The value of genotype-specific reference for transcriptome analyses in barley

• DOI: 10.26508/lsa.202101255
• Publication Date: 2022-05-12T16:20:50Z
• Authors: Wenbin Guo; Max Coulter; Robbie Waugh; Runxuan Zhang
• Keywords: RNA-Seq; Reference Genes

It is increasingly apparent that although different genotypes within a species share "core" genes, they also contain variable numbers of "specific" genes and structures are only present in subset individuals. Using common reference genome may thus lead to loss genotype-specific information the assembled Reference Transcript Dataset (RTD) generation erroneous, incomplete or misleading transcriptomics analysis results. In this study, we RTD (sRTD) reference-based (cRTD) from RNA-seq data cultivated Barke Morex barley, respectively. Our quantitative evaluation showed sRTD has significantly higher diversity transcripts alternative splicing events, whereas cRTD missed 40% it ∼70% accurate transcript assemblies. We found more for quantification as well differential expression analysis. However, gene-level less affected, which be reasonable compromise when high-quality not available.