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The First Eight Mitogenomes of Leaf-Mining Dactylispa Beetles (Coleoptera: Chrysomelidae: Cassidinae) Shed New Light on Subgenus Relationships

. 2021 Nov 08 ; 12 (11) : . [epub] 20211108

Status PubMed-not-MEDLINE Language English Country Switzerland Media electronic

Document type Journal Article

Grant support
31760173, 41971059, 41861007 and 32160314 National Natural Science Foundation of China
[2020]60 Science and Technology Project of Ganzhou City
YCX19A024 Innovation Fund of Postgraduate, Gannan Normal University
DKRVO 2019-2023/5.I.b, National Museum, 00023272 Ministry of Culture of the Czech Republic

The taxonomic classification of Dactylispa, a large genus of leaf-mining beetles, is problematic because it is currently based on morphology alone. Here, the first eight mitochondrial genomes of Dactylispa species, which were used to construct the first molecular phylogenies of this genus, are reported. The lengths of the eight mitogenomes range from 17,189 bp to 20,363 bp. All of the mitochondrial genomes include 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and 1 A + T-rich region. According to the nonsynonymous/synonymous mutation ratio (Ka/Ks) of all PCGs, the highest and the lowest evolutionary rates were found for atp8 and cox1, respectively, which is a common phenomenon among animals. According to relative synonymous codon usage, UUA(L) has the highest frequency. With two Gonophorini species as the outgroup, mitogenome-based phylogenetic trees of the eight Dactylispa species were constructed using maximum likelihood (ML) and Bayesian inference (BI) methods based on the PCGs, tRNAs, and rRNAs. Two DNA-based phylogenomic inferences and one protein-based phylogenomic inference support the delimitation of the subgenera Dactylispa s. str. and Platypriella as proposed in the system of Chen et al. (1986). However, the subgenus Triplispa is not recovered as monophyletic. The placement of Triplispa species requires further verification and testing with more species. We also found that both adult body shape and host plant relationship might explain the subgeneric relationships among Dactylispa beetles to a certain degree.

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Chen S.H., Yu P.Y., Sun C.H., T’an C.H., Zia Y. Fauna Sinica (Insecta: Coleoptera: Hispidae) Science Press; Beijing, China: 1986.

Liao C. Master’s Thesis. Gannan Normal University; Ganzhou, China: 2015. Diversity and Host Relationship of Leaf-Mining Hispine Beetle.

Liao C., Xu J., Dai X., Zhao X. Species diversity of leaf-mining hispines and of their host plants. Ecol. Sci. 2015;34:159–166.

Staines C. Catalog of the Hispines of the World (Coleoptera: Chrysomelidae: Cassidinae) [(accessed on 25 December 2016)]. Available online: https://naturalhistory.si.edu/research/entomology/collections-overview/coleoptera/catalog-hispines-world.

Santiago-Blay J.A. New Developments on the Biology of Chrysomelidae. SPB Academic Publishing; The Hague, the Netherlands: 2004. Leaf-mining chrysomelids; pp. 305–306.

Banwo O.O., Makundi R.H., Abdallah R.S., Mbapila J.C. First Report of Dactylispa lenta Weise (Coleoptera Chrysomelidae) as a Vector of Rice Yellow Mottle Virus. Acta Phytopathol. Entomol. Hung. 2001;36:189–192.

Gupta R., Tara J.S., Chhetry M. Bionomics of Dactylispa Dohertyi (Gestro, 1897), a new pest of apple plantations (Malus domestica Borkh.) in Jammu Region of J & K, India. Munis Entomol. Zool. 2012;7:754–758.

Maulik S. The Fauna of British India including Ceylon and Burma: Coleoptera: Chrysomelidae (Hispinae and Cassidinae) Taylor and Francis; London, UK: 1919.

