Comparative phylogenetic analysis of key chloroplast and nuclear DNA regions of some Brassica species

The genus Brassica includes the economically valuable vegetables and oilseed crops. Understanding the phylogenetic relationships among these species is vital for plant breeding and evolutionary biology research. In this study, the phylogenetic relationships among some Brassica species were comprehensively analyzed using four chloroplast DNA regions (psbA-trnH, matK, rbcL, and rpl32-trnL) and three nuclear ribosomal DNA regions (ITS1, ITS2, and 5.8S). The resolution of each gene region at the species differentiation level was evaluated. The effectiveness of different gene regions in resolving phylogenetic relationships was also compared. The findings revealed that the matK, rpl32-trnL, and ITS regions provided strong genetic relationships, particularly among species such as B. rapa and B. juncea, as well as B. nigra and B. carinata. Among the chloroplast DNA regions, matK and psbA-trnH effectively resolved variety-level relationships. In contrast, nuclear ribosomal DNA regions (ITS1, ITS2, and 5.8S) provided a higher resolution at the species level. Phylogenetic trees constructed using the Maximum Likelihood method and appropriate analytical models provided well-supported clades and evolutionary relationships among Brassica species. Additionally, genetic relationships were visualized using principal component analysis (PCA), and the results of the phylogenetic analyses were confirmed. PCAs were broadly consistent with the phylogenetic trees and revealed genetic differences and similarities among the species. Multiple gen regions played a complementary role in resolving phylogenetic relationships. This study highlighted the importance of focusing on multiple gene regions instead of a single gene region.