Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids.

ABSTRACT: Polyploidy is a widespread phenomenon throughout eukaryotes. Due to the coexistence of duplicated genomes, polyploids offer unique challenges for estimating gene expression levels, which is essential for understanding the massive and various forms of transcriptomic responses accompanying polyploidy. Although previous studies have explored the bioinformatics of polyploid transcriptomic profiling, the causes and consequences of inaccurate quantification of transcripts from duplicated gene copies have not been addressed. Using transcriptomic data from the cotton genus (Gossypium) as an example, we present an analytical workflow to evaluate a variety of bioinformatic method choices at different stages of RNA-seq analysis, from homoeolog expression quantification to downstream analysis used to

SUBMITTER: Hu G 

PROVIDER: S-EPMC7986634 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature