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Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Saturnia japonica

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Abstract

The complete mitochondrial genome (mitogenome) of Saturnia japonica (Lepidoptera: Saturniidae) was sequenced and annotated. It is a circular molecule of 15, 376 bp, composed of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNA), and an adenine (A) + thymine (T)-rich region. All protein-coding genes (PCGs) are initiated by the ATN codon except for cytochrome c oxidase subunit 1 (cox1) gene that is seemingly initiated by the CGA codon. Except for cox2 and nad4, which were terminated by incomplete stop codon T or TA, the rest were terminated by canonical stop codon TAA. The A + T-rich region is high conservative, including ‘ATAGA’ motif followed by a 19 bp poly-T stretch, a microsatellite-like element (AT)9 and also a poly-A element, with a total length of 332 bp. The Asn codon was the most frequently used codon, followed by Ile, Leu2, Lys, Met, Phe, and Tyr, while Cys was the least frequently used codon. Phylogenetic relationships analysis based on the 13 PCGs by using maximum likelihood (ML) and neighbor Joining (NJ) revealed that S. japonica belongs to the Saturniidae family. In this study, the annotation and characteristics of the mitogenome of S. japonica were resolved for the first time, which laid a foundation for species classification and the molecular evolution of Lepidoptera: Saturniidae.

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References

  • Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Saunders NC (1987) Intraspecific Phylogeography: The Mitochondrial DNA Bridge Between Population Genetics and Systematics. Annu Rev Ecol Syst 18(10):489–522

    Article  Google Scholar 

  • Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Res 27(8):1767–1780

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cameron SL (2014) Insect mitochondrial genomics: implications for evolution and phylogeny. Annu Rev Entomol 59:95–117

    Article  CAS  PubMed  Google Scholar 

  • Cameron SL, Whiting MF (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

    Article  CAS  PubMed  Google Scholar 

  • Cao YQ, Ma C, Chen JY, Yang DR (2012) The complete mitochondrial genomes of two ghost moths, Thitarodes renzhiensis and Thitarodes yunnanensis: the ancestral gene arrangement in Lepidoptera. BMC Genomics 13:276

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chai HN, Du YZ, Zhai BP (2012) Characterization of the complete mitochondrial genomes of Cnaphalocrocis medinalis and Chilo suppressalis (Lepidoptera: Pyralidae). Int J Biol Sci 8(4):561–579

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen Y, Gan S, Shao L, Cheng C, Hao J (2016) The complete mitochondrial genome of the Pazala timur (Lepidoptera:Papilionidae: Papilioninae). Mitochondrial DNA Part A 27(1):533–534

    Article  CAS  Google Scholar 

  • Chen YM, Sun JW, Iqbal A, Lv R, Wang H, Zang LS (2020) An investigation of Caligula japonica (Lepidoptera: Saturniidae) egg distribution and associated parasitoids on walnut trees (Juglans regia L.) in northwestern China. Int . Pest Manage 24:1–8

    Google Scholar 

  • Dai L, Qian C, Zhang C, Wang L, Wei G, Li J, Zhu B, Liu C (2015) Characterization of the complete mitochondrial genome of Cerura menciana and comparison with other lepidopteran insects. PLoS ONE 10(8):17

    Google Scholar 

  • Dai LS, Zhu BJ, Qian C, Zhang CF, Li J, Wang L, Wei GQ, Liu CL (2016) The complete mitochondrial genome of the diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae). Mitochondrial DNA Part A 27(2):1512–1513

    Article  CAS  Google Scholar 

  • Dowton M, Castro LR, Austin AD (2002) Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome “morphology.” Invertebr Syst 16(3):345–356

    Article  Google Scholar 

  • Forstén A (1991) Mitochondrial-DNA time-table and the evolution of Equus: comparison of molecular and paleontological evidence. Ann Zool Fenn 28(3/4):301–309

    Google Scholar 

  • Guo J, Miao X, He P, Li M, Wang S, Cui J, Huang C, He L, Zhao J (2019) Babesia gibsoni endemic to Wuhan, China: mitochondrial genome sequencing, annotation, and comparison with apicomplexan parasites. Parasitol Res 118(1):235–243

    Article  PubMed  Google Scholar 

  • Hao J, Sun Q, Zhao H, Sun X, Gai Y, Yang Q (2012) The Complete mitochondrial genome of Ctenoptilum vasava (Lepidoptera: Hesperiidae: Pyrginae) and its phylogenetic implication. Comparat Funct Genom. https://doi.org/10.1155/2012/328049

