Mitochondrial genome of Apis mellifera anatoliaca (Hymenoptera: Apidae) – the Anatolian honey bee

Abstract

Apis mellifera anatoliaca had a mitochondrial genome that was 16,256 bp long, with 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and an AT-rich control region. The phylogenetic tree showed that A. m. anatoliaca was closely related to other subspecies found in Turkey, A. m. caucasica and A. m. meda.

Keywords:

• Mitogenome
• next-generation sequencing
• Turkey

The Anatolian honey bee, Apis mellifera anatoliaca Maa (often misspelled A. m. anatolica), occurs throughout Turkey, along with several other A. mellifera subspecies. This yellow-brown honey bee is important for Turkish beekeeping. Multiple investigators have studied genetic variation in honey bees of Turkey (e.g. Smith et al. 1997; Kekecoglu et al. 2009; Özdil et al. 2012). Morphometrically and biologically, A. anatoliaca belongs to the O-lineage (Ruttner 1988). However, despite high interest in this honey bee, no corresponding distinction has been found in mtDNA data to separate it from the Eastern-Mediterranean C-lineage (Kandemir et al. 2000; Palmer et al. 2000; Kandemir et al. 2006).

Here, we report on the complete mitochondrial genome of A. m. anatoliaca (GenBank accession number: MT188686). The sample sequenced was of a morphometrically identified worker honey bee from the Ruttner Bee Collection at the Bee Research Institute in Oberursel, Germany (Voucher No. 3377, I. Çakmak, Bayburt, Turkey, 2002, 40°15 N, 40°13E). Genomic DNA was extracted and quantified before genomic library preparation and PE-150 sequencing with Illumina Hi-Seq 3000/4000 (San Diego, CA) following Eimanifar et al (2017).

Resulting data were checked for quality with FastQC (Andrews 2010), and then trimmed with Trimmomatic (Bolger et al. 2014). Mapping was performed following Boardman et al (2019) in Geneious Prime 2019.0.4 (Kearse et al. 2012) using the reference mitogenome with the highest pairwise identity (A. m. meda, KY464957). The mitogenome was initially annotated using mitos2 (Bernt et al. 2013), and then manually adjusted to A. m. capensis (KX870183) annotation in Geneious Prime. A manual alignment of the sequences of the 13 protein-coding genes (PCGs) and two ribosomal RNAs (rRNAs) was generated in Mesquite v3.5 (Maddison and Maddison 2018). A phylogenetic estimation was run on CIPRES Science Gateway V. 3.3 (Miller et al. 2010), using RAxML 8.2.10 (Stamatakis 2014) with the GTRGAMMA model and 1000 bootstrap replicates (-f a option). PAUP 4.0a was used to produce P-distances (Swofford 2003).

The mitogenome of A. m. anatoliaca was 16,256 bp long (43.1% A, 9.6% C, 5.6% G, 41.7% T). The 13 PCGS, 22 transfer RNAs (tRNAs), two rRNAs and an AT-rich control region resembled other Apis species. Nine of the PCGs were located on the light strand, while the remaining four were on the heavy strand. Atp8 and atp6 overlapped, sharing 19 bp. Four start codons were used: ATA (co1, nad3), ATC (nad2), ATG (atp6, co3, cytb, nad4) and ATT (atp8, co2, nad1, nad4l, nad5, nad6). All stop codons for PCGs were TAA. The 16S rRNA was 1,372bp (81.7% AT) and the 12S rRNA was 785 bp (84.5% AT) long. The 22 tRNAs varied in length from 63 to 78 bp.

Phylogenetically, A. m. anatoliaca is closest to other subspecies found in Turkey: A. m. caucasica (P-distance: 0.00053) and A. m. meda (P-distance: 0.0068, Figure 1). Together, these three subspecies form an O-lineage clade. The P-distances between A. m. anatoliaca and African bees are greater than 0.01. Sequencing additional mitogenomes from Turkey and surrounding countries would enhance our understanding of the O- and C- honey bee lineages.

Figure 1. Phylogenetic tree showing the relationship between A. m. anatoliaca and 27 other Apis honey bees. The tree is midpoint rooted. Node labels indicate the bootstrap values and unlabeled lineages are 100%. GenBank accession numbers are provided.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This project was financed through cooperative agreements provided by the United States Department of Agriculture, Animal and Plant Health Inspection Service (USDA-APHIS) [AP17PPQS&T00C172 and AP18PPQS&T00C116].