ArticleBMC biology2024
Introgressions lead to reference bias in wheat RNA-seq analysis.
Article in BMC biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 12 citations in OpenAlex.
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- Harnessing Bulk-Segregant Mapping to Identify Trait-Associated Genes in the Allopolyploid Model Plant Nicotiana benthamiana.Plant biotechnology journal · 2026Article
- Temporal and genotype-dependent transcriptomic responses to cold treatment and recovery in winter rapeseed (Frontiers in plant science · 2026Article
- Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement.Nature communications · 2025Article
- Rapid reprogramming and stabilization of homoeolog expression bias in hexaploid wheat biparental populations.Genome biology · 2025Article
- Evaluating Genome Assemblies for Optimized Completeness and Accuracy of Reference Gene Sequences in Wheat, Rye, and Triticale.Plants (Basel, Switzerland) · 2025Article
- Pangenome graph mitigates heterozygosity overestimation from mapping bias: a case study in Chinese indigenous pigs.BMC biology · 2025Article
- Analysis of a global wheat panel reveals a highly diverse introgression landscape and provides evidence for inter-homoeologue chromosomal recombination.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- A Transcriptome Response of Bread Wheat (Plants (Basel, Switzerland) · 2024Article
- Introgressions lead to reference bias in wheat RNA-seq analysis.BMC biology · 2024Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
Abstract
backgroundRNA-seq is a fundamental technique in genomics, yet reference bias, where transcripts derived from non-reference alleles are quantified less accurately, can undermine the accuracy of RNA-seq quantification and thus the conclusions made downstream. Reference bias in RNA-seq analysis has yet to be explored in complex polyploid genomes despite evidence that they are often a complex mosaic of wild relative introgressions, which introduce blocks of highly divergent genes.
resultsHere we use hexaploid wheat as a model complex polyploid, using both simulated and experimental data to show that RNA-seq alignment in wheat suffers from widespread reference bias which is largely driven by divergent introgressed genes. This leads to underestimation of gene expression and incorrect assessment of homoeologue expression balance. By incorporating gene models from ten wheat genome assemblies into a pantranscriptome reference, we present a novel method to reduce reference bias, which can be readily scaled to capture more variation as new genome and transcriptome data becomes available.
conclusionsThis study shows that the presence of introgressions can lead to reference bias in wheat RNA-seq analysis. Caution should be exercised by researchers using non-sample reference genomes for RNA-seq alignment and novel methods, such as the one presented here, should be considered.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.