Skip to main content Skip to main navigation menu Skip to site footer
Type: Article
Published: 2017-10-10
Page range: 574–583
Abstract views: 103
PDF downloaded: 3

The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders

Department of Teacher Training, Daegu Education Training Institute, 121 Dangsan-ro, Dalse-gu, Daegu, 42651, South Korea
Institute for Phylogenomics and Evolution, Kyungpook National University, 1005 KNU Global Plaza, 80 Daehak-ro, Buk-gu, Daegu, 41566, South Korea Institute of Ecology and Biological Resources, Vietnam Academy of Sciences and Technology, No.18, Hoangquocviet Road, Caugiay District, Hanoi, Vietnam
Institute for Phylogenomics and Evolution, Kyungpook National University, 1005 KNU Global Plaza, 80 Daehak-ro, Buk-gu, Daegu, 41566, South Korea
Institute for Phylogenomics and Evolution, Kyungpook National University, 1005 KNU Global Plaza, 80 Daehak-ro, Buk-gu, Daegu, 41566, South Korea
Freshwater Biodiversity Research Division, Nakdonggang National Institute of Biological Resources, 14 Sangju, Gyeongsangbuk-do, Republic of Korea
Institute for Phylogenomics and Evolution, Kyungpook National University, 1005 KNU Global Plaza, 80 Daehak-ro, Buk-gu, Daegu, 41566, South Korea Department of Biology Education, Teachers College, Kyungpook National University, 1005 KNU Global Plaza, 80 Daehak-ro, Buk-gu, Daegu, 41566, South Korea
Myriapoda Anaulaciulus koreanus millipedes mitochondrial genome gene arrangement Korea

Abstract

The millipede Anaulaciulus koreanus (Verhoeff, 1937), belonging to the family Julidae, is an endemic species of the Korean fauna. In this study, we sequence and annotate the mitochondrial genome of A. koreanus. The complete mitochondrial genome of this species is 14,916 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes (16S and 12S rRNA), and a large non-coding region. The genome has a very high A+T content (71.1%), less than of the species Brachycybe lecontii Wood, 1864 (order Platydesmida; 76.6%) and Sphaerotheriidae sp. (order Sphaerotheriida; 71.2%). In comparison with the mitochondrial gene arrangement of eight other millipede species, the whole mitochondrial gene arrangement of A. koreanus is most similar to the nemasomatid species, Antrokoreana gracilipes Verhoeff, 1938, but differs from those of the other diplopod orders. The absence of tRNACys between the ND2 and COI regions is unique to the order Polydesmida, whereas the translocation of tRNATyr to between ND2 and COI is exclusive to the Sphaerotheriida. It is also shown that the translocation of tRNAThr between ND4L and ND1 may be a synapomorphy to support a close relationship of two orders Spirobolida and Spirostreptida.

 

References

  1. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 3389–3402.
    https://doi.org/10.1093/nar/25.17.3389

    Brehm, A., Harris, D.J., Hernandez, M., Cabrera, V.M., Larruga, J.M., Pinto, F.M. & Gonzalez, A.M. (2001) Structure and evolution of the mitochondrial DNA complete control region in the Drosophila subobscura subgroup. Insect Molecular Biology, 10, 573–578.
    https://doi.org/10.1046/j.0962-1075.2001.00295.x

    Brewer, M.S. & Bond, J.E. (2013) Ordinal-Level Phylogenomics of the Arthropod Class Diplopoda (Millipedes) Based on an Analysis of 221 Nuclear Protein-Coding Loci Generated Using Next-Generation Sequence Analyses. PLoS ONE, 8 (11), e79935.
    https://doi.org/10.1371/journal.pone.0079935

    Brewer, M.S., Swafford, L., Spruill, C.L. & Bond, J.E. (2013) Arthropod Phylogenetics in light of three novel millipedes (Myriapoda: Diplopoda) mitochondrial genomes with comments on the appropriateness of mitochondrial genome sequence data for inferring deep level relationships. Plos ONE, 8 (7), e68005.
    https://doi.org/10.1371/journal.pone.0068005

    Cao, L., Kenchington, E., Zouros, E. & Rodakis, G.C. (2004) Evidence that the large noncoding sequence is the main control region of maternally and paternally transmitted mitochondrial genomes of the marine mussel (Mytilus spp.). Genetics, 167 (2), 835–850.
    https://doi.org/10.1534/genetics.103.026187

