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

Author:

Zhang Ren-Gang123,Shang Hong-Yun12,Jia Kai-Hua4ORCID,Ma Yong-Peng12ORCID

Affiliation:

1. State Key Laboratory of Plant Diversity and Specialty Crops/Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations , Kunming Institute of Botany, , Kunming 650201 Yunnan , China

2. Chinese Academy of Sciences , Kunming Institute of Botany, , Kunming 650201 Yunnan , China

3. University of Chinese Academy of Sciences , Beijing 101408 Beijing , China

4. Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences , Jinan 250100 Shandong , China

Abstract

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 the controversial issue regarding the progenitors of the octoploid strawberry. The results of both methodologies reaffirm Fragaria vesca and Fragaria iinumae as progenitors of the octoploid strawberry. Finally, we propose recommendations for enhancing the accuracy of subgenome phasing in future studies, recognizing the potential of integrated tools for advanced complex allopolyploidy research and offering a new roadmap for robust subgenome-based phylogenetic analysis.

Funder

National Key Research and Development Program

Key Basic Research Programs of Yunnan Province

PSESP in Yunnan Province

Publisher

Oxford University Press (OUP)

Subject

Molecular Biology,Information Systems

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