Endang Rahmat, Laura Anindita, Jeremiah Tobias Hutabarat, Rudi Nirwantono, Argandita Meiftasari, Anca Awal Sembada, Roggers Gang, Muhammad Yogi Saputra, Refsya Azanti Putri
Coleus amboinicus Lour., commonly known as “Torbangun” in Indonesia, is a culturally significant herb widely used as a natural galactagogue in Indonesia, yet its complete plastome sequence remains uncharacterized. This study reports the first complete chloroplast (cp) genome of an Indonesian C. amboinicus Lour. isolate, generated using Oxford Nanopore Technology (ONT) and annotated to identify its coding regions, repeat structures, simple sequence repeats (SSRs), and nucleotide variations. ONT PromethION sequencing produced 280,433 reads, with an N50 of 11,452 bp. The cp genome was assembled to 152,510 bp with the canonical quadripartite structure, consisting of an LSC region (83,374 bp), an SSC region (17,693 bp), and two IR regions (IRa and IRb) of 25,721 bp and 25,722 bp, respectively. The genome encodes 113 unique genes, containing 79 protein-coding genes, 30 tRNAs, and 4 rRNAs, with a GC content of 37.74%. Structural analysis revealed 51 SSR motifs, predominantly AT-biased, and 104 long repeats dominated by palindromic structures. Sliding-window analysis identified eight divergent hotspot regions, including psbA, rps16, atpI, psbM, rpl16-rps3, ndhF, ccsA-ndhD, and ycf1, with elevated sequence variation, indicating their potential as molecular markers for species identification. Codon usage analysis showed strong AU-ending bias, with AUU (Ile) the most frequent codon (RSCU = 1.49). Phylogenetic reconstruction established C. amboinicus Lour. as a sister species to C. hadiensis Forssk., with perfect support at all major nodes. These findings provide essential genomic resources for C. amboinicus Lour., establishing a basis for future uses in species authentication, molecular marker development, and biotechnological exploration. © The Author(s), under exclusive licence to Springer Nature B.V. 2026.
Biotechnology Department, Faculty of Engineering, Bina Nusantara University, Jakarta, 11480, Indonesia; School of Life Sciences and Technology, Institut Teknologi Bandung, West Java, Bandung, 40132, Indonesia; National Agricultural Research Organization, National Semi-Arid Resources Research Institute, Soroti, Uganda; Department of Chemistry, Faculty of Science, Institut Teknologi Sumatera, Lampung, Indonesia; Department of Pharmacy, Faculty of Science, Institut Teknologi Sumatera, Lampung, Indonesia