Introgressions lead to reference bias in wheat RNA-seq analysis.

ABSTRACT:

Background

RNA-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.

Results

Here 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 inco

SUBMITTER: Coombes B 

PROVIDER: S-EPMC10921782 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature