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Type: Article
Published: 2020-08-03
Page range: 533–552
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The mitochondrial genome of Smerinthus planus (Lepidoptera: Sphingidae) and its comparative analysis with other Lepidoptera species

College of Life Sciences, Anhui Agricultural University, 130 ChangJiang West Road, Hefei, 230036, China.
College of Life Sciences, Anhui Agricultural University, 130 ChangJiang West Road, Hefei, 230036, China.
College of Life Sciences, Anhui Agricultural University, 130 ChangJiang West Road, Hefei, 230036, China.
State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Tian Sheng Road, Beibei, Chongqing, 400715, China.
College of Life Sciences, Anhui Agricultural University, 130 ChangJiang West Road, Hefei, 230036, China.
College of Life Sciences, Anhui Agricultural University, 130 ChangJiang West Road, Hefei, 230036, China.
College of Life Sciences, Anhui Agricultural University, 130 ChangJiang West Road, Hefei, 230036, China.
College of Life Sciences, Anhui Agricultural University, 130 ChangJiang West Road, Hefei, 230036, China.
College of Life Sciences, Anhui Agricultural University, 130 ChangJiang West Road, Hefei, 230036, China.
College of Life Sciences, Anhui Agricultural University, 130 ChangJiang West Road, Hefei, 230036, China.
Mitochondrial genome database evolution phylogenetic analysis Lepidoptera

Abstract

In the present study, the complete mitochondrial genome of Smerinthus planus Walker (Lepidoptera: Sphingidae) was sequenced and analyzed to add additional traits for expanding our knowledge on systematics and phylogenetics of world-wide studied Sphingidae moths. The mitochondrial genome is a circular double-stranded DNA molecule, 15368 bp in size. It includes 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, twenty-two transfer RNA (tRNA) genes, and an adenine (A) + thymine (T) rich region. All the PCGs start with the typical ATN start codons, except for the nad5 gene, which initiates with TTA. The codon usage analysis revealed that Phe, Ile, Lys, Leu, Asn, and Tys were the most common amino acids, while Cys and Trp were least common. Among the 13 PCGs, nine genes harbor the complete termination codon TAA, whereas the remaining four genes (nad1, cob, nad4, and nad3) terminate with TAG. The A+T rich region of S. planus is 318 bp. This region displays the highest A+T rich content, accounting for 91.50%, with both AT skew (-0.09) and GC skew (-0.26) are negative. Like other Lepidopterans, the A+T-rich region of the S. planus also contains some conserved regions, including the motif ‘ATAGA’ followed by an 18 bp poly-T stretch, a microsatellite-like (AT)8 and a poly-A element. Phylogenetic relationships, based on nucleotide sequences from the genomes of 31 species, confirmed that S. planus belong to the Sphingidae family. This study is aimed to improve the mitochondrial genome database of moths and provide valuable information for studying the genetic evolution and phylogeny of Lepidopteran species.

References

  1. Beard, C.B., Hamm, D.M. & Collins, F.H. (1993) The mitochondrial genome of the mosquito Anopheles gambiae: DNA sequence, genome organization, and comparisons with mitochondrial sequences of other insects. Insect molecular biology, 2 (2), 103–124.

    https://doi.org/10.1111/j.1365-2583.1993.tb00131.x

    Benson, G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic acids research, 27 (2), 573–580.
    https://doi.org/10.1093/nar/27.2.573

    Boore, J.L. (1999) Animal mitochondrial genomes. Nucleic acids research, 27 (8), 1767–1780.

    https://doi.org/10.1093/nar/27.8.1767

    Cameron, S.L. & Whiting, M.F. (2008) The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths. Gene, 408 (1–2), 112–123.

    https://doi.org/10.1016/j.gene.2007.10.023

    Dai, L.S., Li, S., Yu, H.M., Wei, G.Q., Wang, L., Qian, C., Zhang, C.F., Li, J., Sun, Y., Zhao, Y., Zhu, B.J. & Liu, C.L. (2017) Mitochondrial genome of the sweet potato hornworm, Agrius convolvuli (Lepidoptera: Sphingidae), and comparison with other Lepidoptera species. Genome, 60 (2), 128–138.

