Comparative description of mitochondrial genomes of the honey bee Apis (Hymenoptera: Apidae): four new genome sequences and Apis phylogeny using whole genomes and individual genes

We sequenced four complete mitochondrial genomes (mt genomes) of members of the honey bee genus Apis (A. cerana, A. dorsata, A. laboriosa, and A. mellifera ligustica). These four and other available mt genome sequences of Apis were used to scrutinize the within-genus genomic characteristics, gene arrangement, and phylogenetic relationships of Apis. Furthermore, phylogenetic performance of 15 individual genes and two concatenated gene combinations were tested to locate suitable genes for Apis phylogeny. Phylogenetic reconstruction using all concatenated protein-coding genes (PCGs) and rRNAs strongly supported the presence of three lineages in Apis: the sister lineages of cavity-nesting honey bees (A. cerana, A. mellifera, A. nigrocincta, and A. koschevnikovi) and the giant honey bees (A. dorsata and A. laboriosa), and a divergent lineage consisting of the dwarf honey bees (A. florea and A. andreniformis). Apis mt genomes revealed two gene arrangements, trnE-trnS(1) or trnS(1)-trnE in the tRNA block at the A+T-rich region and ND2 junction. The gene arrangement found in Apis are consistent with two independent derivations because the same arrangement was shared between non-sister species. Several number of two gene concatenation, along with the individual gene ND4, confirmed the current whole mt genome-based phylogeny with relatively strong support, signifying that these single and two gene combinations are sufficient for an extended within-genus phylogeny of Apis, without inclusion of additional genes.