ArticleNucleic acids research2025
SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Chromosome-level genome assemblies of Brownlowia tersa and Brownlowia argentata (Brownlowioideae: Malvaceae).Scientific data · 2026Article
- Genomics meets metabolomics: decodingHorticulture research · 2026Article
- Phylogenomic Insights into High Conservation and Lineage-Specific Expansion of the ABAPT Gene Family in Plants.International journal of molecular sciences · 2026Article
- High-quality genome ofPlant diversity · 2026Article
- quota_Anchor: a strand and whole genome duplication-aware collinear gene identification tool.aBIOTECH · 2026Article
- High-quality genome assembly ofHorticulture research · 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
- Telomere-to-telomere genome assembly and 3D chromatin architecture ofHorticulture 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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Authors and funding
10 authors.
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Abstract
With the explosive growth of whole-genome datasets, accurate detection of orthologous synteny has become crucial for reconstructing evolutionary history. However, current methods for identifying orthologous synteny face great limitations, particularly in scaling with varied polyploidy histories and accurately removing out-paralogous synteny. In this study, we developed a scalable and robust approach, based on the Orthology Index (OI), to effectively identify orthologous synteny. Our evaluation across a large-scale empirical dataset with diverse polyploidization events demonstrated the high reliability and robustness of the OI method. Simulation-based benchmarks further validated the accuracy of our method, showing its superior performance against existing methods across a wide range of scenarios. Additionally, we explored its broad applications in reconstructing the evolutionary histories of plant genomes, including the inference of polyploidy, identification of reticulation, and phylogenomics. In conclusion, OI offers a robust, interpretable, and scalable approach for identifying orthologous synteny, facilitating more accurate and efficient analyses in plant evolutionary genomics.
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