    https://doi.org/10.1139/gen-2016-0058

    Dai, L.S., Qian, C., Zhang, C.F., Wang, L., Wei, G.Q., Li, J., Zhu, B.J. & Liu, C.L. (2015) Characterization of the complete mitochondrial genome of Cerura Menciana and comparison eith other lepidopteran insects. PLoS One, 10 (8), e0132951.

    https://doi.org/10.1371/journal.pone.0132951

    Dai, L.S., Zhu, B.J., Liu, Q.N., Wei, G.Q. & Liu, C.L. (2013) Characterization of the complete mitochondrial genome of Bombyx mori strain H9 (Lepidoptera: Bombycidae). Gene, 519 (2), 326–334.

    https://doi.org/10.1016/j.gene.2013.02.002

    Dai, L.S., Zhu, B.J., Qian, C., Zhang, C.F., Li, J., Wang, L., Wei, G.Q. & Liu, C.L. (2016) The complete mitochondrial genome of the diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae). Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis, 27 (2), 1512–1513.

    https://doi.org/10.3109/19401736.2014.953116

    De Ré, F.C., Wallau, G.L., Robe, L.J. & Loreto, E.L. (2014) Characterization of the complete mitochondrial genome of flower-breeding Drosophila incompta (Diptera, Drosophilidae). Genetica, 142 (6), 525–535.

    https://doi.org/10.1007/s10709-014-9799-9

    Fagua, G., Condamine, F.L., Brunet, B., Clamens, A.L., Laroche, J., Levesque, R.C., Cusson, M. & Sperling, F. (2018) Convergent herbivory on conifers by Choristoneura moths after boreal forest formation. Molecular phylogenetics and evolution, 123, 35–43.

    https://doi.org/10.1016/j.ympev.2018.01.013

    Fan, C., Xu, C., Li, J., Lei, Y., Gao, Y., Xu, C. & Wang, R. (2016) Complete mitochondrial genome of a satyrid butterfly, Ninguta schrenkii (Lepidoptera: Nymphalidae). Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis, 27 (1), 80–81.

    https://doi.org/10.3109/19401736.2013.873909

    Gong, Y.J., Wu, Q.L. & Wei, S.J. (2013) Complete mitogenome of the Argyrogramma agnata (Lepidoptera: Noctuidae). Mitochondrial DNA, 24 (4), 391–393.

    https://doi.org/10.3109/19401736.2013.763241

    Han, Y., Huang, Z., Tang, J., Chiba, H. & Fan, X. (2018) The complete mitochondrial genomes of two skipper genera (Lepidoptera: Hesperiidae) and their associated phylogenetic analysis. Scientific reports, 8 (1), 15762.

    https://doi.org/10.1038/s41598-018-34107-1

    Inoue, J.G., Miya, M., Tsukamoto, K. & Nishida, M. (2001) Complete mitochondrial DNA sequence of Conger myriaster (Teleostei: Anguilliformes): novel gene order for vertebrate mitochondrial genomes and the phylogenetic implications for anguilliform families. Journal of molecular evolution, 52 (4), 311–320.

    https://doi.org/10.1007/s002390010161

    Jiang, S.T., Hong, G.Y., Yu, M., Li, N., Yang, Y., Liu, Y.Q. & Wei, Z.J. (2009) Characterization of the complete mitochondrial genome of the giant silkworm moth, Eriogyna pyretorum (Lepidoptera: Saturniidae). International journal of biological sciences, 5 (4), 351–365.

    https://doi.org/10.7150/ijbs.5.351

    Junqueira, A.C., Lessinger, A.C., Torres, T.T., da Silva, F.R., Vettore, A.L., Arruda, P. & Azeredo Espin, A.M. (2004) The mitochondrial genome of the blowfly Chrysomya chloropyga (Diptera: Calliphoridae). Gene, 339, 7–15.

