Comparative Chloroplast Genome Study of in China Sheds Light on Plastome Characterization and Phylogenetic Relationships.

Background: Mill., a morphologically diverse herbaceous perennial genus of Zingiberaceae, is distributed mainly in tropical to warm-temperate Asia. In China, species of have crucial medicinal, edible, and horticultural values; however, their phylogenetic relationships remain unclear.

Methods: To address this issue, the complete plastomes of the 29 accessions were assembled and characterized. Comparative plastome analysis and phylogenetic analysis were conducted to develop genomic resources and elucidate the intraspecific phylogeny of .

Results: The newly reported plastomes ranged from 161,495 to 163,880 bp in length with highly conserved structure. Results of comparative analysis suggested that IR expansions/contractions and changes of repeats were the main reasons that influenced the genome size of the plastome. A large number of SSRs and six highly variable regions (, , , -, -, and -) have been identified, which could serve as potential DNA markers for future population genetics or phylogeographic studies on this genus. The well-resolved plastome phylogeny suggested that could be divided into three clades, corresponding to sect. (sect. + sect. ) and sect. .

Conclusions: Overall, this study provided a robust phylogeny of plants in China, and the newly reported plastome data and plastome-derived markers will be of great significance for the accurate identification, protection, and agricultural management of resources in the future.