Chloroplast Genome Assembly and DNA Variation Detection of Amomum villosum Lour. and Alpinia kwangsiensis T.L.Wu & S.J.Chen

Background: Amomum villosum, known for its anti-inflammatory and antibacterial effects, is a traditional medicinal plant used for gastrointestinal disorders. However, Alpinia kwangsiensis, a related species with lower pharmacological efficacy, is often used as an adulterant, warranting accurate molecular identification.<br/>Methods and Results: In this study, we analyzed the complete chloroplast genomes of A. villosum and A. kwangsiensis using an Illumina NextSeq 1000 sequencer and a NOVOPlasty assembler to identify polymorphic regions for DNA marker development. The genome of A. villosum (164,070 bp) comprised large and small single-copy regions and two inverted repeats, whereas that of A.<br/>kwangsiensis (162,449 bp) displayed a similar structure with size differences. Moreover, the gene content of the two species slightly varied, with A. villosum and A. kwangsiensis encoding 133 and 130 genes, respectively. Our comparative analysis involving related Amomum (Wurfbainia) and Alpinia accessions clarified the taxonomic relationships. We identified small insertions/deletions and single-nucleotide polymorphisms as potential species-specific DNA marker candidates <br/>Conclusion: The results of this study provide essential chloroplast genomic resources for authenticating medicinal materials and support future marker-assisted methods for the identification of A. villosum and related species.