Complete chloroplast genome of and a comparative analysis with members of the family Zingiberaceae.

Unlabelled: (L.) Mansf. is a medically important ginger species of the family Zingiberaceae but its genomic information on molecular phylogeny and identification is scarce. In this work, the chloroplast genome of was sequenced, characterized and compared to the other Zingiberaceae species to provide chloroplast genetic resources and to determine its phylogenetic position in the family. The chloroplast genome of was 163,817 bp in length and consisted of a large single-copy (LSC) region of 88,302 bp, a small single-copy (SSC) region of 16,023 bp and a pair of inverted repeats (IRA and IRB) of 29,746 bp each. The chloroplast genome contained 113 unique genes, including 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Several genes had atypical start codons, while most amino acids exhibited biased usage of synonymous codons. Comparative analyses with various chloroplast genomes of Zingiberaceae taxa revealed several highly variable regions (, , , , and ) in the LSC and SSC regions in the chloroplast genome of that could be utilized as molecular markers for DNA barcoding and species delimitation. Phylogenetic analyses based on shared protein-coding genes revealed that formed a distinct lineage with Mood & L.M.Prince, in a subclade that also contained the genera and . These findings constitute the first chloroplast genome information of that could be a reference for phylogenetic analysis and identification of genus within the Zingiberaceae family.

Supplementary Information: The online version contains supplementary material available at 10.1007/s40415-022-00845-w.