Plastid phylogenomics and species discrimination in the "Chinese" clade of <i>Roscoea</i> (Zingiberaceae)

<i>Roscoea</i> is an alpine or subalpine genus from the pan-tropical family Zingiberaceae, which consists of two disjunct groups in geography, namely the "Chinese" clade and the "Himalayan" clade. Despite extensive research on the genus, <i>Roscoea</i> species remain poorly defined and relationships between these species are not well resolved. In this study, we used plastid genomes of nine species and one variety to resolve phylogenetic relationships within the "Chinese" clade of <i>Roscoea</i> and as DNA super barcodes for species discrimination. We found that <i>Roscoea</i> plastid genomes ranged in length from 163,063 to 163,796 bp, and encoded 113 genes, including 79 protein-coding genes, 30 tRNA genes, four rRNA genes. In addition, expansion and contraction of the IR regions showed obvious infraspecific conservatism and interspecific differentiation. Plastid phylogenomics revealed that species belonging to the "Chinese" clade of <i>Roscoea</i> can be divided into four distinct subclades. Furthermore, our analysis supported the independence of <i>R</i>. <i>cautleoides</i> var. <i>pubescens</i>, the recovery of <i>Roscoea pubescens</i> Z.Y. Zhu, and a close relationship between <i>R</i>. <i>humeana</i> and <i>R</i>. <i>cautloides</i>. When we used the plastid genome as a super barcode, we found that it possessed strong discriminatory power (90%) with high support values. Intergenic regions provided similar resolution, which was much better than that of protein-coding regions, hypervariable regions, and DNA universal barcodes. However, plastid genomes could not completely resolve <i>Roscoea</i> phylogeny or definitively discriminate species. These limitations are likely related to the complex history of <i>Roscoea</i> speciation, poorly defined species within the genus, and the maternal inheritance of plastid genomes.