Phylogenetic Analysis of Acacia nilotica and Coffea arabica Using Protein Sequences from the Chloroplast RBCL Gene

The genus Acacia is important economically to local communities in sub-Saharan Africa for its medicinal and beverage usage. The bark extract is used for making a coffee-like concoction, which is named by locals as ‘Wild coffee’ due to its brown color. The objective of this study was to compare the evolutionary analysis of A. nilotica and C. arabica -based amino acids sequence of the ribulose-1,5-bisphosphate carboxylase. The results showed that A. nilotica and C. arabica are polyphyletic and the subspecies A. nilotica and A. n. hemispherica formed the sister group, same as the species C. arabica, C. salvatrix, and C. racemosa.  The chloroplast-encoded rbcL gene, which encodes the large subunit of ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco), is a valuable marker for investigating the evolutionary relationships between plant species. In this study, we conducted a phylogenetic analysis of two economically and ecologically significant plants, Acacia nilotica and Coffea arabica, using protein sequences derived from the chloroplast rbcL gene. A multiple sequence alignment of the rbcL protein sequences was performed, and a maximum likelihood phylogenetic tree was constructed using the RAxML algorithm. The tree was rooted using a Thiotrichales bacterium as an outgroup sequence to establish the evolutionary context. Branch support values were calculated to assess the statistical robustness of the inferred relationships. The results of the phylogenetic analysis revealed the evolutionary relationship between Acacia nilotica and Coffea arabica within the context of other plant taxa. The phylogenetic tree provided insights into their shared ancestry, divergence time, and taxonomic placement within the larger plant kingdom. We identified conserved regions in the rbcL protein sequences, reflecting functional importance, as well as divergent regions, suggesting potential adaptive evolution. The significance of our study lies in understanding the evolutionary history and taxonomic position of these economically important plant species. This knowledge has implications for biodiversity conservation, crop improvement, and ecosystem management. The study also highlights the utility of the rbcL gene as a valuable tool for investigating plant phylogenetics. In conclusion, our phylogenetic analysis using the rbcL protein sequences provides valuable insights into the evolutionary relationship between Acacia nilotica and Coffea arabica. This research contributes to our understanding of plant evolution and has practical applications in various fields, from agriculture to conservation.