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

文献类型： 外文期刊

作者： Zhang, Ren-Gang 3 ; Shang, Hong-Yun 3 ; Jia, Kai-Hua 2 ; Ma, Yong-Peng 1 ;

作者机构： 1.Chinese Acad Sci, Kunming Inst Bot, State Key Lab Plant Divers & Specialty Crops, Yunnan Key Lab Integrat Conservat Plant Species Ex, 132,Lanhei Rd, Kunming 650201, Yunnan, Peoples R China

2.Shandong Acad Agr Sci, Inst Crop Germplasm Resources, 23788,Ind North Rd, Jinan 250100, Shandong, Peoples R China

3.Chinese Acad Sci, Kunming Inst Bot, State Key Lab Plant Divers & Specialty Crops, Yunnan Key Lab Integrat Conservat Plant Species Ex, Kunming, Peoples R China

4.Univ Chinese Acad Sci, Beijing, Peoples R China

5.Shandong Acad Agr Sci, Inst Crop Germplasm Resources, Jinan, Peoples R China

关键词： subgenome phasing; WGDI; SubPhaser; complex allopolyploidy

期刊名称：BRIEFINGS IN BIOINFORMATICS （ 影响因子：9.5； 五年影响因子：10.6 ）

ISSN： 1467-5463

年卷期： 2024 年 25 卷 1 期

页码：

收录情况： SCI

摘要： 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.

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