ArticleBriefings in bioinformatics2023
Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations.
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- A haplotype-complete chromosome-level assembly of octoploid Urochloa humidicola cv. Tully reveals multiple genomic compositions and evolutionary histories in the species.G3 (Bethesda, Md.) · 2026Article
- Analysis of a near telomere-to-telomere genome of Phellodendron amurense reveals insights into berberine biosynthesis.Nature communications · 2025Article
- Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae.bioRxiv : the preprint server for biology · 2025Article
- A nearly complete haplotype-phased genome assembly of nerve plant (Horticulture research · 2025Article
- Reticulate allopolyploidy and subsequent dysploidy drive evolution and diversification in the cotton family.Nature communications · 2025Article
- SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics.Nucleic acids research · 2025Article
- Phytop: a tool for visualizing and recognizing signals of incomplete lineage sorting and hybridization using species trees output from ASTRAL.Horticulture research · 2025Article
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Corrections and comments
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Authors and funding
4 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.