Skip to main content Skip to main navigation menu Skip to site footer
Published: 2022-05-18

Seven new mitochondrial genomes of phytophagous scarab beetles (Coleoptera: Scarabaeidae) and phylogenetic implications

Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210024, China. 2Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China. 3Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, P.R. China.
Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210024, China.
Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China. Hainan Yazhou Bay Seed Lab, Building 1, No.7 Yiju Road, Yazhou District, Sanya 572000, Hainan, China
Coleoptera Scarabaeidae phytophagous scarab lineage mitochondrial genomes deep phylogenetic relationships


Among Scarabaeidae, the phytophagous scarab lineage including Melolonthinae, Cetoniinae, Dynastinae, and Rutelinae is considered important due to its members’ roles as agricultural pests or pollinators. In this study, the near-complete mitochondrial genomes of seven species from six genera in the phytophagous scarab lineage were newly sequenced: Anomala russiventris (Fairmaire, 1893); Apogonia cf. basalis (Moser, 1915); Apogonia splendida (Boheman, 1858); Coenochilus striatus (Westwood, 1874); Trichogomphus mongol (Arrow, 1908); Sophrops subrugatus (Moser, 1921) and Tetraserica leishanica (Liu, Bai, Yang & Ahrens, 2014). The complete mitochondrial genomes from the 6 species include 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and 1 control region, which have a highly conserved gene arrangement, except for Tr. mongol with the rearrangement of 2 tRNA genes (tRNA-Ile and tRNA-Gln), which is a potential identified subfamily-level character of Dynastinae. In order to test whether the mitogenomic data are suited for high-level phylogenetic inferences, the substitution saturation and heterogeneity were analyzed. The results showed no sign that the phylogenetic inferences were biased by substitution saturation or the low heterogeneity of the sequence composition for most pairwise comparisons between the sequences for the entire dataset (13 PCGs) and the amino acids dataset (13 PCGs_AA). Based on the combined data of 13 PCGs and 13 PCGs_AA from the mitogenomes of 37 taxa, the phylogeny of the phytophagous lineage was explored using RAxML and Bayesian methods. The results confirmed that Cetoniinae, Rutelinae, and Dynastinae are monophyletic, and that the latter two are sister groups. Melolonthinae is a paraphyletic group, and its tribes, Diplotaxini, Euchirini, Melolonthini, Rhizotrogini, and Sericini, are a monophyletic group. The subfamily rank of Dynastinae and the tribe rank of Anomalini and Adoretini are supported.



  1. Ahrens, D. (2006) The phylogeny of Sericini and their position within the Scarabaeidae based on morphological characters (Coleoptera: Scarabaeidae). Systematic Entomology, 31 (1), 113–144.
    Ahrens, D. & Vogler, A.P. (2008) Towards the phylogeny of chafers (Sericini): analysis of alignment-variable sequences and the evolution of segment numbers in the antennal club. Molecular Phylogenetics and Evolution, 47 (2), 783–798.
    Ahrens, D., Scott, M. & Vogler, A.P. (2011) The phylogeny of monkey beetles based on mitochondrial and ribosomal RNA genes (Coleoptera: Scarabaeidae: Hopliini). Molecular Phylogenetics and Evolution, 60 (3), 408–415.
    Ahrens, D., Schwarzer, J. & Vogler, A.P. (2014) The evolution of scarab beetles tracks the sequential rise of angiosperms and mammals. Proceedings the Royal Society B-Biological Sciences, 281 (1791), 20141470.
    Ayivi, S.P.G., Tong, Y., Storey, K.B., Yu, D.N. & Zhang, J.Y. (2021) The Mitochondrial Genomes of 18 New Pleurosticti (Coleoptera: Scarabaeidae) Exhibit a Novel trnQ-NCR-trnI-trnM Gene Rearrangement and Clarify Phylogenetic Relationships of Subfamilies within Scarabaeidae. Insects, 12, 1025.
    Ballard, J.W. & Whitlock, M.C. (2004) The incomplete natural history of mitochondria. Molecular Ecology, 13 (4), 729–744.
    Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., Lesin, V.M., Nikolenko, S.I., Pham, S., Prjibelski, A.D., Pyshkin, A.V., Sirotkin, A.V., Vyahhi, N., Tesler, G., Alekseyev, M.A. & Pevzner, P.A. (2012) SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology, 19 (5), 455–477.
