Complete Mitochondrial Genome Characterization and Phylogenomics of the Stingless Bee, Heterotrigona itama (Apidae: Meliponini)

With increasing demand for stingless bee honey, meliponiculture has gained widespread attention. <i>Heterotrigona itama</i> is one of the most economically important species. However, excessive exploitation for commercial purposes has led to population declines, and the species is now considered vulnerable in Thailand. Despite its ecological and economic significance, genomic and taxonomic information on <i>H. itama</i> remains limited. In this study, we sequenced and characterized the complete mitochondrial genome (mitogenome) of <i>H. itama</i> to explore its genome structure and phylogenetic position. The circular mitogenome is 15,318 bp in length and consists of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. The genome exhibits a strong A+T bias (75.41%), which affects codon usage and amino acid composition. Isoleucine, methionine, and phenylalanine were the most commonly encoded amino acids. Gene arrangement was highly conserved and closely resembled that of <i>Tetragonula</i> species. Phylogenetic analyses confirmed that <i>H. itama</i> clusters with other stingless bees and is more closely related to bumblebees than to honeybees. Several gene rearrangements suggest a high degree of mitogenomic plasticity. This study provides essential genomic resources for future studies in systematics, phylogenetics, population genetics, and conservation of stingless bees in the Meliponini tribe.