Characterization and phylogenetic relationships analysis of the complete chloroplast genome of Capsicum annuum (Solanaceae)

Capsicum annuum is one of the oldest domesticated crops in the Americas, which is also the most widely grown spice crop in the world. The complete chloroplast genome of C. annuum has been assembled and annotated in this paper. Its length was 156,781 bp, containing a large single-copy region of 87,367 bp, a small single-copy region of 17,850 bp, and a pair of IR regions of 25,782 bp in each. The whole chloroplast genome of C. annuum contains 135 genes, including 89 protein-coding genes (PCGs), 38 transfer RNA genes (tRNAs), and 8 ribosome RNA genes (rRNAs). The overall nucleotide composition is: A of 30.8%, T of 31.5%, C of 19.1% and G of 18.6%, with a total GC content of the chloroplast genome 37.7% and AT of 62.3%. Phylogenetic relationship analysis was based on 10 plant species using the maximum-likelihood (ML) methods, which showed that the position of C. annuum clustered with C. galapagoense.