNA在Illumina HiSeq 2000測(cè)序平臺(tái)上進(jìn)行4G深度的轉(zhuǎn)錄組從頭測(cè)序，運(yùn)用兩個(gè)組裝程序?qū)y(cè)序數(shù)據(jù)進(jìn)行拼接,，最終發(fā)現(xiàn)Trinity method的組裝結(jié)果在本研究中優(yōu)于SOAPdenovo軟件,。
通過(guò)Trinity method獲得了118,064條unigene，其平均長(zhǎng)度為500 bp,、N50為599 bp,、平均測(cè)序深度為33.25倍的。進(jìn)一步對(duì)這些unigene進(jìn)行注解發(fā)現(xiàn)有7,408條unigene和3個(gè)代謝途徑與CCN的拮抗調(diào)控相關(guān),。該轉(zhuǎn)錄組數(shù)據(jù)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(dá)分析,、基因組和功能基因組等領(lǐng)域研究的基礎(chǔ)和公共信息平臺(tái),，同時(shí)，再結(jié)合多基因組學(xué)工具（multigenomic tools）,，將有力促進(jìn)對(duì)CCN抗性機(jī)理,、根部發(fā)育和小麥進(jìn)化機(jī)制的了解,。
該研究結(jié)果近期發(fā)表在BMC Genomics刊物上。(生物谷Bioon.com)
doi:10.1186/1471-2164-13-133
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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.
