ArticleBMC genomics2013
Analysis and annotation of the hexaploid oat seed transcriptome.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Genome-wide identification of oatFrontiers in genetics · 2025Article
- A first de novo transcriptome assembly of feijoa (Acca sellowiana [Berg] Burret) reveals key genes involved in flavonoid biosynthesis.The plant genome · 2024Article
- Transcriptome and metabolome analyses reveal regulatory networks associated with nutrition synthesis in sorghum seeds.Communications biology · 2024Article
- Transcriptome analysis of ovules offers early developmental clues after fertilization in3 Biotech · 2023Article
- Article
- OMICS in Fodder Crops: Applications, Challenges, and Prospects.Current issues in molecular biology · 2022Review
- Article
- Analysis of oat seed transcriptome with regards to proteins involved in celiac disease.Scientific reports · 2022Article
- Identification of Pueraria spp. through DNA barcoding and comparative transcriptomics.BMC plant biology · 2022Article
- Multiple Antioxidative and Bioactive Molecules of Oats (Antioxidants (Basel, Switzerland) · 2021Review
- Synergistic Effect of Methyl Jasmonate and Abscisic Acid Co-Treatment on Avenanthramide Production in Germinating Oats.International journal of molecular sciences · 2021Article
- Comparative de novo transcriptome analysis of barley varieties with different malting qualities.Functional & integrative genomics · 2020Article
- Functional dissection of HGGT and HPT in barley vitamin E biosynthesis via CRISPR/Cas9-enabled genome editing.Annals of botany · 2020Article
- Heritable temporal gene expression patterns correlate with metabolomic seed content in developing hexaploid oat seed.Plant biotechnology journal · 2020Article
- Evaluation of duplicated reference genes for quantitative real-time PCR analysis in genome unknown hexaploid oat (Plant methods · 2020Article
- Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species.BMC bioinformatics · 2019Article
- Charting oat (Avena sativa) embryo and endosperm transcription factor expression reveals differential expression of potential importance for seed development.Molecular genetics and genomics : MGG · 2019Article
- The Biosynthetic Pathway of Major Avenanthramides in Oat.Metabolites · 2019Article
- Preparation and Characterization of Avenin-Enriched Oat Protein by Chill Precipitation for Feeding Trials in Celiac Disease.Frontiers in nutrition · 2019Article
- PK-profiling method for identifying the expression of resistance-associated genes in partially resistant oats to crown rust.BMC plant biology · 2018Article
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext generation sequencing provides new opportunities to explore transcriptomes. However, challenges remain for accurate differentiation of homoeoalleles and paralogs, particularly in polyploid organisms with no supporting genome sequence. In this study, RNA-Seq was employed to generate and characterize the first gene expression atlas for hexaploid oat.
resultsThe software packages Trinity and Oases were used to produce a transcript assembly from nearly 134 million 100-bp paired-end reads from developing oat seeds. Based on the quality-parameters employed, Oases assemblies were superior. The Oases 67-kmer assembly, denoted dnOST (de novo Oat Seed Transcriptome), is over 55 million nucleotides in length and the average transcript length is 1,043 nucleotides. The 74.8× sequencing depth was adequate to differentiate a large proportion of putative homoeoalleles and paralogs. To assess the robustness of dnOST, we successfully identified gene transcripts associated with the biosynthetic pathways of three compounds with health-promoting properties (avenanthramides, tocols, β-glucans), and quantified their expression.
conclusionsTo our knowledge, this study provides the first direct performance comparison between two major assemblers in a polyploid organism. The workflow we developed provides a useful guide for comparable analyses in other organisms. The transcript assembly developed here is a major advance. It expands the number of oat ESTs 3-fold, and constitutes the first comprehensive transcriptome study in oat. This resource will be a useful new tool both for analysis of genes relevant to nutritional enhancement of oat, and for improvement of this crop in general.
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