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

Abstract

BackgroundAegilops 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.ResultsUsing 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.ConclusionsWe 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.

De novo transcriptome assembly of Ipomoea nil using Illumina sequencing for gene discovery and SSR marker identification

“…Additionally, the cDNA library was constructed using pooled RNA samples from four representative tissue types. Since the aims of this project were to generate as many cDNA sequences as possible, pooling was a cost-effective strategy based on statistical and practical considerations (Sloan et al 2012;Xu et al 2012).…”

Deyeuxia angustifolia's trancriptional response to elevated CO2 concentration in Sanjiang plain, Northeast China

“…High-quality RNA samples were sent to the Biomarker Technology Company (Beijing, China) for cDNA library construction and sequencing using an Illumina HiSeq TM 2000 (Illumina, San Diego, CA, USA). The cDNA library construction method and Illumina deep-sequencing processes were the same as described by Xu et al [11].…”

Molecular Cloning and Characterization of Two Genes Encoding Tryptophan Decarboxylase from Aegilops variabilis with Resistance to the Cereal Cyst Nematode (Heterodera avenae) and Root-Knot Nematode (Meloidogyne naasi)

“…variabilis accession No. 1 were germinated as reported previously (Xu et al 2012). The seedlings were transferred to a greenhouse under 24°C (day) and 20°C (night) with a photoperiod of 16 h. Samples of roots, stems, leaves of 20-day-old seedlings and roots, stems, leaves, flower buds, flowers of mature plants at 3 days after flowering (DAF) were frozen immediately in liquid nitrogen and stored at −80°C for further analysis.…”