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Open Access Highly Accessed Research article

De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode

De-Lin Xu12, Hai Long1*, Jun-Jun Liang12, Jie Zhang12, Xin Chen12, Jing-Liang Li12, Zhi-Fen Pan1, Guang-Bing Deng1 and Mao-Qun Yu1*

Author Affiliations

1 Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China

2 Graduate University of the Chinese Academy of Sciences, Beijing, China

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BMC Genomics 2012, 13:133  doi:10.1186/1471-2164-13-133

Published: 11 April 2012



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.


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.


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.