Robust identification of orthologous synteny with theOrthology Indexand its applications in reconstructing the evolutionary history of plant genomes

Abstract

AbstractWith the explosive growth of whole-genome datasets, accurate detection of orthologous synteny has become crucial for the reconstruction of evolutionary history based on these datasets. However, the methods of identifying orthologous synteny currently available for plants have great limitations: the methods are difficult to scale with varying polyploidy and the accurate removal of out-paralogy is challenging, given the high complexity of plant genomes. In this study, we developed a scalable and robust approach, the Orthology Index (OI), to accurately identify orthologous synteny by calculating the proportion of orthologs within syntenic blocks. Interestingly, our evaluation of a comprehensive dataset comprising nearly 100 known cases with diverse polyploidy and speciation events revealed that the technique is highly reliable in the identification of orthologous synteny, with an OI threshold value of 0.6 as a cutoff. This discovery highlights OI as a potentially universal criterion for the identification of orthologous synteny. In addition, we demonstrate its broad applications in reconstructing plant genome evolutionary histories, including inference of polyploidy, identification of reticulation, and phylogenomics. The index has been packaged in an all-in-one toolkit (freely available fromhttps://github.com/zhangrengang/OrthoIndex) to facilitate its use in these applications. In conclusion, OI offers a robust, interpretable, and scalable approach for the automated identification of orthologous synteny, significantly expanding our analytical capabilities in plant evolutionary genomics.