    Bernt, M., Donath, A., Jühling, F., Externbrink, F., Florentz, C., Fritzsch, G., Pütz, J., Middendorf, M. & Stadler, P.F. (2013) MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution, 69 (2), 313–319.
    Breeschoten, T., Doorenweerd, C., Tarasov, S. & Vogler, A.P. (2016) Phylogenetics and biogeography of the dung beetle genus Onthophagus inferred from mitochondrial genomes. Molecular Phylogenetics and Evolution, 105, 86–95.
    Browne, D.J. & Scholtz, C.H. (1998) Evolution of the scarab hindwing articulation and wing base: a contribution toward the phylogeny of the Scarabaeidae (Scarabaeoidea: Coleoptera). Systematic Entomology, 23 (4), 307–326.
    Cameron, S.L., Sullivan, J., Song, H., Miller, K.B. & Whiting, M.F. (2009) A mitochondrial genome phylogeny of the Neuropterida (lace-wings, alderflies and snakeflies) and their relationship to the other holometabolous insect orders. Zoologica Scripta, 38 (6), 575–590.
    Cameron, S.L. (2014) Insect Mitochondrial Genomics: Implications for Evolution and Phylogeny. Annual Review of Entomology, 59, 95–117.
    Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution, 17 (4), 540–552.
    Cheng, C.T., Jeng, M.L., Tsai, J.F., Li, C.K. & Wu, L.W. (2021) Two mitochondrial genomes of Taiwanese rhinoceros beetles, Oryctes rhinoceros and Eophileurus chinensis (Coleoptera: Scarabaeidae). Mitochondrial DNA Part B, 6 (8), 2260–2262.
    Choi, E.H., Mun, S., Baek, S.Y., Hwang, J. & Hwang, U.W. (2020) The complete mitochondrial genome of a whiter-spotted flower chafer, Protaetia brevitarsis (Coleoptera: Scarabaeidae). Mitochondrial DNA Part B, 5 (3), 3602–3604.
    Coca-Abia, M. (2007) Phylogenetic relationships of the subfamily Melolonthinae (Coleoptera, Scarabaeidae). Insect Systematics & Evolution, 38 (4), 447–472.
    Erichson, W.F. (1847) Naturgeschichte der Insecten Deutschlands. Erste Abtheilung. Coleoptera. Vol. 3. Nicolaischen Buchhandlung, Berlin, 481–640 pp.
    Frew, A., Barnett, K., Nielsen, U.N., Riegler, M., & Johnson, S.N. (2016) Belowground ecology of scarabs feeding on grass roots: current knowledge and future directions for management in Australasia. Frontiers in Plant Science, 7, 321.
    Filipović, I., Hereward, J.P., Rašić, G., Devine, G.J., Furlong, M.J. & Etebari, K. (2021) The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing. PeerJ, 9, e10552.
    Grant, J.R. & Stothard, P. (2008) The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Research, 36, 181–184.
    Gunter, N.L., Weir, T.A., Slipinksi, A., Bocak, L. & Cameron, S.L. (2016) If Dung Beetles (Scarabaeidae: Scarabaeinae) Arose in Association with Dinosaurs, Did They Also Suffer a Mass Co-Extinction at the K-Pg Boundary? PLoS One, 11 (5), e0153570.
    Howden, H.F. (1982) Larval and adult characters of Frickius Germain, its relationship to the Geotrupini, and a phylogeny of some major taxa in the Scarabaeoidea (Insecta: Coleoptera). Canadian Journal of Zoology, 60 (11), 2713–2724.
    Jin, J.J., Yu, W.B., Yang, J.B., Song, Y., dePamhilis, C.W., Y., Yi, T.S. & Li, D.Z. (2018) GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology, 21 (1), 241.
    Katoh, K. & Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution, 30 (4), 772–780.
    Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P. & Drummond, A. (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28 (12), 1647–1649.
    Kim, M.J., Kim, K.G. & Kim, I. (2013) Description of Nearly Completed Mitochondrial Genome Sequences of the Garden Chafer Polyphylla laticollis manchurica, Endangered in Korea (Insecta: Coleoptera). International Journal of Industrial Entomology, 27 (1), 185–202.
