Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations.

ABSTRACT: Accurate subgenome phasing is crucial for understanding the origin, evolution and adaptive potential of polyploid genomes. SubPhaser and WGDI software are two common methodologies for subgenome phasing in allopolyploids, particularly in scenarios lacking known diploid progenitors. Triggered by a recent debate over the subgenomic origins of the cultivated octoploid strawberry, we examined four well-documented complex allopolyploidy cases as benchmarks, to evaluate and compare the accuracy of the two software. Our analysis demonstrates that the subgenomic structure phased by both software is in line with prior research, effectively tracing complex allopolyploid evolutionary trajectories despite the limitations of each software. Furthermore, using these validated methodologies, we revisited t

SUBMITTER: Zhang RG 

PROVIDER: S-EPMC10772947 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature