Complete Chloroplast Genome Sequence of the Endemic and Medicinal Plant Zingiber salarkhanii: Comparative Analysis and Phylogenetic Relationships

<i>Zingiber salarkhanii</i> (Zingiberaceae family) is an endemic species of Bangladesh. It possesses biological effects, including analgesic, anxiolytic, cytotoxic, and antioxidant properties. Although genomic data on <i>Zingiber</i> is scarce, the entire chloroplast (cp) genome has been extensively used as a molecular marker to resolve phylogenetic issues. The genome size is 163,980 bp, and it has a standard quadripartite structure, with an average GC content of 36.91%. The genome contains 138 genes (113 unique), comprising 90 protein-coding genes, 79 unique genes, 48 noncoding genes (34 unique), 40 transfer RNAs (tRNAs), and eight ribosomal RNAs (rRNAs). Codon usage analysis of the cp revealed 14 high-frequency codons besides 18 optimal codons in this species. A repetitive study revealed 211 simple sequence repeats (SSRs), predominantly A/T mononucleotide repeats. Sequence alignment indicated that variable regions were primarily located in the single-copy regions. Sequence comparison showed that most variable regions were located within the single-copy regions, and nucleotide diversity (π = 0-0.11289) indicated overall low divergence with 11 mutation hotspots. Phylogenetic investigations using both coding sequences and complete cp genomes indicated that <i>Z. salarkhanii</i> is most closely related to the <i>Zingiber</i> genus. Phylogenetic investigations using both coding genes and complete cp genomes placed <i>Z. salarkhanii</i> within the core <i>Zingiber</i> lineage, revealing its closest relationship to <i>Z. recurvatum</i> rather than to the genus. It conducted an extensive analysis of many cp genomic characteristics for phylogenetic significance, including overall genome architecture, codon usage bias, repetitive sequences, inverted repeat borders, and phylogenetic reconstruction. These findings provide a basis for further research to elucidate the molecular evolutionary dynamics of individual population variability within the species and genus. The plastome reported here also provides an essential genomic reference for future work on population variation and species differentiation within <i>Zingiber</i>.