    Kim, M.J., Jeong, S.Y., Jeong, J.C., Kim, S.S. & Kim, I. (2016) Complete mitochondrial genome of the endangered flower chafer Osmoderma opicum (Coleoptera: Scarabaeidae). Mitochondrial DNA Part B, 1 (1), 148–149.
    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.
    Kück, P., Meid, S.A., Groß, C., Wägele, J.W. & Misof, B. (2014) AliGROOVE–visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support. BMC Bioinformatics, 15 (294), 1–15.
    Lanfear, R., Frandsen, P.B., Wright, A.M., Senfeld, T. & Calcott, B. (2016) PartitionFinder 2: newmethods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution, 34 (3), 772–773.
    Li, Z., Li, X., Song, N., Tang, H. & Yin, X. (2020) The Mitochondrial Genome of Amara aulica (Coleoptera, Carabidae, Harpalinae) and Insights into the Phylogeny of Ground Beetles. Genes, 11 (2), 181.
    Mayer, C., Soka, G. & Picker, M. (2006) The importance of monkey beetle (Scarabaeidae: Hopliini) pollination for Aizoaceae and Asteraceae in grazed and ungrazed areas at Paulshoek, Succulent Karoo, South Africa. Journal of Insect conservation, 10 (4), 323–333.
    McKenna, D.D., Farrell, B.D., Caterino, M.S., Farnum, C.W., Hawks, D.C., Maddison, D.R., Seago, A.E., Short, A.E.Z., Newton, A.F. & Thayer, M.K. (2015) Phylogeny and evolution of Staphyliniformia and Scarabaeiformia: forest litter as a stepping stone for diversification of nonphytophagous beetles. Systematic Entomology, 40 (1), 35–60.
    Miller, M.A., W. Pfeiffer, T. & Schwartz, T. (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Gateway Computing Environments Workshop (GCE). New Orleans, LA, p. 1–8.
    Nie, R.E., Yang, M.X., Xue, H.J., Yang, Y.R., Tong, Y.J., Qiu, T.F., Bai, M. & Yang, X.K. (2017) The application and effectiveness of a flight interception trap for insect collecting. Chinese Journal of Applied Entomology, 54 (3), 530–535.
    Nie, R.E., Breeschoten, T., Timmermans, M.J.T.N., Nadein, K., Xue, H.J., Bai, M., Huang, Y., Yang, X.K. & Vogler, A.P. (2018) The phylogeny of Galerucinae (Coleoptera: Chrysomelidae) and the performance of mitochondrial genomes in phylogenetic inference compared to nuclear rRNA genes. Cladistics, 34 (2), 113–130.
    Nie, R.E., Andújar, C., Gómez-Rodríguez, C., Bai, M., Xue, H.J., Tang, M., Yang, C.T., Tang, P., Yang, X.K. & Vogler, A. P. (2020) The phylogeny of leaf beetles (Chrysomelidae) inferred from mitochondrial genomes. Systematic Entomology, 45 (1), 188–204.
    Nie, R.E., Vogler, A.P., Yang, X.K. & Lin, M.Y. (2021) Higher-level phylogeny of longhorn beetles (Coleoptera: Chrysomeloidea) inferred from mitochondrial genomes. Systematic Entomology, 46 (1), 56–70.
    Rambaut, A., Drummond, A.J., Xie, D., Baele, G. and Suchard, M.A., 2018. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Software for Systematics and Evolution. 67, 901–904.
    Ronquist, F., Teslenko, M., Mark, P.V.D., 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.
    Rubinoff, D. & Holland, B.S. (2005) Between Two Extremes: Mitochondrial DNA is neither the Panacea nor the Nemesis of Phylogenetic and Taxonomic Inference. Systematic Biology, 54 (6), 952–961.
    Schattner, P., Brooks, A.N. & Lowe T.M. (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Research, 33, 686–689.
    Scholtz, C.H. (1988) Biology of Sparrmannia flava Arrow (Scarabaeidae: Melolonthinae). The Coleopterists Bulletin, 42 (1), 57–62.
