A likelihood ratio test for detecting shifts in homeolog expression ratios in allopolyploids.

ABSTRACT: Allopolyploids arise through hybridization between related species, carrying multiple sets of chromosomes from distinct progenitors, referred to as subgenomes. Within allopolyploids, duplicated genes across subgenomes, called homeologs, are thought to enhance environmental robustness by shifting their expression ratios depending on environmental and developmental changes. However, existing methods for detecting such ratio shifts, including HomeoRoq and Fisher's exact test, are limited to allopolyploids with two subgenome sets and thus cannot handle more complex cases. We present the HOmeolog Bias Identification Test (HOBIT), a statistical method for detecting shifts in homeolog expression ratios across different conditions using RNA-seq count data. HOBIT performs a likelihood ratio test fo

SUBMITTER: Sun J 

PROVIDER: S-EPMC12676099 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature