Complete mitochondrial genome of the Japanese bumblebee, Bombus hypocrita hypocrita (Insecta: Hymenoptera: Apidae)

Abstract

In the present report, we describe the complete mitochondrial genome of the common bumblebee, Bombus hypocrita hypocrita, from the Otome Plateau, in Yamanashi Prefecture, Japan. The mitochondrial genome of B. h. hypocrita is a circular molecule of 15,795 bp. It contains 13 protein-coding, 22 tRNA and two rDNA genes. The protein-coding genes had ATA, ATG or ATT as the initiation codon and were terminated by the typical stop codon TAA, except for ND4 and Cytb. All the tRNA genes typically formed a cloverleaf secondary structure, except for trnE and trnS1.

Keywords:

• Illumina’s Next Seq 500
• bumblebee
• genetic diversity
• conservation

The Asian orange-tailed bumblebee, Bombus hypocrita, is an important bumblebee species for ecosystem and agriculture and is distributed in Far East Asia (Matsumura et al. 2004). Mitochondrial DNA information is very important for species identification and phylogenetic analysis of the bumblebees (Cameron et al. 2007). To our knowledge, this study is the first to successfully determine the sequence of mitochondrial DNA of B. hypocrita hypocrita (accession number AP017662).

Adult B. h. hypocrita females were collected from the Otome Plateau in Yamanashi Prefecture, Japan (Specimen is stored in the National Museum of Nature and Science, Japan accession number: NSMT-I-HYM74236). The genomic DNA isolated from the worker was sequenced using Illumina’s Next Seq 500 (Illumina). The resultant reads were assembled and analyzed using MITOS web server (Bernt et al. 2013, Germany) and MEGA6 software (Tamura et al. 2013, Japan). Phylogenetic analysis was performed based on the nucleotide sequences of the 13 protein-coding genes using TREEFINDER software (Jobb et al. 2004, Germany).

The B. h. hypocrita mitochondrial genome forms a 15,795 bp closed loop. This mitochondrial genome represents a typical hymenopteran mitochondrial genome and matches the B. h. sapporensis (Hong et al. 2008; Takahashi et al. 2016) genomes in that it comprises 13 protein-coding, 22 putative tRNA, and two rDNA genes. The average AT content of the B. h. hypocrita mitochondrial genome was 85%. Similar to the other bumblebee mitochondrial genomes (Cha et al. 2007; Du et al. 2015), the heavy strand (H-strand) was predicted to contain nine protein-coding and 13 tRNA genes, and the light strand (L-strand) was predicted to contain four protein-coding, nine tRNA and two rDNA genes. The genes, ATP8 and ATP6, shared 19 nucleotides, ND4 and ND4L shared one nucleotide, and ND6 and Cytb shared 13 nucleotide. Six protein-coding genes of the B. h. hypocrita mitochondrial genome started with ATA, ATP6, COIII, ND4 and Cytb started with ATG, and COII, ND5 and ND4L started with ATT; these starting codons have been found to be common in the B. hypocrita mitochondrial genome (Hong et al. 2008; Takahashi et al. 2016). The stop codon in each of these protein-coding genes was either TAA or TAT, except for Cytb, which had TAG, as in other bumblebees.

The complete mitochondrial DNA sequences of 13 mitochondrial protein-coding genes from 14 closely related taxa were analyzed using maximum likelihood method to investigate the phylogenetic relationships within Apinae (Figure 1). The phylogenetic analyses strongly supported the basic topology recoverable from molecular and morphological analyses, grouping the eusocial bee into three major clusters: bumblebee, honeybee and stingless bee. The nucleotide substitution rate between the subspecies of the mitochondrial genomes of B. h. hypocrita and B. h. sapporensis was 96.1% (14073/14646). In Japan, the population of B. hypocrita has reduced due to the genetic pollution of crossing, alien diseases, and competition for nesting-site or feed with the invasive species, Bombus terrestris (Goka 2010). The data generated in the present study would help in understanding the genetic diversity of the population and would aid in the conservation of this species.

Figure 1. Phylogenetic relationships (determined using the method of maximum likelihood) among the members of Apinae (Order: Hymenoptera) based on the nucleotide sequence of 13 protein-coding genes regions in the mitochondrial genome. The numbers beside the nodes are percentages of 1000 bootstrap values. The Melipona species was used as an outgroup. Alphanumeric terms indicate the GenBank accession numbers.

Acknowledgements

This work was supported by the Science and technology research promotion program for agriculture, forestry, fisheries and food industry (27013B) under Ministry of Agriculture, Forestry and Fisheries of Japan. We are grateful to Mr. A. Uehara, Mr. H. Kubota and Ms. A. Kubota.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.