Integrated Syntenic and Phylogenomic Analyses of Polyploidy Events in Monocots

Unraveling widespread polyploidy events throughout plant evolution is needed to infer the wide impacts of polyploidization on diversification, speciation, and other evolutionary innovations. Many polyploidy events have been identified in Poales and Ziniberates, but the timing and nature of these ancient events remains unclear. We employed an integrated approach of syntenic and phylogenomic analyses to improve the resolution of WGDs in monocot lineages. Firstly, a comprehensive phylogenomic analyses were performed on 11,503 gene clusters and the number of ancient duplications were detected along the internal branches of the monocot phylogeny. We also investigated the inter-genomic synteny blocks of Musa and Oryza, and dated the duplications of anchor genes located on systemic blocks phylogenetically. It supports three rounds of WGDs in Musa lineage and two, potentially three, ancient WGDs in the history of grass lineages after their divergence. The newly developed SynTree approach provides a fast automated way to analyze multi-taxa genome alignment data and obtain an approximate overview of their WGD landscape. Finally, by integrating syntenic and phylogenomic evidence, we were able to improve the currently knowledge of genome duplication history in monocot lineages.