Uhmann E. LXV.—Hispinae aus dem Britischen Museum.—VIII. Teil. 156. Beitrag zur Kenntnis der Hispinae (Coleopt., Chrysom.) Ann. Mag. Nat. Hist. 1954;7:497–518. doi: 10.1080/00222935408651750. DOI

Boore J.L. Animal mitochondrial genomes. Nucleic Acids Res. 1999;27:1767–1780. doi: 10.1093/nar/27.8.1767. PubMed DOI PMC

Cameron S.L. Insect mitochondrial genomics: Implications for evolution and phylogeny. Annu. Rev. Entomol. 2014;59:95–117. doi: 10.1146/annurev-ento-011613-162007. PubMed DOI

Sayadi A., Immonen E., Tellgren-Roth C., Arnqvist G. The Evolution of Dark Matter in the Mitogenome of Seed Beetles. Genome Biol. Evol. 2017;9:2697–2706. doi: 10.1093/gbe/evx205. PubMed DOI PMC

Zhang D.-X., Szymura J.M., Hewitt G.M. Evolution and structural conservation of the control region of insect mitochondrial DNA. J. Mol. Evol. 1995;40:382–391. doi: 10.1007/BF00164024. PubMed DOI

Zhang D.-X., Hewitt G.M. Insect Mitochondrial Control Region: A Review of its Structure, Evolution and Usefulness in Evolutionary Studies. Biochem. Syst. Ecol. 1997;25:99–120. doi: 10.1016/S0305-1978(96)00042-7. DOI

Curole J.P., Kocher T.D. Mitogenomics: Digging deeper with complete mitochondrial genomes. Trends Ecol. Evol. 1999;14:394–398. doi: 10.1016/S0169-5347(99)01660-2. PubMed DOI

DeSalle R., Schierwater B., Hadrys H. MtDNA: The small workhorse of evolutionary studies. Front. Biosci. Landmark. 2017;22:873–887. doi: 10.2741/4522. PubMed DOI

Wilson A.C., Cann R.L., Carr S.M., George M., Gyllensten U.B., Helm-Bychowski K.M., Higuchi R.G., Palumbi S.R., Prager E.M., Sage R.D., et al. Mitochondrial DNA and two perspectives on evolutionary genetics. Biol. J. Linn. Soc. 1985;26:375–400. doi: 10.1111/j.1095-8312.1985.tb02048.x. DOI

Saccone C., Gissi C., Reyes A., Larizza A., Pesole G. Mitochondrial DNA in metazoa: Degree of freedom in a frozen event. Genes. 2002;286:3–12. doi: 10.1016/S0378-1119(01)00807-1. PubMed DOI

Xiao L., Zhang S., Long C., Guo Q., Xu J., Dai X., Wang J. Complete Mitogenome of a Leaf-Mining Buprestid Beetle, Trachys auricollis, and Its Phylogenetic Implications. Genes. 2019;10:992. doi: 10.3390/genes10120992. PubMed DOI PMC

Dai X., Xu J., Jiang Z. Bionomics of Dactylispa approximata on Lophatherum gracile. North. Hortic. 2012;22:125–127.

Lee C. The taxonomic status of Dactylispa taiwana Takizawa, 1978 (Coleoptera: Chrysomelidae: Cassidinae) Genus. Int. J. Invertebr. Taxon. 2009;1:109–110.

Wen L.U., Zhang Y., Huang C. Study on the economic threshold of Dactylispa setifera (Chapuis) J. Agric. Biol. Sci. 2003;22:29–31.

Zheng X.L., Zhang Y.J., Wang Y.L., Dong Z.S., Da-Xing H.U., Wen L.U., University G. Observation on digestive system in Dactylispa setifera Chapuis(Coleoptera:Hispidae) J. South. Agric. 2016;47:223–226.

Zaitsev Y.M. The immature stages of the leaf-beetle genus Dactylispa (Coleoptera, Chrysomelidae) from Vietnam. Entomol. Rev. 2012;92:305–314. doi: 10.1134/S0013873812030074. DOI

Coil D., Jospin G., Darling A.E. A5-miseq: An updated pipeline to assemble microbial genomes from Illumina MiSeq data. Quant. Biol. 2014;31:1–3. doi: 10.1093/bioinformatics/btu661. PubMed DOI

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., et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 2012;19:455–477. doi: 10.1089/cmb.2012.0021. PubMed DOI PMC

Coordinators N.R. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2018;46:D8–D13. doi: 10.1093/nar/gkx1095. PubMed DOI PMC

Kurtz S., Phillippy A., Delcher A.L., Smoot M., Shumway M., Antonescu C., Salzberg S.L. Versatile and open software for comparing large genomes. Genome Biol. 2004;5:1–9. doi: 10.1186/gb-2004-5-2-r12. PubMed DOI PMC

Walker B.J., Abeel T., Shea T., Priest M., Abouelliel A., Sakthikumar S., Cuomo C.A., Zeng Q., Wortman J., Young S.K., et al. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE. 2014;9:e112963. doi: 10.1371/journal.pone.0112963. PubMed DOI PMC

