The complete mitochondrial genome of the West African honey bee Apis mellifera adansonii (Insecta: Hymenoptera: Apidae).

The complete mitochondrial genome of the West African honey bee Apis mellifera adansonii consisted of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. It was 16,466 bp and consisted of 84.7% AT nucleotides. This subspecies had a similar mitogenome to those of other southern African honey bees, namely A. m. scutellata, A. m. capensis, and A. m. monticola.

The West African honey bee, A. m. adansonii (Latreille, 1804), is a small, yellow honey bee found throughout West Africa, including Nigeria, Burkina Faso, and Congo. Mitochondrial DNA studies on the tRNA-Ile and ND2 gene regions and a microsatellite study both showed that A. m. adansonii is closely related to honey bees with which it shares geographic borders: A. m. scutellata, A. m. monticola, and A. m. capensis (Arias and Sheppard 1996; Franck et al. 2001). Using a single gene region, these four subspecies were found to be genetically very similar (Arias and Sheppard 1996). Here, we sequenced the mitochondrial genome of a worker A. m. adansonii from the Ruttner Bee Collection at the Bee Research Institute in Oberursel, Germany (Voucher No. 1284, H. Himsel, 1985, Gaya, Niger, 11°52′48N 3°27E). Subspecies identity was confirmed morphometrically and the GenBank accession number is MN585109.

Genomic DNA was extracted, quantified and sequenced (PE-150bp, Illumina Hi-Seq 3000/4000, San Diego, CA) following Eimanifar et al. (2017). Raw sequencing data were quality controlled using FastQC (Andrews 2010). Reads were trimmed with Trimmomatic (Bolger et al. 2014) before mapping was performed in Geneious Prime 2019.0.4 (Biomatters Ltd., Auckland, New Zealand) (Kearse et al. 2012). We followed the stringent mapping practice described in Boardman et al. (2019), using A. m. capensis (KX870183) as the reference genome. The assembled mitochondrial genome was annotated using mitos2 (Bernt et al. 2013) and then manually adjusted to A. m. capensis in Geneious. Sequences from the 13 protein-coding genes (PCGs) and two ribosomal RNAs (rRNAs) were extracted and manually aligned to other Apis sequences in Mesquite version 3.5 (Maddison and Maddison 2018). Phylogenetic analysis was completed using RAxML version 8.2.10 GTRGAMMA model (1000 bootstrap replicates, -f, a option) (Stamatakis 2014) on CIPRES Science Gateway version 3.3 (Miller et al. 2010) and P-distances were calculated using PAUP 4.0a (Swofford 2003).

The complete mitogenome of A. m. adansonii was 16,466 bp (base composition: 43.2% A, 41.5% T, 5.6% C, and 9.6% G). As expected, the mitogenome has 13 PCGs, 22 transfer RNA (tRNA) genes, two rRNA genes, and one putative control region (CR). The light strand encoded nine PCGs (nad2, co1, co2, atp8, atp6, co3, nad3, nad6, and cytb), with the remaining four (nad1, nad4, nad4l, and nad5) on the heavy strand. Nineteen nucleotides were shared between atp8 and atp6. Four start codons were used: ATT (co2, atp8, nad5, nad4l, nad6, and nad1), ATG (atp6, co3, nad4, and cytb), ATA (co1 and nad3) and ATC (nad2), and all 13 PCGs used a TAA stop codon. The 22 tRNAs varied in length from 62 bp (tRNA-Gln) to 79 bp (tRNA-Thr). The 16S rRNA was 1,327 bp (84.2% AT) and the 12S rRNA was 785 bp (81% AT).

Phylogenetically, the closest subspecies to A. m. adansonii were the African honey bees (A. m. scutellata hybrid, KJ601784, P-distance: 0.00137), A. m. capensis (KX870183, P-distance: 0.00267), A. m. scutellata (KY614238, P-distance: 0.00274), and A. m. monticola (MF678581, P-distance: 0.0032) (Figure 1). Ruttner (1988) suggested that A. m. adansonii is similar to A. m. litorea, so sequencing this subspecies would further clarify our understanding of sub-Saharan honey bee evolution and diversity.

Figure 1.

Phylogenetic relationships between A. m. adansonii and 22 other Apis honey bees (GenBank accession numbers provided). African A-lineage honey bees are shown with (A). The tree is midpoint rooted. Node labels indicate bootstrap values, with unlabeled lineages representing 100%.