    https://doi.org/10.1016/j.gene.2004.06.031

    Kim, S.R., Kim, M.I., Hong, M.Y., Kim, K.Y., Kang, P.D., Hwang, J.S., Han, Y.S., Jin, B.R. & Kim, I. (2009) The complete mitogenome sequence of the Japanese oak silkmoth, Antheraea yamamai (Lepidoptera: Saturniidae). Molecular biology reports, 36 (7), 1871–1880.

    https://doi.org/10.1007/s11033-008-9393-2

    Kim, M.J., Wang, A.R., Park, J.S. & Kim, I. (2014) Complete mitochondrial genomes of five skippers (Lepidoptera: Hesperiidae) and phylogenetic reconstruction of Lepidoptera. Gene, 549 (1), 97–112.

    https://doi.org/10.1016/j.gene.2014.07.052

    Kumar, S., Stecher, G. & Tamura, K. (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular biology and evolution, 33 (7), 1870–1874.

    https://doi.org/10.1093/molbev/msw054

    Li, F.B., Zhang, H.X., Shen, W.F., Xu, X.Y., Wang, W., Chen, J.E., He, L.H. & Meng, Z.Q. (2015) Complete mitochondrial genome of the common cutworm Spodoptera litura (Lepidoptera: Noctuidae). Mitochondrial DNA, 26 (6), 838–839.

    https://doi.org/10.3109/19401736.2013.855918

    Li, J., Lin, R.R., Zhang, Y.Y., Hu, K.J., Zhao, Y.Q., Li, Y., Huang, Z.R., Zhang, X., Geng, X.X. & Ding, J.H. (2018) Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera, Sphingidae). ZooKeys, 754, 127–139.

    https://doi.org/10.3897/zookeys.754.23404

    Li, J., Zhang, Y., Hu, K., Zhao, Y., Lin, R., Li, Y., Huang, Z., Zhang, X., Geng, X. & Ding, J. (2018) Mitochondrial genome characteristics of two Sphingidae insects (Psilogramma increta and Macroglossum stellatarum) and implications for their phylogeny. International journal of biological macromolecules, 113, 592–600.

    https://doi.org/10.1016/j.ijbiomac.2018.02.159

    Liao, F., Wang, L., Wu, S., Li, Y.P., Zhao, L., Huang, G.M., Niu, C.J., Liu, Y.Q. & Li, M.G. (2010) The complete mitochondrial genome of the fall webworm, Hyphantria cunea (Lepidoptera: Arctiidae). International journal of biological sciences, 6 (2), 172–186.

    https://doi.org/10.7150/ijbs.6.172

    Liu, Q., Jiang, X., Hou, X., Yang, H. & Chen, W. (2018) The mitochondrial genome of Ephestia elutella (Insecta: Lepidoptera: Pyralidae). Mitochondrial DNA Part B, 3 (1), 189–190.

    https://doi.org/10.1080/23802359.2018.1436993

    Liu, Q.N., Zhu, B.J., Dai, L.S., Wei, G.Q. & Liu, C.L. (2012) The complete mitochondrial genome of the wild silkworm moth, Actias selene. Gene, 505 (2), 291–299.

    https://doi.org/10.1016/j.gene.2012.06.003

    Liu, Q.N., Zhu, B.J., Dai, L.S. & Liu, C.L. (2013) The complete mitogenome of Bombyx mori strain Dazao (Lepidoptera: Bombycidae) and comparison with other lepidopteran insects. Genomics, 101 (1), 64–73.

    https://doi.org/10.1016/j.ygeno.2012.10.002

    Liu, Q.N., Zhu, B.J., Dai, L.S., Wang, L., Qian, C., Wei, G.Q. & Liu, C.L. (2016) The complete mitochondrial genome of the common cutworm, Spodoptera litura (Lepidoptera: Noctuidade). Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis, 27 (1), 122–123.

