Eur. J. Entomol. 115: 650-657, 2018 | DOI: 10.14411/eje.2018.064

The draft genome sequence of the Japanese honey bee, Apis cerana japonica (Hymenoptera: Apidae)Original article

Kakeru YOKOI1, Hironobu UCHIYAMA2, Takeshi WAKAMIYA3, Mikio YOSHIYAMA4, Jun-Ichi TAKAHASHI3, Tetsuro NOMURA3, Tsutomu FURUKAWA5, Shunsuke YAJIMA2,5, Kiyoshi KIMURA4,*
1 Insect Genome Research and Engineering Unit, Division of Applied Genetics, Institute of Agrobiological Sciences (NIAS), National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan; e-mail: yokoi123@affrc.go.jp
2 NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan; e-mails: hu202456@nodai.ac.jp, yshun@nodai.ac.jp
3 Department of Life Sciences, Kyoto Sangyo University, Kyoto, Motoyama, Kamigamo, Kita-ku, Kyoto, 603-8555 Japan; e-mail: jit@cc.kyoto-su.ac.jp, nomurat@cc.kyoto-su.ac.jp
4 Honeybee Research Group, Division of Animal Breeding and Reproduction, National Institute of Livestock and Grassland Science (NILGS), National Agriculture and Food Research Organization (NARO), Tsukuba, 2 Ikenodai, Tsukuba, Ibaraki 305-0901, Japan; e-mail: yoshiyam@affrc.go.jp
5 Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan

Honey bees are not only important for honey production but also as pollinators of wild and cultivated plants. The Eastern honeybee (Apis cerana) is more resistant to several pathogens than the Western honeybee (Apis mellifera), and the genomes of two strains of the nominotypical subspecies, A. cerana cerana, northern (Korea) and southern (China) strains, have been sequenced. Apis cerana japonica, another subspecies of A. cerana, shows many specific features (e.g. mildness, low honey production and frequently absconds) and it is important to study the molecular biological and genetic aspects of these features. To accelerate the genetic research on A. cerana japonica, we sequenced the genome of this subspecies. The draft genome sequence of A. cerana japonica presented here is of high quality in terms of basic genome status (e.g. N50 is 180 kbp, total length is 211 Mbp, and largest contig length is 1.31 Mbp) and BUSCO results. The gene set of A. cerana japonica was predicted using AUGUSTUS software and the set of genes was annotated using Blastp and InterProScan, and GO terms were added to each gene. The number of genes is higher than in A. mellifera and in the two strains of A. cerana cerana sequenced previously. A small number of transposable elements and repetitive regions were found in A. cerana japonica, which are also in the genomes of A. mellifera and the northern and southern strains of A. cerana cerana. Apis cerana is resistant to several pathogens that seriously damage A. mellifera. We searched for 41 orthologs related to the IMD and Toll pathways, which have key roles in the immune reaction to invading pathogens. Some orthologs were not identified in the genome of the northern strain of A. cerana cerana. This indicates that the Toll and IMD pathways function in the same way as in A. mellifera and Drosophila melanogaster. Use of the draft genome sequence of A. cerana japonica provided herein and those of the other Apis (sub)species may help to accelerate comparative research on the genome of honey bees.

Keywords: Hymenoptera, Apidae, Apis cerana japonica, genome sequence, transposable elements, innate immune genes

Received: June 4, 2018; Revised: September 25, 2018; Accepted: September 25, 2018; Published online: November 14, 2018  Show citation

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YOKOI, K., UCHIYAMA, H., WAKAMIYA, T., YOSHIYAMA, M., TAKAHASHI, J., NOMURA, T., ... KIMURA, K. (2018). The draft genome sequence of the Japanese honey bee, Apis cerana japonica (Hymenoptera: Apidae). EJE, 115, Article 650-657. https://doi.org/10.14411/eje.2018.064
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