Comparison and phylogenetic analyses of nine complete chloroplast genomes of zingibereae

Abstract

Zingibereae is a large tribe in the family Zingiberaceae, which contains plants with important medicinal, edible, and ornamental values. Although tribes of Zingiberaceae are well circumscribed, the circumscription of many genera within Zingibereae and the relationships among them remain elusive, especially for the genera of Boesenbergia, Curcuma, Kaempferia and Pyrgophyllum. In this study, we investigated the plastome variation in nine species representing five genera of Zingibereae. All plastomes showed a typical quadripartite structure with lengths ranging from 162,042 bp to 163,539 bp and contained 132–134 genes, consisting of 86–88 coding genes, 38 transfer RNA genes and eight ribosomal RNA genes. Moreover, the characteristics of the long repeats sequences and simple sequence repeats (SSRs) were detected. In addition, we conducted phylogenomic analyses of the Zingibereae and related taxa with plastomes data from additional 32 species from Genbank. Our results confirmed that Stahlianthus is closely related to Curcuma, supporting the idea of merging it into Curcuma. Kaempferia, Boesenbergia and Zingiber were confirmed as close relatives and grouped together as the Kaempferia group. Pyrgophyllum is not allied with the Curcuma clade but instead is embedded within the Hedychium clade. Our results demonstrate the power of plastid phylogenomics in improving the phylogenetic relationships within Zingibereae and provide a new insight into plastome evolution in Zingibereceae.