    Cha, S.Y., Yoon, H.J., Lee, E.M., Yoon, M.H., Hwang, J.S., Jin, B.R., Han, Y.S. & Kim, I. (2007) The complete nucleotide sequence and gene organization of the mitochondrial genome of the bumblebee, Bombus igntitus (Hymenoptera: Apidae). Gene, 392, 206–220.
    https://doi.org/10.1016/j.gene.2006.12.031

    Choi, E.H., Park, S.J., Jang, K.H. & Hwang, U.W. (2007) Complete mitochondrial genome of a Chinese scorpion Mesobuthus martensii (Chelicerata, Scorpiones, Buthidae). DNA Sequence, 18 (6), 461–473.
    https://doi.org/10.1080/10425170701289883

    Clayton, D.A. (1984) Transcription of the mammalian mitochondrial genome. Annual Review of Biochemistry, 53, 573–594.
    https://doi.org/10.1146/annurev.bi.53.070184.003041

    Dong, Y., Xu, J.J., Hao, S.J. & Sun, H.Y. (2012) The complete mitochondrial genome of the giant pill millipede, Sphaerotheriidae sp. (Myriapoda: Diplopoda: Sphaerotheriida). Mitochondrial DNA, 23 (5), 333–335.
    https://doi.org/10.3109/19401736.2012.683184

    Dong, Y., Zhu, L., Bai, Y., Ou, Y. & Wang, C. (2016) Complete mitochondrial genomes of two plat-backed millipedes by next-generation sequencing (Diplopoda, Polydesmida). ZooKeys, 637, 1–20.
    https://doi.org/10.3897/zookeys.637.9909

    Enghoff, H., Dohle, W. & Blower, J.G. (1993) Anamorphosis in millipedes (Diplopoda): the present state of knowledge with some developmental and phylogenetic considerations. Zoological Journal of the Linnean Society, 109, 103–234.
    https://doi.org/10.1111/j.1096-3642.1993.tb00305.x

    Enghoff, H. (1984) Phylogeny of millipedes - a cladistic analysis. Journal of Zoological Systematics and Evolutionary Research, 22, 8–26. https://doi.org/10.1111/j.14390469.1984.tb00559.x

    Fernández, R., Edgecombe, G.D. & Giribet, G. (2016) Exploring phylogenetic relationships within Myriapoda and the effects of matrix composition and occupancy on phylogenomic reconstruction. Systematic Biology, 65 (5), syw041.
    https://doi.org/10.1093/sysbio/syw041

    Hoffman, R.L. (1980) Classification of the Diplopoda. Muséum D'Histoire Naturelle, Genève, 237 pp.

    Hopkin, S.P. & Read, H.J. (1992) The biology of millipedes. Oxford University Press, Oxford, 246 pp.

    Hwang, U.W., Friedrich, M., Tautz, D., Park, C.J. & Kim, W. (2001) Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature, 413 (6852), 154–157.
    https://doi.org/10.1038/35093090

    Jang, K.H. & Hwang, U.W. (2009) Complete mitochondrial genome of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata): Phylogenetic position of Bryozoan and phylogeny of lophophorates within the Lophotrochozoa. BMC Genomics, 10, 167.
    https://doi.org/10.1186/1471-2164-10-167

    Kambhampati, S. & Smith, P.T. (1995) PCR primers for the amplification of four insect mitochondrial gene fragments. Insect Molecular Biology, 4, 233–236.
    https://doi.org/10.1111/j.1365-2583.1995.tb00028.x

    Kumazawa, Y. & Nishida, M. (1993) Sequence evolution of mitochondrial tRNA genesand deep-branch animal phylogenetics. Journal of Molecular Evolution, 37 (4), 380–398.
    https://doi.org/10.1007/BF00178868

    Lavrov, D., Boore, J. & Brown, W. (2002) Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss. Molecular Biology and Evolution, 19, 163.

    https://doi.org/10.1093/oxfordjournals.molbev.a004068

    Lim, J.T. & Hwang, U.W. (2006) The Complete Mitochondrial Genome of Pollicipes mitella (Crustacea, Maxillopoda, Cirripedia): Non-monophylies of Maxillopoda and Crustacea. Molecules and Cells, 22 (3), 314–322.

