Yong H.S.Song S.L.Chua K.O.Liew Y.J.M.Chan K.G.Lim P.E.Eamsobhana P.Mahidol University2026-03-112026-03-112026-12-01Molecular Biology Reports Vol.53 No.1 (2026)03014851https://repository.li.mahidol.ac.th/handle/123456789/115630Background: Geniotrigona thoracica is one of the commonest stingless bee species for pollination services and commercial meliponiculture in Thailand, Malaysia, and Indonesia. Methods and Results: Its complete mitochondrial genome exhibits genome duplication, heteroplasmy and gene rearrangement. It comprises a 16,045-bp “canonical” mitogenome; and a 32,092-bp genome comprising two segments, the 16,045-bp “canonical” genome and its “duplicated-rearranged” genome. The “canonical” genome contains 39 genes—13 protein-coding genes (PCGs), 2 rRNA genes, and 24 tRNA genes (trnK and trnM are duplicated). All the 13 PCGs as well as the two rRNA genes and 19 tRNA genes are located on the majority (J) strand. The “duplicated-rearranged” genome comprises a short segment of tRNA genes in close proximity to the control region (trnM–trnK–trnI–trnA–trnK–trnM–control region) and a long inverted segment of 33 genes (13 PCGs, 2 rRNAs and 18 tRNAs of the nad2 to trnS2 segment of the “canonical” genome). Based on 15 mt-genes and 13 PCGs, G. thoracica forms a subclade with the lineage consisting of Heterotrigona and Lepidotrigona. Conclusions: This phylogenetic relationship concurs with earlier findings based on over 2500 ultra-conserved element (UCE) loci as well as mitochondrial and nuclear genes, indicating mitogenome is suitable for taxon differentiation and phylogenetic study. In addition, the geographic isolates of G. thoracica from Malaysia and Thailand are genetically variable.Biochemistry, Genetics and Molecular BiologyArticleSCOPUS10.1007/s11033-026-11603-62-s2.0-10503171833115734978