Grant J.R., Stothard P. The CGView Server: A comparative genomics tool for circular genomes. Nucleic Acids Res. 2008;36:W181–W184. doi: 10.1093/nar/gkn179. PubMed DOI PMC

Nabil-Fareed A., Petty N.K., Zakour N.L.B., Beatson S.A. BLAST Ring Image Generator (BRIG): Simple prokaryote genome comparisons. BMC Genom. 2011;12:1–10. PubMed PMC

Librado P., Rozas J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25:1451–1452. doi: 10.1093/bioinformatics/btp187. PubMed DOI

Zhang D., Gao F., Jakovlić I., Zou H., Zhang J., Li W.X., Wang G.T. PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol. Ecol. Res. 2020;20:348–355. doi: 10.1111/1755-0998.13096. PubMed DOI

Katoh K., Standley D.M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 2013;30:772–780. doi: 10.1093/molbev/mst010. PubMed DOI PMC

Lanfear R., Frandsen P.B., Wright A.M., Senfeld T., Calcott B. PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses. Mol. Biol. Evol. 2017;34:772–773. doi: 10.1093/molbev/msw260. PubMed DOI

Nguyen L.T., Schmidt H.A., von Haeseler A., Minh B.Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 2015;32:268–274. doi: 10.1093/molbev/msu300. PubMed DOI PMC

Ronquist F., Teslenko M., van der Mark P., Ayres D.L., Darling A., Hohna S., Larget B., Liu L., Suchard M.A., Huelsenbeck J.P. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 2012;61:539–542. doi: 10.1093/sysbio/sys029. PubMed DOI PMC

Lartillot N., Rodrigue N., Stubbs D., Richer J. PhyloBayes MPI: Phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol. 2013;62:611–615. doi: 10.1093/sysbio/syt022. PubMed DOI

Lartillot N., Lepage T., Blanquart S. PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics. 2009;25:2286–2288. doi: 10.1093/bioinformatics/btp368. PubMed DOI

Miller M.A., Pfeiffer W., Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees; Proceedings of the 2010 Gateway Computing Environments Workshop (GCE); New Orleans, LA, USA. 14 November 2010; pp. 1–8.

Guo Q., Xu J., Liao C., Dai X., Jiang X. Complete mitochondrial genome of a leaf-mining beetle, Agonita chinensis Weise (Coleoptera: Chrysomelidae) Mitochondrial DNA B Resour. 2017;2:532–533. doi: 10.1080/23802359.2017.1365650. PubMed DOI PMC

Zhang S., Guo Q., Xu J., Wang X., Dai X. The complete mitochondrial genome of Downesia tarsata (Coleoptera: Chrysomelidae: Cassidinae) Mitochondrial DNA B Resour. 2021;6:1073–1074. doi: 10.1080/23802359.2021.1899862. PubMed DOI PMC

Yuan M.L., Zhang Q.L., Zhang L., Guo Z.L., Liu Y.J., Shen Y.Y., Shao R. High-level phylogeny of the Coleoptera inferred with mitochondrial genome sequences. Mol. Phylogenet. Evol. 2016;104:99–111. doi: 10.1016/j.ympev.2016.08.002. PubMed DOI

Ojala D., Montoya J., Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature. 1981;290:470–474. doi: 10.1038/290470a0. PubMed DOI

Wang H.L., Yang J., Boykin L.M., Zhao Q.Y., Li Q., Wang X.W., Liu S.S. The characteristics and expression profiles of the mitochondrial genome for the Mediterranean species of the Bemisia tabaci complex. BMC Genom. 2013;14:401. doi: 10.1186/1471-2164-14-401. PubMed DOI PMC

Boore J.L. Complete Mitochondrial Genome Sequence of the Polychaete Annelid Platynereis dumerilii. Mol. Biol. Evol. 2001;18:1413–1416. doi: 10.1093/oxfordjournals.molbev.a003925. PubMed DOI

Chen S.C., Wang X.Q., Li P.W., Hu X., Wang J.J., Peng P. The Complete Mitochondrial Genome of Aleurocanthus camelliae: Insights into Gene Arrangement and Genome Organization within the Family Aleyrodidae. Int. J. Mol. Sci. 2016;17:1843. doi: 10.3390/ijms17111843. PubMed DOI PMC

