The Complete Mitochondrial Genome of Geniotrigona thoracica (Apidae: Meliponini): Phylogenomic Implications and Mitochondrial Gene Rearrangement Patterns

The stingless bee Geniotrigona thoracica is an ecologically and economically important pollinator in Southeast Asia, yet comprehensive genomic resources for this species remain limited. In this study, we sequenced, assembled, and annotated the complete mitochondrial genome (mitogenome) of G. thoracica to investigate its genomic architecture and phylogenetic position. The circular mitogenome is 16,061 bp in length and comprises the typical set of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. The genome exhibits a strong A + T bias, consistent with other hymenopteran mitogenomes, and codon usage patterns reflect this nucleotide composition. Most tRNAs display the canonical cloverleaf secondary structure, although minor structural variations were observed. Comparative analyses revealed several gene rearrangements, including transposition and inversion events, suggesting lineage-specific rearrangements, including transposition of the cox1–trnL–cox2–trnD–atp8–atp6–cox3 block and transposition with inversion of the trnF–nad5–nad4–nad4l–trnP block, relative to the ancestral hymenopteran gene order. Phylogenomic analyses based on concatenated mitochondrial genes strongly supported the monophyly of Meliponini and placed G. thoracica within a well-supported Indo-Malayan clade, closely related to Tetragonula, Heterotrigona, and Lepidotrigona. Furthermore, stingless bees were recovered as more closely related to bumblebees than to honeybees, consistent with previous studies. Overall, this study provides a complete, annotated mitogenomic resource for G. thoracica and contributes to a better understanding of mitochondrial genome evolution, phylogenetic relationships, and biogeographic patterns in stingless bees.