Complete chloroplast genome sequence of Buchanania latifolia: genome structure, and phylogeny of basal Anacardiaceae family relationships

Abstract The chloroplast (cp) genomes are valuable resource with multiple applications, encompassing species identification, phylogenetic reconstruction, and evolutionary investigations. In this study, the complete chloroplast genome sequence of Buchanania latifolia was de novo sequenced, assembled and annotated. The chloroplast genome of B. latifolia exhibits a typical quadripartite structure, with a total length of 160,088 bp, containing 88 protein-coding sequences (CDS), 37 tRNA genes, and 8 rRNA genes, with an overall GC content of 37.7%. A total of 99 SSR loci and 63 repeat sequences were identified, which can be utilized for marker development, phylogenetic and population studies of B. latifolia. Codon usage analysis revealed a preference for Leu codons ending with A/U. Additionally, the study investigated IR boundaries, DNA polymorphism, positive selection suites, and phylogenetic position. Comparative analysis with five other species from the Anacardiaceae family confirmed the nearly identical and highly conserved chloroplast genome features of B. latifolia, which can be valuable for understanding the plastid evolution and evolutionary relationships within Anacardiaceae. Phylogenetic analysis reveals that B. latifolia is positioned at the base of Anacardiaceae, sister to Choerospondias axillaris, Lannea coromandelica, and Sclerocarya birrea. These findings could provide important genetic information for further research into breeding of Anacardiaceae, phylogeny, and evolution of B. latifolia.