Analysis of the complete mitochondrial genome of Apis nigrocincta (Insecta: Hymenoptera: Apidae) on Sangihe Island in Indonesia

The cavity-nesting honeybee, Apis nigrocincta, only inhabits the tropical forests of Sulawesi, Sangihe and Mindanao Islands, which are designated as biodiversity hotspots and one of the important areas for biological conservation. In the present study, for the first time, we analyzed the complete mitochondrial genome of A. nigrocincta from two regions in Sangihe Island, Indonesia. The mitochondrial genome of A. nigrocincta consists of a circular molecule of approximately 1.5 kb that includes 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and one AT-rich control region. Two A. nigrocincta had AT mitochondrial genome contents of approximately 84.57 and 84.23%. Start codons ATT, ATG and ATA were found in 13 PCGs. Stop codons TAA and TAG were observed in 12 PCGs and the ND2 gene, respectively. The heavy (H)-strand was predicted to have 9 PCGs and 14 tRNA genes, while the light (L)-strand was predicted to contain 4 PCGs, 8 tRNA, and 2 rRNA genes. All tRNA genes formed typical cloverleaf secondary structures, except for tRNA-Ser(AGN) and tRNA-His. The 104 mutation sites that differed between the A. nigrocincta from two regions in Sangihe Island, Indonesia were evenly distributed throughout the mitochondrial genome. The phylogenetic relationship, inferred using 13 PCGs (based on the maximum likelihood), was consistent with that reported in previous studies that predicted a sister relationship between A. nigrocincta and A. cerana. We discovered that the genetic distance between the A. nigrocincta varieties on Sangihe Island is 0.0067, indicating that they maintained a high genetic diversity on this island.