Characterization and Phylogenetic Analysis of the Chloroplast Genome of Carissa spinarum L. (Rauvolfioideae,...

Carissa spinarum L. (Rauvolfioideae, Apocynaceae), a thorny shrub indigenous to arid regions of South Asia (including Pakistan), is traditionally used to treat fever, diabetes, and inflammation. This study presents the first de novo assembly of the complete chloroplast (cp) genome of C. spinarum. The genome comprises 154,654 base pairs (bp) and displays the typical quadripartite structure, consisting of a large single-copy (LSC) region (84,929 bp), a small single-copy (SSC) region (18,123 bp), and a pair of inverted repeats (IRa and IRb; 25,801 bp each). Annotation identified 113 unique genes, including 79 protein-coding genes (CDSs), 30 transfer RNAs (tRNAs), and four ribosomal RNAs (rRNAs), with 16 genes duplicated in the IRs (five CDSs, four rRNAs, and seven tRNAs). Relative synonymous codon usage (RSCU) analysis revealed a strong bias tuoward codons ending in A/T (RSCU ≥ 1), while those ending in C/G were underrepresented (RSCU < 1). Amino acid frequency analysis showed lysine as the most frequently encoded and cysteine as the least abundant. We identified numerous simple sequence repeats (SSRs), with mononucleotide repeats being the most abundant, followed by tetranucleotide repeats, then by trinucleotide repeats; most SSRs were A/T-rich, consistent with the high overall AT content of the cp genome. Phylogenomic analysis across 19 genera placed C. spinarum within the tribe Carisseae, clarified intertribal relationships, and supported the polyphyly of Willughbeieae. As the first cp genome resource for this species, our study provides a valuable foundation for future conservation efforts and evolutionary studies within Rauvolfioideae and the broader Apocynaceae family.