The Carniolan Honeybee from Slovenia—A Complete and Annotated Mitochondrial Genome with Comparisons to Closely Related Apis mellifera Subspecies

SIMPLE SUMMARY: The western honeybee, Apis mellifera, is a globally distributed bee species with many recognised subspecies, one of which is Apis mellifera carnica, the Carniolan honeybee. Apis m. carnica is native to southern Central Europe and parts of the Balkans, with the locus classicus in Slovenia. It is also widely popular with beekeepers in parts of Central and Northern Europe and other parts of the world, including the USA, Canada, and even New Zealand. In Slovenia, A. m. carnica is protected, with measures to conserve the subspecies’ autochthonous domestic population in place. Such efforts depend heavily upon genomic and phylogenetic information. In this study, we sequenced and annotated the mitochondrial genome of a specimen from Slovenia and compared the obtained data with a previously published sample of the A. m. carnica from Austria and the closely related Italian honeybee A. m. ligustica. We found several features unique to the new mitochondrial genome. We also phylogenetically analyzed the relationship between our sequence and the selected available A. mellifera mitochondrial sequences. The acquired position of the sequenced A. m. carnica from Slovenia on the phylogenetic tree brings new evidence for close relationships among C and O lineages and reflects their recent historical matrilinear ancestry. ABSTRACT: The complete mitochondrial genome of the Carniolan honeybee (Apis mellifera carnica) from Slovenia, a homeland of this subspecies, was acquired in two contigs from WGS data and annotated. The newly obtained mitochondrial genome is a circular closed loop of 16,447 bp. It comprises 37 genes (13 protein coding genes, 22 tRNA genes, and 2 rRNA genes) and an AT-rich control region. The order of the tRNA genes resembles the order characteristic of A. mellifera. The mitogenomic sequence of A. m. carnica from Slovenia contains 44 uniquely coded sites in comparison to the closely related subspecies A. m. ligustica and to A. m. carnica from Austria. Furthermore, 24 differences were recognised in comparison between A. m. carnica and A. m. ligustica subspecies. Among them, there are three SNPs that affect translation in the nd2, nd4, and cox2 genes, respectively. The phylogenetic placement of A. m. carnica from Slovenia within C lineage deviates from the expected position and changes the perspective on relationship between C and O lineages. The results of this study represent a valuable addition to the information available in the phylogenomic studies of A. mellifera—a pollinator species of worldwide importance. Such genomic information is essential for this local subspecies’ conservation and preservation as well as its breeding and selection.