ArticleLife science alliance2022
The value of genotype-specific reference for transcriptome analyses in barley.
Article in Life science alliance, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- Temporal and genotype-dependent transcriptomic responses to cold treatment and recovery in winter rapeseed (Frontiers in plant science · 2026Article
- Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.Bioinformatics advances · 2026Article
- Genetic Signatures of Competitive Performance in Burmese Gamecocks: A Transcriptomic Analysis.Biology · 2025Article
- A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity.Nature genetics · 2025Article
- The cap-binding complex modulates ABA-responsive transcript splicing during germination in barley (Hordeum vulgare).Scientific reports · 2024Article
- Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs.International journal of molecular sciences · 2023Review
- High-quality reference transcriptome construction improves RNA-seq quantification inFrontiers in genetics · 2022Article
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Authors and funding
4 authors.
Funding
Abstract
It is increasingly apparent that although different genotypes within a species share "core" genes, they also contain variable numbers of "specific" genes and different structures of "core" genes that are only present in a subset of individuals. Using a common reference genome may thus lead to a loss of genotype-specific information in the assembled Reference Transcript Dataset (RTD) and the generation of erroneous, incomplete or misleading transcriptomics analysis results. In this study, we assembled genotype-specific RTD (sRTD) and common reference-based RTD (cRTD) from RNA-seq data of cultivated Barke and Morex barley, respectively. Our quantitative evaluation showed that the sRTD has a significantly higher diversity of transcripts and alternative splicing events, whereas the cRTD missed 40% of transcripts present in the sRTD and it only has ∼70% accurate transcript assemblies. We found that the sRTD is more accurate for transcript quantification as well as differential expression analysis. However, gene-level quantification is less affected, which may be a reasonable compromise when a high-quality genotype-specific reference is not available.
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