    https://doi.org/10.3109/19401736.2013.873934

    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/25.5.955

    Lu, H.F., Su, T.J., Luo, A.R., Zhu, C.D. & Wu, C.S. (2013) Characterization of the complete mitochondrion genome of diurnal Moth Amata emma (Butler) (Lepidoptera: Erebidae) and its phylogenetic implications. PloS One, 8 (9), e72410.

    https://doi.org/10.1371/journal.pone.0072410

    Pan, M., Yu, Q., Xia, Y., Dai, F., Liu, Y., Lu, C., Zhang, Z. & Xiang, Z. (2008) Characterization of mitochondrial genome of Chinese wild mulberry silkworm, Bombyx mandarina (Lepidoptera: Bombycidae). Science in China, Series C, Life Sciences, 51 (8), 693–701.

    https://doi.org/10.1007/s11427-008-0097-6

    Peters, M.J. & Marcus, J.M. (2016) Taxonomy as a hypothesis: Testing the status of the Bermuda buckeye butterfly Junonia coenia bergi (Lepidoptera: Nymphalidae). Systematic Entomology.

    https://doi.org/10.1111/syen.12214

    Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D.L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M.A. & Huelsenbeck, J.P. (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic biology, 61 (3), 539–542.

    https://doi.org/10.1093/sysbio/sys029

    Shi, Q.H., Xing, J.H., Liu, X.H. & Hao, J.S. (2018) The complete mitochondrial genome of comma, polygonia c-aureum (Lepidoptera: Nymphalidae: Nymphalinae). Mitochondrial DNA Part B, 3 (1), 53–55.

    https://doi.org/10.1080/23802359.2017.1419091

    Sun, Q.Q., Sun, X.Y., Wang, X.C., Gai, Y.H., Hu, J., Zhu, C.D. & Hao, J.S. (2012) Complete sequence of the mitochondrial genome of the Japanese buff-tip moth, Phalera flavescens (Lepidoptera: Notodontidae). Genetics and molecular research: GMR, 11 (4), 4213–4225.

    https://doi.org/10.4238/2012.September.10.2

    Sun, Y., Chen, C., Gao, J., Abbas, M.N., Kausar, S., Qian, C., Wang, L., Wei, G., Zhu, B.J. & Liu, C.L. (2017) Comparative mitochondrial genome analysis of Daphnis nerii and other lepidopteran insects reveals conserved mitochondrial genome organization and phylogenetic relationships. PloS One, 12 (6), e0178773.

    https://doi.org/10.1371/journal.pone.0178773

    Sun, Y., Zhang, J., Li, Q., Liang, D., Abbas, M.N., Qian, C., Wang, L., Wei, G., Zhu, B.J. & Liu, C.L. (2017) Mitochondrial genome of Abraxas suspecta (Lepidoptera: Geometridae) and comparative analysis with other Lepidopterans. Zootaxa, 4254 (5), 501–519.

    https://doi.org/10.11646/zootaxa.4254.5.1

    Taanman, J.W. (1999) The mitochondrial genome: structure, transcription, translation and replication. Biochimica et Biophysica Acta (BBA)—Bioenergetics, 1410 (2), 103–123.

    https://doi.org/10.1016/s0005-2728(98)00161-3

    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

    Wolstenholme, D.R. (1992) Animal mitochondrial DNA: structure and evolution. International review of cytology, 141, 173–216.

    https://doi.org/10.1016/s0074-7696(08)62066-5

    Wu, Y.P., Li, J., Zhao, J.L., Su, T.J., Luo, A.R., Fan, R.J., Chen, M.C., Wu, C.S. & Zhu, C.D. (2012) The complete mitochondrial genome of the rice moth, Corcyra cephalonica. Journal of insect science, 12, 72.

    https://doi.org/10.1673/031.012.7201

    Xu, W., Jameson, D., Tang, B. & Higgs, P.G. (2006) The relationship between the rate of molecular evolution and the rate of genome rearrangement in animal mitochondrial genomes. Journal of molecular evolution, 63 (3), 375–392.

