Analysis of whole chloroplast genomes from three medicinal Amomum species

Amomum xanthioides, A. villosum and A. longiligulare are three medicinally important herbs that are widely cultivated in southeast Asia. The ripe fruits of all three species are not only used worldwide in treatments for gastrointestinal diseases, but are also popular condiments in cooked food. In this study, we determined and analyzed the complete chloroplast (cp) genome sequences of these three Amomum species. The sizes of the cp genomes of A. xanthioides, A. villosum and A. longiligulare were 161,889 bp, 162,355 bp, and 161,990 bp, respectively. The cp genomes of all three species displayed a typical quadripartite structure. The cp genomes of A. xanthioides, A. villosum, and A. longiligulare encoded a total of 139, 138, and 139 genes, respectively, of which 118, 117, and 118 genes were single-copy genes. These included 92 protein-coding genes, eight rRNAs, as well as 39, 38, and 39 tRNAs, respectively. A comparative analysis revealed that the cp genomes of the three Amomum species had similar characteristics and patterns of organization. However, they also varied in terms of gene content, the expansion of inverted repeats, codon usage, repeat sequences, and simple sequence repeats. A phylogenetic analysis strongly supported a sister relationship between A. xanthioides and A. villosum. Overall, the results advance understanding of the relationships among the three medicinally valuable Amomum species, and provide basic molecular information to aid conservation efforts as well as research in phylogenetics and systematics.