Abstract
In this study, we performed a comparative analysis of 11 newly and 110 published data from the Zingiberaceae family, including their structure, codon usage, nucleotide polymorphisms, divergence time, and selection pressures. Our findings revealed a conserved structure across Zingiberaceae species' chloroplast genomes, with no significant expansion or contraction observed during diversification. We identified four regions within protein-coding genes (atpH, rpl32, ndhA, and ycf1) and one intergenic region (psac-ndhE) prone to mutations, which could serve as valuable molecular markers for phylogeography and population genetics studies. Additionally, our analysis indicated that natural selection predominantly influences codon usage in Zingiberaceae chloroplast genes. Phylogenetic analysis supported the division of Zingiberaceae into two subfamilies. Our results confirmed that Globba is more closely related to Curcuma than to Hedychium, while Hedychium is more closely related to Pommereschea-Rhynchanthus than to Cautleya. Divergence time estimations revealed two rapid divergences in Zingiberoideae species, possibly influenced by rapid uplift of the Tibetan Plateau and a cooling event in the Late Miocene caused by a decrease in CO2 levels. Ancestral range reconstruction results support that Zingiberaceae species originated in Africa during the Cretaceous, and subsequently spread to Southeast Asia and India. Most protein-coding genes in Zingiberaceae undergo negative selection, except for the ycf2 gene. Furthermore, we identified two positively selected genes (matK and ndhB) in high-altitude Roscoea species, potentially crucial for their adaptation to highland environments. In summary, our study provided new perspectives for studying the intricate phylogenetic relationships and their adaptive evolution within the Zingibeaceae family.