Allotetraploidization event of Coptis chinensis shared by all Ranunculales

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.