    Lowe, T.M. & Eddy, S.R. (1997) tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Research, 25 (5), 955–964.
    https://doi.org/10.1093/nar/25.5.0955

    Miyazawa, H., Ueda, C., Yahata, K. & Su, Z.-H. (2014) Molecular phylogeny of Myriapoda provides insights into evolutionary patterns of the mode in post-embryonic development. Scientific Reports, 4, 4127.
    https://doi.org/10.1038/srep04127

    Ojala, D., Merkel, C., Geltand, R. & Attardi, G. (1980) The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell, 22, 393–403.
    https://doi.org/10.1016/0092-8674(80)90350-5

    Ojala, D., Montoya, J. & Attardi, G. (1981) tRNA punctuation model of RNA processing in human mitochondria. Nature, 290, 470–474.
    https://doi.org/10.1038/290470a0

    Park, S.J., Choi, E.H., Hwang, J.S. & Hwang, U.W. (2016) The complete mitochondrial genome of a centipede Bothropolys sp. (Chilopoda, Lithobiomorpha, Lithobiidae)’. Mitochondrial DNA, 27 (3), 2268–2269.

    Park, S.J., Lee, Y.S. & Hwang, U.W. (2007) The complete mitochondrial genome of the sea spider Achelia bituberculata (Pycnogonida, Ammotheidae): arthropod ground pattern of gene arrangement. BMC Genomics, 8 (1), 343.
    https://doi.org/10.1186/1471-2164-8-343

    Schultheis, A.S., Weigt, L.A. & Hendricks, A.C. (2002) Arrangement and structural conservation of the mitochondrial control region of two species of Plecoptera: utility of tandem repeat-containing regions in studies of population genetics and evolutionary history. Insect Molecular Biology, 11, 605–610.
    https://doi.org/10.1046/j.1365-2583.2002.00371.x

    Shear, W. (2011) Class Diplopoda de Blainville in Gervais, 1844. Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa, 3148, 159–164.

    Shelley, R.M. & Golovatch, S.I. (2011) Atlas of Myriapod Biogeography. I. Indigenous Ordinal and Supra-Ordinal Distributions in the Diplopoda: Perspectives on Taxon Origins and Ages, and a Hypothesis on the Origin and Early Evolution of the Class. Insecta Mundi, 0158, 1–134.

    Sierwald, P. & Bond, J.E. (2007) Current status of the myriapod class diplopoda (Millipedes): Taxonomic diversity and phylogeny. Annual Review of Entomology, 52, 401–420.
    https://doi.org/10.1146/annurev.ento.52.111805.090210

    Sierwald, P., Shear, W.A., Shelley, R.M. & Bond, J.E. (2003) Millipede phylogeny revisited in the light of the enigmatic order Siphoniulida. Journal of Zoological Systematics and Evolutionary Research, 41, 87–99.
    https://doi.org/10.1046/j.1439-0469.2003.00202.x

    Simon, C., Frati, F., Beckenbach, A., Crespi, B., Liu, H. & Flook, P. (1994) Evolution, weighting and a compilation of conserved polymerase chain reaction primers. Annals of the Entomological Society of America, 87, 651–701.
    https://doi.org/10.1093/aesa/87.6.651

    Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25 (24), 4876–4882.
    https://doi.org/10.1093/nar/25.24.4876

    Verhoeff, K.W. (1937) Zur Kenntnis ostasiatischer Diplopoden. II. Zoologischer Anzeiger, 119 (1/2), 33–40.

    Woo, H.J., Lee, Y.S., Park, S.J., Lim, J.T., Jang, K.H., Choi, E.H., Choi, Y.G. & Hwang, U.W. (2007) Complete mitochondrial genome of a troglobite millipede Antrokoreana gracilipes (Diplopoda, Juliformia, Julida), and juliformian phylogeny. Molecules and Cells, 23 (2), 182–191.

    Woo, H.J. (2009) Comparative analysis of mitochondrial genomes of Superorder Juliformia (Myriapoda, Diplopoda) and phylogenetic relationships of juliformian orders. PhD thesis, Kyungpook National University, Daegu, 119 pp.

    Zhang, D., Szymura, J.M. & Hewitt, G.M. (1995) Evolution and structural conservation of the control region of insect mitochondrial DNA. Journal of Molecular Evolution, 40, 382–391.
    https://doi.org/10.1007/BF00164024

    Zhang, D.X. & Hewitt, G.M. (1997) Insect mitochondrial control region: a review of its structure, evolution and usefulness in evolutionary studies. Biochemical Systematics and Ecology, 25, 99–120.
    https://doi.org/10.1016/S0305-1978(96)00042-7