Su T., Liang A. Comparative analysis of seven mitochondrial genomes of Phymatostetha (Hemiptera: Cercopidae) and phylogenetic implications. Int. J. Biol. Macromol. 2019;125:1112–1117. doi: 10.1016/j.ijbiomac.2018.12.174. PubMed DOI

Ren L., Shang Y., Yang L., Shen X., Chen W., Wang Y., Cai J., Guo Y. Comparative analysis of mitochondrial genomes among four species of muscid flies (Diptera: Muscidae) and its phylogenetic implications. Int. J. Biol. Macromol. 2019;127:357–364. doi: 10.1016/j.ijbiomac.2019.01.063. PubMed DOI

Hong M.Y., Jeong H.C., Kim M.J., Jeong H.U., Lee S.H., Kim I. Complete mitogenome sequence of the jewel beetle, Chrysochroa fulgidissima (Coleoptera: Buprestidae) Mitochondrial DNA. 2009;20:46–60. doi: 10.1080/19401730802644978. PubMed DOI

Amorim I.C., Melo A.S., Cruz G.A.d.S., Wallau G.d.L., Moura R.d.C.d. Dichotomius (Luederwaldtinia) schiffleri (Coleoptera: Scarabaeidae) mitochondrial genome and phylogenetic relationships within the superfamily Scarabaeoidea. Mitochondrial DNA Part B. 2017;2:887–888. doi: 10.1080/23802359.2017.1407695. PubMed DOI PMC

Sheffield N.C., Song H., Cameron S.L., Whiting M.F. A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles. Mol. Biol. Evol. 2008;25:2499–2509. doi: 10.1093/molbev/msn198. PubMed DOI PMC

Hurst L.D. The Ka/Ks ratio:diagnosing the form of sequence evolution. Trends Genet. 2002;18:486–487. doi: 10.1016/S0168-9525(02)02722-1. PubMed DOI

Jeffares D.C., Tomiczek B., Sojo V., dos Reis M. A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome. Methods Mol. Biol. 2015;1201:65–90. doi: 10.1007/978-1-4939-1438-8_4. PubMed DOI

Zhang Z., Li J., Zhao X.-Q., Wang J., Wong G.K.-S., Yu J. KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging. Genom. Proteom. Bioinform. 2006;4:259–263. doi: 10.1016/S1672-0229(07)60007-2. PubMed DOI PMC

Nie R.-E., Yang X.-K. Research progress in mitochondrial genomes of Coleoptera. Acta Biochim. Biophys. Sin. 2014;57:860–868.

Hebert P.D., Ratnasingham S., de Waard J.R. Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proc. Biol. Sci. 2003;270((Suppl. 1)):S96–S99. doi: 10.1098/rsbl.2003.0025. PubMed DOI PMC

Oliveira D.C., Raychoudhury R., Lavrov D.V., Werren J.H. Rapidly evolving mitochondrial genome and directional selection in mitochondrial genes in the parasitic wasp nasonia (hymenoptera: Pteromalidae) Mol. Biol. Evol. 2008;25:2167–2180. doi: 10.1093/molbev/msn159. PubMed DOI PMC

Smietanka B., Burzynski A., Wenne R. Comparative genomics of marine mussels (Mytilus spp.) gender associated mtDNA: Rapidly evolving atp8. J. Mol. Evol. 2010;71:385–400. doi: 10.1007/s00239-010-9393-4. PubMed DOI

Shen X., Li X., Sha Z., Yan B., Xu Q. Complete mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus (Crustacea: Decapoda: Caridea): Gene rearrangement and phylogeny within Caridea. Sci. China Life Sci. 2012;55:591–598. doi: 10.1007/s11427-012-4348-1. PubMed DOI

Chaboo C.S. Biology and phylogeny of the Cassidinae Gyllenhal sensu lato (tortoise and leaf-mining beetles) Coleoptera Chrysomelid. Bull. Am. Mus. Nat. Hist. 2007;305:1–250. doi: 10.1206/0003-0090(2007)305[1:BAPOTC]2.0.CO;2. DOI

Wilf P., Labandeira C.C., Kress W.J., Staines C.L., Windsor D.M., Allen A.L., Johnson K.R. Timing the radiations of leaf beetles: Hispines on gingers from latest cretaceous to recent. Science. 2000;289:291–294. doi: 10.1126/science.289.5477.291. PubMed DOI

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