Characterization of the First Complete Plastome of Zingiber emeiense: Insights Into Its Phylogenetic Position

Zingiber emeiense Z. Y. Zhu is an endemic medicinal species restricted to Mount Emei in southwestern China. However, the lack of genomic resources has led to its frequent misclassification and has impeded evolutionary studies. Here, we assembled and characterized the first two complete chloroplast genomes (plastomes) of Z. emeiense. The two plastomes were identical in sequence and structure, each with a total length of 163,865 bp and exhibiting a typical quadripartite structure. Each plastome comprised a large single-copy (LSC) region of 88,191 bp, a small single-copy (SSC) region of 15,750 bp, and a pair of inverted repeats (IR) of 29,962 bp each. Each genome encoded 134 functional genes, including 86 protein-coding genes, 40 tRNA genes, and eight rRNA genes, with an overall GC content of 36.04%. Comparative plastome analyses revealed that IR boundary variation and repeat sequence differences were major sources of genome size variation within Zingiber. Seven hypervariable regions (psbM, trnT-UGU, ycf1, petA-psbJ, ndhF, psaC-ndhE, and rps19) were identified as potential molecular markers. Likelihood-based selection analyses revealed that plastid gene evolution was primarily driven by purifying selection, but ten genes showed signatures of positive selection; ycf1, petD, and rpl2 exhibited lineage-specific positive selection on the Z. emeiense clade. Phylogenomic reconstruction based on 70 complete plastomes placed Z. emeiense within sect. Cryptanthium, where it was strongly supported as a sister clade to Zingiber smilesianum and Zingiber teres. This study provides essential genomic resources for conservation and taxonomic studies of this endemic species.