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

Abstract We developed a scalable and robust approach, the Orthology Index (OI), to accurately identify orthologous synteny by calculating the proportion of pre-inferred orthologs within syntenic blocks. Our evaluation of a comprehensive dataset comprising nearly 100 known cases with diverse polyploidy events revealed that the approach is highly reliable and robust in the identification of orthologous synteny. This discovery highlights OI as a potentially universal criterion for the automated identification of orthologous synteny. Additionally, we demonstrate its broad applications in reconstructing plant genome evolutionary histories, including polyploidy and reticulation inference, and phylogenomics. The index is packaged in an all-in-one toolkit (https://github.com/zhangrengang/OrthoIndex).