The Complete Chloroplast Genome of Curcuma bakerii, an Endemic Medicinal Plant of Bangladesh: Insights into Genome Structure, Comparative Genomics, and Phylogenetic Relationships

<b>Background</b>: <i>Curcuma bakerii</i> is a species of the family Zingiberaceae, endemic to Bangladesh. This genus of rhizomatous plants is widely distributed in tropical regions worldwide and is valued for its medicinal, aromatic, and culinary properties. <b>Methods</b>: The complete chloroplast (cp) genome of <i>C. bakerii</i> was reconstructed using high-throughput sequencing data. Subsequently, the genome was functionally annotated, assembled, and analyzed to clarify its evolutionary dynamics and structural organization. <b>Results</b>: The study's findings indicate that the genome size is 162,189 base pairs (bp) and that it has a normal quadripartite structure with a large single-copy (LSC) region also comprises a small single-copy (SSC) region and two inverted repeats (IRa and IRb). The GC content of the genome was 36.18%, consisting of 135 genes: 88 protein-coding, 39 tRNA, and 8 rRNA. The codon usage analysis revealed 22 high-frequency and five optimal codons indicative of codon bias. Analysis of repetitive sequences revealed 213 Simple Sequence Repeats (SSRs), most of which were A/T. Additionally, seven mutation hotspots were reported, with 68.08% of single-nucleotide polymorphisms (SNPs) detected in the coding region and 31.91% in the noncoding region. Nonsynonymous substitutions accounted for 63.78%, while synonymous substitutions accounted for 36.11%. <b>Conclusions</b>: Based on this study, cp genome sequencing is a useful tool for understanding the intrageneric relationships among <i>Curcuma</i> species. The research presents a complete cp genome of <i>C. bakerii</i> from Bangladesh and provides a useful genomic resource for the molecular evolution, phylogeny, and genetic diversity study of the genus <i>Curcuma</i>.