Coptis chinensis Franch., also named Chinese goldthread is a member of Ranunculaceae in the order Ranunculales and represents an important lineage of early eudicots with traditional medicinal value. In our study, by using syntenic analysis combined with phylogenomic analysis of C. chinensis and four other representative genomes from basal and core eudicots, we confirmed that the WGD event in C. chinensis was shared by Aquilegia coerulea and Papaver somniferum L. and quickly occurred after Ranunculales diverged from other eudicots, likely a Ranunculales common tetraploidization (RCT). The synonymous nucleotide substitutions at synonymous sites distribution of syntenic blocks across these genomes showed that the evolutionary rate of the P. somniferum genome is faster than that of the C. chinensis genome by approximately 13.7%, possibly due to Papaveraceaes having an additional special tetraploidization event (PST). After Ks correction, the RCT dated to 115–130 million years ago (MYA), which was close to the divergence of Ranunculaceaes and Papaveraceaes approximately 115.45–130.51 MYA. Moreover, we identified homologous genes related to polyploidization and speciation and constructed multiple sequence alignments with different reference genomes. Notably, the event-related subgenomes in the basal genomes all showed genomic fractionation bias, suggesting a likely allopolyploid nature of the RCT, PST and T-Alpha and T-Beta events in Tetracentron sinense. In addition, we detected that the sixteen P450 subfamilies were markedly expanded in the genomes of Ranunculales, and most of them were related to the RCT and PST events. We constructed a new platform for Early Eudicot Comparative Genomic Research (http://www.cgrpoee.top/index.html) to store more information. In summary, our findings support the WGD of C. chinensis shared by Ranunculales, which is likely an allotetraploidization event. This present effort offered new insights into the evolution of key polyploidization events and the genes related to secondary metabolites during the diversification of early eudicots.

Chinese mahogany (Toona sinensis) is of considerable medical and economic importance, and its genome has been deciphered. However, the process underlying its polyploidy is unclear, and the chromosomal evolutionary trajectory is poorly understood. Here, by reanalysing the T. sinensis genome, we found evidence of a tetraploidization event (T. sinensis special tetraploidization, TST) that occurred approximately 15–17 million years ago (MYA) after the core eudicot-common hexaploidization (ECH or gamma) event. We characterized the synonymous nucleotide substitution rates (Ks values) of collinear genes and found that T. sinensis genes affected by the TST evolve at a slower rate than Acer yangbiense genes. Furthermore, we identified homologous genes related to polyploidization and speciation and constructed multiple alignments with different reference genomes. Notably, the significant balance of gene retention and loss characterized in the two TST-derived subgenomes suggests an autopolyploid nature of the TST. Moreover, we deduced the chromosomal karyotypes of the two subgenomes and identified 7 chromosomal fusions that have shaped the T. sinensis genome; more information is available on a newly constructed karyotype platform (http://www.cgrpoee.top/Toona_sinensis/index.html). The T. sinensis genome preserves the ancestral chromosome structure of dicotyledons well and could serve as a good reference for understanding genomic changes in other Meliaceae and Sapindales plants. In addition, we verified that tandem duplication and the ECH have promoted the expansion of terpene synthase (TPS) genes; conversely, the TST seems to have inhibited expansion of these genes. This present effort has clarified the polyploidy events of the T. sinensis genome, filled gaps in the history of karyotype evolution, and laid a solid foundation for further genomic studies in the Meliaceae research community and beyond.