    Scholtz, C.H. & Grebennikov, V.V. (2016) 15. Scarabaeoidea Latreille, 1802. In: Beutel R. G. & Kristensen N. P. (Eds.), Handbook of Zoology, Arthropoda: Insecta, Coleoptera, Beetles. Volume 1. Morphology and Systematics (Archostemata, Adephaga, Myxophaga, Polyphaga partim) 2nd edition. De Gruyter, Berlin, pp. 443–525.
    Shao, L.L., Huang, D.Y., Sun, X.Y., Hao, J.S., Cheng, C.H., Zhang, W. & Yang, Q. (2014) Complete mitochondrial genome sequence of Cheirotonus jansoni (Coleoptera: Scarabaeidae). Genetics and Molecular Research, 13 (1), 1047–1058.
    Sharp, P.M. & Li, W.H. (1986) An evolutionary perspective on synonymous codon usage in unicellular organisms. Journal of Molecular Evolution, 24 (1–2), 28–38.
    Song, N. & Zhang, H. (2018) The Mitochondrial Genomes of Phytophagous Scarab Beetles and Systematic Implications. Journal of Insect Science, 18 (6), 1–11.
    Smith, A.B.T., Hawks, D.C. & Heraty, J.M. (2006) An Overview of the Classification and Evolution of the Major Scarab Beetle Clades (Coleoptera: Scarabaeoidea) Based on Preliminary Molecular Analyses. The Coleopterists Bulletin, 60 (5), 35–46.[35:AOOTCA]2.0.CO;2
    Stamatakis, A. (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30 (9), 1312–1313.
    Timmermans, M.J., Barton, C., Haran, J., Ahrens, D., Culverwell, C.L., Ollikainen, A., Dodsworth, S., Foster, P.G., Bocak, L. & Vogler, A.P. (2016) Family-Level Sampling of Mitochondrial Genomes in Coleoptera: Compositional Heterogeneity and Phylogenetics. Genome Biology and Evolution, 8 (1), 161–175.
    Wickham, H. (2009) ggplot2: Elegant Graphics for Data Analysis (Use R). Springer: New York, NY, USA, Volume 10, p. 978.
    Xia, X. (2018) DAMBE 7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution. Molecular Biology and Evolution, 35 (6), 1550–1552.
    Yang, C., Zhu, E.J., He, Q.J., Yi, C.H., Hu, S.J. & Wang, X.B. (2020) Complete mitochondrial genome of the Endangered long-armed scarab Cheirotonus gestroi (Coleoptera: Euchiridae). Mitochondrial DNA Part B, 5 (1), 869–870.
    Yang, W., Zhang, Y., Feng, S., Liu, L. & Li, Z. (2018) The first complete mitochondrial genome of the Japanese beetle Popillia japonica (Coleoptera: Scarabaeidae) and its phylogenetic implications for the superfamily Scarabaeoidea. International Journal of Biological Macromolecules, 118, 1406–1413.
    Yang, X.Z., Zhang, L., Feng, R.Q., Zhang, L.J., Luo, F.Z. & Yuan, M.L. (2018) Mitochondrial genome of Amphimallon solstitiale (Coleoptera: Scarabaeidae: Melolonthinae) and phylogenetic analysis. Mitochondrial DNA Part B, 4 (1), 110–111.
    Yu, X.L., Tan, W., Zhang, H.Y., Jiang, W.L., Gao, H., Wang, W.X., Liu, Y.X., Wang, Y. & Tian, X.X. (2019) Characterization of the Complete Mitochondrial Genome of Harpalus sinicus and Its Implications for Phylogenetic Analyses. Genes, 10 (9), 724.
    Yuan, M.L., Zhang. Q.L., Zhang. L., Guo. Z.L., Liu. Y.J., Shen. Y.Y. & Shao, R. (2016) High-level phylogeny of the Coleoptera inferred with mitochondrial genome sequences, Molecular Phylogenetics and Evolution, 11 (2016), 99–111.
    Zhang, D., Gao, F., Jakovlić, I., Zou, H., Zhang, J., Li, W.X. & Wang, G.T. (2020) PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Molecular Ecology Resources, 20 (1), 348–355.
    Zhou, Y.T., Yan, J.Y. & Qi, H.X. (2021) Complete mitochondrial genome of Polyphylla gracilicornis (Coleoptera: Scarabaeoidea). Mitochondrial DNA Part B, 6 (2), 435–436.