    https://doi.org/10.1007/s00239-005-0246-5

    Yang, L., Wei, Z.J., Hong, G.Y., Jiang, S.T. & Wen, L.P. (2009) The complete nucleotide sequence of the mitochondrial genome of Phthonandria atrilineata (Lepidoptera: Geometridae). Molecular biology reports, 36 (6), 1441–1449.

    https://doi.org/10.1007/s11033-008-9334-0

    Yang, X., Cameron, S.L., Lees, D.C., Xue, D. & Han, H. (2015) A mitochondrial genome phylogeny of owlet moths (Lepidoptera: Noctuoidea), and examination of the utility of mitochondrial genomes for lepidopteran phylogenetics. Molecular phylogenetics and evolution, 85, 230–237.

    https://doi.org/10.1016/j.ympev.2015.02.005

    Yang, X., Yang, X., Xue, D. & Han, H. (2016) The complete mitochondrial genome of Endoclita signifer (Lepidoptera, Hepialidae). Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis, 27(6), 4620–4621.

    https://doi.org/10.3109/19401736.2015.1101585

    Yang, M., Song, L., Shi, Y., Yin, Y., Wang, Y., Zhang, P., Chen, J., Lou, L. & Liu, X. (2019) The complete mitochondrial genome of a medicinal insect, Hydrillodes repugnalis (Lepidoptera: Noctuoidea: Erebidae), and related phylogenetic analysis. International journal of biological macromolecules, 123, 485–493.

    https://doi.org/10.1016/j.ijbiomac.2018.10.149

    Yang, L., Dai, J., Gao, Q., Yuan, G., Liu, J., Sun, Y., Sun, Y., Wang, L., Qian, C., Zhu, B., Liu, C. & Wei, G. (2020a) Characterization of the complete mitochondrial genome of Orthaga olivacea Warre (Lepidoptera Pyralidae) and comparison with other Lepidopteran insects. PloS One, 15 (3), e0227831.

    https://doi.org/10.1371/journal.pone.0227831

    Yang, M., Song, L., Zhou, L., Shi, Y., Song, N. & Zhang, Y. (2020b) Mitochondrial genomes of four satyrine butterflies and phylogenetic relationships of the family Nymphalidae (Lepidoptera: Papilionoidea). International journal of biological macromolecules, 145, 272–281.

    https://doi.org/10.1016/j.ijbiomac.2019.12.008

    Yin, J., Hong, G.Y., Wang, A.M., Cao, Y.Z. & Wei, Z.J. (2010) Mitochondrial genome of the cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) and comparison with other Lepidopterans. Mitochondrial DNA, 21 (5), 160–169.

    https://doi.org/10.3109/19401736.2010.503242

    Yin, J., Wang, A.M., Hong, G.Y., Cao, Y.Z. & Wei, Z.J. (2011) Complete mitochondrial genome of Chilo suppressalis (Walker) (Lepidoptera: Crambidae). Mitochondrial DNA, 22 (3), 41–43.

    https://doi.org/10.3109/19401736.2011.605126

    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 (2), 99–120.

    https://doi.org/10.1016/S0305-1978(96)00042-7

    Zhang, M., Gao, Z., Yin, J., Zhang, T., Zhang, X., Yuan, D., Li, T., Zhong, Y., Ma, E. & Ren, Z. (2019) Complete mitochondrial genome of two Thitarodes species (Lepidoptera, Hepialidae), the host moths of Ophiocordyceps sinensis and phylogenetic implications. International journal of biological macromolecules, 140, 794–807.

    https://doi.org/10.1016/j.ijbiomac.2019.08.182

    Zhu, W., Yan, J., Song, J. & You, P. (2018) The first mitochondrial genomes for Pyralinae (Pyralidae) and Glaphyriinae (Crambidae), with phylogenetic implications of Pyraloidea. PloS One, 13 (3), e0194672.

    https://doi.org/10.1371/journal.pone.0194672