ArticleBMC genomics2012
De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Manipulation of the Expression of Tryptophan Decarboxylase Boosts Grain Functional Quality and Stress Resilience Capacity of Wheat.Plant biotechnology journal · 2025Article
- Transcriptional profiling of wheat (Triticum aestivum L.) during a compatible interaction with the cereal cyst nematode Heterodera avenae.Scientific reports · 2019Article
- Wheat genetic resources in the post-genomics era: promise and challenges.Annals of botany · 2018Review
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- TheFrontiers in plant science · 2018Article
- Transcriptional responses of wheat and the cereal cyst nematode Heterodera avenae during their early contact stage.Scientific reports · 2017Article
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- RNA-seq Analysis of Cold and Drought Responsive Transcriptomes ofFrontiers in plant science · 2017Article
- De novo assembly and characterization of the leaf, bud, and fruit transcriptome from the vulnerable tree Juglans mandshurica for the development of 20 new microsatellite markers using Illumina sequencing.Molecular genetics and genomics : MGG · 2016Article
- Effects of drought and salt-stresses on gene expression in Caragana korshinskii seedlings revealed by RNA-seq.BMC genomics · 2016Article
- Transcriptomic analysis reveals the gene expression profile that specifically responds to IBA during adventitious rooting in mung bean seedlings.BMC genomics · 2016Article
- Comparative Transcriptome Analysis of Resistant and Susceptible Common Bean Genotypes in Response to Soybean Cyst Nematode Infection.PloS one · 2016Article
- Dual RNA-Sequencing of Eucalyptus nitens during Phytophthora cinnamomi Challenge Reveals Pathogen and Host Factors Influencing Compatibility.Frontiers in plant science · 2016Article
- Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome.PloS one · 2016Article
- Transcriptome sequencing, annotation and polymorphism detection in the hop bush, Dodonaea viscosa.BMC genomics · 2015Article
- Large-scale identification of wheat genes resistant to cereal cyst nematode Heterodera avenae using comparative transcriptomic analysis.BMC genomics · 2015Article
- De novo transcriptome assembly of Ipomoea nil using Illumina sequencing for gene discovery and SSR marker identification.Molecular genetics and genomics : MGG · 2015Article
- Pathways associated with lignin biosynthesis in lignomaniac jute fibres.Molecular genetics and genomics : MGG · 2015Article
- Article
- De novo assembly of transcriptome sequencing in Caragana korshinskii Kom. and characterization of EST-SSR markers.PloS one · 2015Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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