Structural Variations in Complete Mitogenome of Stingless Bees Serve as Auxiliary Molecular Markers for Generic Systematics

For this study, mitochondrial-level research was conducted into the stingless bee species Lepidotrigona arcifera in order to assemble the complete mitogenome sequence of L. arcifera, analyze its structural characteristics, and provide a more reliable and valuable taxonomic basis for resolving the complex phylogeny of Meliponini tribe. We obtained the complete mitogenome of L. arcifera, spanning 15,260 bp in length and comprising thirteen protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), twenty-two transfer RNAs (tRNAs), and a control region (D-loop). Phylogenetic analysis showed that L. arcifera has the closest genetic relationship with Lepidotrigona flavibasis (genus Lepidotrigona), followed by Lepidotrigona terminata (genus Lepidotrigona), and then Tetragonula pagdeni (genus Tetragonula), consistent with our previous findings. We further conducted a comparative analysis of structural variations across mitogenomes, revealing significant divergence in gene order and transcriptional orientation. The thirty-eight mitochondrial genes were categorized into four blocks (I-IV) and the D-loop. An inversion within Block IV distinguished L. arcifera from its closest relative L. flavibasis. Conserved block order was highly consistent within Melipona. Notably, Frieseomelitta varia (genus Frieseomelitta) and Tetragonisca angustula (genus Tetragonisca) formed a distinct clade and shared an identical block arrangement, which differed from other species. This study presents the first complete mitogenome sequence of L. arcifera, enriching the genomic resources for this taxon. More importantly, it reveals extensive mitochondrial gene rearrangements in stingless bees, suggesting that such structural variations represent valuable auxiliary molecular markers for stingless bee species classification.