    Article  Google Scholar 

  • Hassanin A (2006) Phylogeny of Arthropoda inferred from mitochondrial sequences: strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution. Mol Phylogenet Evol 38(1):100–116

    Article  CAS  PubMed  Google Scholar 

  • Jiang ST, Hong GY, Yu M, Li N, Yang Y, Liu YQ, Wei ZJ (2009) Characterization of the complete mitochondrial genome of the giant silkworm moth, Eriogyna pyretorum (Lepidoptera: Saturniidae). Int J Biol Sci 5(4):351–365

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Junqueira AC, Lessinger AC, Torres TT, Silva FRD, Vettore AL, Arruda P, Espin AMLA (2004) The mitochondrial genome of the blowfly Chrysomya chloropyga (Diptera: Calliphoridae). Gene 339:7–15

    Article  CAS  PubMed  Google Scholar 

  • Kawaguchi A, Nishida M (2001) Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Mol Biol Evol 18(11):1993–2009

    Article  PubMed  Google Scholar 

  • Kim I, Lee EM, Seol KY, Yun EY, Lee YB, Hwang JS, Jin BR (2006) The mitochondrial genome of the Korean hairstreak, Coreana raphaelis (Lepidoptera: Lycaenidae). Insect Mol Biol 15(2):217–225

    Article  CAS  PubMed  Google Scholar 

  • Kim MJ, Choi SW, Kim I (2015) Saturnia jonasii Butler, 1877 on Jejudo Island, a new saturnid moth of South Korea with DNA data and morphology (Lepidoptera: Saturniidae). Zootaxa 3946(3):374–386

    Article  PubMed  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111–120

    Article  CAS  PubMed  Google Scholar 

  • Liao F, Wang L, Wu S, Li YP, Zhao L, Huang GM, Niu CJ, Liu YQ, Li MG (2010) The complete mitochondrial genome of the fall webworm, Hyphantria cunea (Lepidoptera: Arctiidae). Int J Biol Sci 6(2):172–186

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu QN, Zhu BJ, Dai LS, Liu CL (2013) The complete mitogenome of Bombyx mori strain Dazao (Lepidoptera: Bombycidae) and comparison with other Lepidopteran insects. Genomics 101:64–73

    Article  CAS  PubMed  Google Scholar 

  • Liu S, Xue D, Cheng R, Han H (2014) The complete mitogenome of Apocheima cinerarius (Lepidoptera: Geometridae: Ennominae) and comparison with that of other Lepidopteran insects. Gene 547(1):136–144

    Article  CAS  PubMed  Google Scholar 

  • Li SY, Du ZJ, Qi I (2014) Wild silkworm series II-Saturnia japonica. Sci Seric 35(2):85–87

    Google Scholar 

  • Lu HF, Su TJ, Luo AR, Zhu CD, Wu CS (2013) Characterization of the complete mitochondrion genome of Diurnal Moth Amata emma (Butler) (Lepidoptera: Erebidae) and its phylogenetic implications. PLoS ONE 8(9):48

    Google Scholar 

  • Lowe TM, Eddy SR (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mcknight ML, Shaffer HB (1997) Large, rapidly evolving intergenic spacer in the mitochondrial DNA of the salamander family Ambystomatidae (Amphibia: Caudata). Mol Biol Evol 14(11):1167–1176

    Article  CAS  PubMed  Google Scholar 

  • Ramirez-Rios V, Franco-Sierra ND, Alvarez JC, Saldamando-Benjumea CI, Villanueva-Mejia DF (2016) Mitochondrial genome characterization of Tecia solanivora (Lepidoptera: Gelechiidae) and its phylogenetic relationship with other Lepidopteran insects. Gene 581(2):107–116

    Article  CAS  PubMed  Google Scholar 

  • Rand DM (1993) Endotherms, ectotherms, and mitochondrial genome-size variation. J Mol Evol 37(3):281–295

    Article  CAS  PubMed  Google Scholar 

  • Shadel GS, Clayton DA (1993) Mitochondrial transcription initiation. Variation and conservation. J Biol Chem 268(22):16083–16086

    Article  CAS  PubMed  Google Scholar 

  • Song H, Sheffield NC, Cameron SL, Miller KB, Whiting MF (2010) When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics. Syst Entomol 35(3):429–448

    Article  Google Scholar 

  • Sun Y, Chen C, Gao J, Abbas MN, Kausar S, Qian C, Wang L, Wei G, Zhu BJ, Liu CL (2017) Comparative mitochondrial genome analysis of Daphnis nerii and other Lepidopteran insects reveals conserved mitochondrial genome organization and phylogenetic relationships. PLoS ONE 12(6):19

    CAS  Google Scholar 

  • Sun YX, Wang L, Wei GQ, Qian C, Dai LS, Sun Y, Abbas MN, Zhu BJ, Liu CL (2016) Characterization of the complete mitochondrial genome of Leucoma salicis (Lepidoptera: Lymantriidae) and comparison with other lepidopteran insects. Sci Rep 15(6):39153

    Article  CAS  Google Scholar 

  • Swofford, DL (2003) PAUP*: Phylogenetic analysis using parsimony, Version 4. 0 b10. (Sinauer 2003).

