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

• Main Authors: Xu De-Lin, Long Hai, Liang Jun-Jun, Zhang Jie, Chen Xin, Li Jing-Liang, Pan Zhi-Fen, Deng Guang-Bing, Yu Mao-Qun
• Format: Article
• Language: English
• Published: BMC 2012-04-01
• Series: BMC Genomics
• Online Access: http://www.biomedcentral.com/1471-2164/13/133

<p>Abstract</p> <p>Background</p> <p><it>Aegilops variabilis</it> No.1 is highly resistant to cereal cyst nematode (CCN). However, a lack of genomic information has restricted studies on CCN resistance genes in <it>Ae</it>. <it>variabilis</it> and has limited genetic applications in wheat breeding.</p> <p>Results</p> <p>Using RNA-Seq technology, we generated a root transcriptome at a sequencing depth of 4.69 gigabases of <it>Ae. variabilis</it> 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.</p> <p>Conclusions</p> <p>We conducted high-resolution transcriptome profiling related to root development and the response to CCN infection in <it>Ae</it>. <it>variabilis</it> No.1. This research facilitates further studies on gene discovery and on the molecular mechanisms related to CCN resistance.</p>