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

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