  • Taanman JW (1999) The mitochondrial genome: structure, transcription, translation and replication. Biochim Biophys Acta 1410(2):103–123

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25(24):4876–4882

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wei SJ, Shi BC, Gong YJ, Li Q, Chen XX (2013) Characterization of the mitochondrial genome of the diamondback moth Plutella xylostella (Lepidoptera: Plutellidae) and phylogenetic analysis of advanced moths and butterflies. DNA Cell Biol 32(4):173–187

    Article  CAS  PubMed  Google Scholar 

  • Wich GN, Hummel H, Jarsch M, Bär U, Böck A (1986) Transcription signals for stable RNA genes in Methanococcus. Nucleic Acids Res 14(6):2459

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wolstenholme DR (1992) Animal mitochondrial DNA: structure and evolution. Int Rev Cytol 141(6):173

    Article  CAS  PubMed  Google Scholar 

  • Wu LW, Lees DC, Yen SH, Lu CC, Hsu YF (2010) The complete mitochondrial genome of the near-threatened swallowtail, Agehana maraho (Lepidoptera: Papilionidae): evaluating sequence variability and suitable markers for conservation genetic studies. Entomol News 121(3):267–280

    Article  Google Scholar 

  • Wu QL, Cui WX, Wei SJ (2015) Characterization of the complete mitochondrial genome of the black cutworm Agrotis ipsilon (Lepidoptera: Noctuidae). Mitochondrial DNA Part A 26(1):139–140

    Article  CAS  Google Scholar 

  • Wu YP, Zhao JL, Su TJ, Li J, Yu F, Chesters D, Fan RJ, Chen MC, Wu CS, Zhu CD (2012) The complete mitochondrial genome of Leucoptera malifoliella Costa (Lepidoptera: Lyonetiidae). DNA Cell Biol 31(10):1508–1522

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Z, Wang X, Li R, Guo R, Zhang W, Song W, Hao C, Wang H, Li M (2015) The mitochondrial genome of Dastarcus helophoroides (Coleoptera: Bothrideridae) and related phylogenetic analyses. Gene 560(1):15–24

    Article  CAS  PubMed  Google Scholar 

  • Zhu BJ, Liu QN, Dai LS, Wang L, Sun Y, Lin KZ, Wei GQ, Liu CL (2013) Characterization of the complete mitochondrial genome of Diaphania pyloalis (Lepidoptera: Pyralididae). Gene 527(1):283–291

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This work was supported by the grant from the National Natural Science Foundation of China (31472147); the fund for Anhui International Joint Research and Development Center of Sericulture Resources Utilization (2017R0101); and the foundation for Innovative Research Groups of Anhui Agricultural University (ANRC2019032).

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  1. Jiang Liu and Junjun Dai have contributed equally to this work.

Authors and Affiliations

  1. School of Life Sciences, Anhui Agricultural University, Hefei, 230036, People’s Republic of China

    Jiang Liu, Jinjin Jia, Yemei Zong, Yahao Sun, Ying Peng, Lei Wang, Cen Qian, Baojian Zhu & Guoqing Wei

  2. Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230061, People’s Republic of China

    Junjun Dai

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  1. Jiang Liu
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Appendix

Appendix

See appendix Figs. 7 and 8; Table 5.

Fig. 7
figure 7figure 7

Codon distribution in the mitogenome of Lepidoptera. CDspT codons per thousand codons

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Fig. 8
figure 8figure 8

The Relative Synonymous Codon Usage (RSCU) of the mitogenome of eight superfamilies in the Lepidoptera. Codon families are plotted on the X-axis. Codons indicated above the bar are not present in the mitogenome

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Table 5 Composition and skewness in different Lepidopteran mitogenomes
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Liu, J., Dai, J., Jia, J. et al. Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Saturnia japonica. Biochem Genet 60, 914–936 (2022). https://doi.org/10.1007/s10528-021-10129-9

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