The first complete chloroplast genome of Calamus erectus (Arecaceae): Phylogenetic placement and divergence time estimation

Abstract

Calamus erectus Roxb. is a medicinally important and vulnerable shrub native to Bangladesh. Despite its ecological and ethnobotanical importance, no complete chloroplast genome has been reported for this species. In this study, we characterized the complete plastome of C. erectus. The assembled plastome was 157,887 bp in length and exhibited a typical quadripartite circular structure, comprising a large single-copy (85,756 bp), a small single-copy (17,593 bp), and a pair of inverted repeats (27,269 bp each). The plastome encoded 131 genes, consisting of 86 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. Seventy simple sequence repeats were identified, mostly mononucleotides (49). A codon usage analysis exhibited a strong preference for codons ending in the adenine or uracil base, reflecting an overall A/T bias in the genome. Plastome-based phylogenetic analyses placed C. erectus within the monophyletic tribe Calameae and indicated a close relationship with C. exilis. A molecular dating analysis indicated that C. erectus diverged approximately 7.6 million years ago during the Tortonian age, while the subfamily Calamoideae originated about 46.2 million years ago in the early Miocene. These findings provide the first complete cp genome resource for C. erectus, offering a foundation for further phylogenomic and conservation studies within Arecaceae.