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

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(7)

Published: April 10, 2025

Abstract With the explosive growth of whole-genome datasets, accurate detection orthologous synteny has become crucial for reconstructing evolutionary history. However, current methods identifying face great limitations, particularly in scaling with varied polyploidy histories and accurately removing out-paralogous synteny. In this study, we developed a scalable robust approach, based on Orthology Index (OI), to effectively identify Our evaluation across large-scale empirical dataset diverse polyploidization events demonstrated high reliability robustness OI method. Simulation-based benchmarks further validated accuracy our method, showing its superior performance against existing wide range scenarios. Additionally, explored broad applications plant genomes, including inference polyploidy, identification reticulation, phylogenomics. conclusion, offers robust, interpretable, approach synteny, facilitating more efficient analyses genomics.

Language: Английский

Robust identification of orthologous synteny with the Orthology Index and its applications in reconstructing the evolutionary history of plant genomes

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 23, 2024

Abstract With the explosive growth of whole-genome datasets, accurate detection orthologous synteny has become crucial for reconstruction evolutionary history. However, currently available methods identification have great limitations: are difficult to scale with varying polyploidy histories, and removal out-paralogy is challenging. In this study, we developed a scalable robust approach, Orthology Index ( OI ), identify synteny. Our evaluation large-scale dataset diverse polyploidization events demonstrated that technique highly reliable. This discovery highlights as potentially unified criterion synteny, further validated using simulation-based benchmarks. addition, explore its broad applications in reconstructing histories plant genomes, including inference polyploidy, reticulation, phylogenomics. conclusion, offers robust, interpretable, approach identifying significantly enhancing our analytical prowess genomics.

Language: Английский