Complete chloroplast genome characterization of Curcuma xanthorrhiza Roxb. from Indonesia with comparative analysis against related Curcuma species

Curcuma xanthorrhiza Roxb., commonly referred to as Javanese turmeric or “Temulawak,” was officially designated as Indonesia’s flagship medicinal plant in 2023 by the Indonesian Ministry of Health. However, to date, no complete plastome sequence derived from an Indonesian isolate has been reported. Despite its substantial cultural and pharmacological importance, genomic resources for this species remain scarce. This study presents the first comprehensive characterization of the chloroplast (cp.) genome of an Indonesian C. xanthorrhiza isolate and assesses its phylogenetic placement within the genus Curcuma. Complete plastome sequencing was performed with Oxford Nanopore Technologies (ONT) and annotated to identify coding regions, repeat structures, SSRs, and nucleotide variations. The cp. genome is 162,139 bp in length and carries a quadripartite structure made up of a large single-copy (LSC) region (86,973), a small single-copy (SSC) region (15,736 bp), and two inverted repeats (IRs) of 29,714 and 29,716 bp. This plastome has 113 total genes annotated, including 79 protein-coding genes, and several conserved genes such as rbcL and matK , which support its future use in DNA barcoding. Divergent hotspot regions, including rps16 , petN , ndhF , and psaC , were identified, indicating their potential as high-resolution molecular markers. Codon usage analysis showed a strong A/T-ending bias, with UUU (Phe) being the most prevalent codon and UUA (Leu) with the highest relative usage (RSCU = 1.91). Phylogenetic reconstruction placed C. xanthorrhiza in a highly supported clade with C. zedoaria and C. elata , identifying the three species with the most recent common ancestor (MRCA) and high evolutionary proximity. Altogether, this work makes an essential contribution to the genomic resources available for C. xanthorrhiza , particularly from Indonesia, providing a plastome reference for future applications in species identification, marker development, and conservation genomics.