SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics

文献类型： 外文期刊

第一作者： Zhang, Ren-Gang

作者： Zhang, Ren-Gang;Shang, Hong-Yun;Zhou, Min-Jie;Shu, Heng;Ma, Yong-Peng;Zhang, Ren-Gang;Shang, Hong-Yun;Zhou, Min-Jie;Shu, Heng;Milne, Richard Ian;Almeida-Silva, Fabricio;Chen, Hengchi;Van de Peer, Yves;Almeida-Silva, Fabricio;Chen, Hengchi;Van de Peer, Yves;Jia, Kai-Hua;Van de Peer, Yves;Van de Peer, Yves

作者机构：

期刊名称：NUCLEIC ACIDS RESEARCH （ 影响因子：13.1； 五年影响因子：16.8 ）

ISSN： 0305-1048

年卷期： 2025 年 53 卷 7 期

页码：

收录情况： SCI

摘要： 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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