Comparative Phylogenetic Analysis of Six Angiosperm Families Using rbcL and matK Chloroplast Markers

Abstract

Chloroplast DNA markers such as rbcL and matK are widely used in plant molecular systematics due to their complementary evolutionary properties. In this study, we conducted a comparative phylogenetic analysis of six major angiosperm families—Apiaceae, Asteraceae, Fabaceae, Lamiaceae, Orchidaceae, and Rosaceae—using publicly available rbcL and matK sequences. A total of 600 sequences (50 species per family per gene) were retrieved from GenBank. Sequence alignment was performed using MAFFT v7 via Biopython scripts, and Maximum Likelihood phylogenies were constructed using MEGA 11. Tree visualization and annotation were carried out in iTOL v7. Both rbcL and matK markers successfully recovered monophyletic family-level groupings, validating their utility in higher-level phylogenetic inference. However, matK-based trees consistently demonstrated higher resolution, especially at genus and species levels. In families such as Fabaceae and Lamiaceae, matK resolved well-supported clades (e.g., Glycine, Vigna, Salvia, Mentha), whereas rbcL exhibited unresolved polytomies and lower bootstrap support. Even in families where rbcL performed moderately well (e.g., Asteraceae, Orchidaceae), matK provided greater phylogenetic clarity, particularly among terminal clades. A visual bootstrap analysis revealed average support values of 66.1% for rbcL trees and approximately 82.0% for matK trees. These results underscore the stronger phylogenetic signal and discriminatory power of matK in resolving recent divergence events and complex lineages. While rbcL remains useful for deeper phylogenetic relationships due to its conserved nature, matK is better suited for fine-scale taxonomic resolution. Our findings reinforce the importance of marker selection in phylogenetic studies and support the combined use of rbcL and matK in multilocus frameworks. These results also highlight the potential of publicly available sequence data and reproducible pipelines for advancing plant evolutionary research.