Published December 31, 2018 | Version v1
Journal article Open

Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods

  • 1. Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
  • 2. Department of Ecology and Evolution, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China & State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
  • 3. Netherlands Biodiversity Centre Naturalis, 2300 RA Leiden, The Netherlands
  • 4. Authority of Bangxi Nature Reserve, Baisha 572821, Hainan, China
  • 5. Authority of Jianfengling National Nature Reserve, Ledong 572542, Hainan, China
  • 6. College of Life Sciences, Lanzhou University, Lanzhou 730000, China

Description

Sun, Xiaoya, Wang, Yanhui, Chen, Pingping, Wang, Hesheng, Lu, Lixiang, Ye, Zhen, Wu, Yanzhuo, Li, Teng, Bu, Wenjun, Xie, Qiang (2018): Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods. Zoological Systematics 43 (4): 356-386, DOI: 10.11865/zs.201833

Files

source.pdf

Files (3.9 MB)

Name Size Download all
md5:e324e026f90f2f6102dd05c5eca9d01b
3.9 MB Preview Download

Linked records

Additional details

Identifiers

LSID
urn:lsid:plazi.org:pub:E324E026F90F2F61FFDDFFC5FFA9D01B

References

  • Andujar, C., Arribas, P., Ruzicka, F., Crampton-Platt, A., Timmermans, M.J.T.N., Vogler, A.P. 2015. Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics. Molecular Ecology, 24: 3603-3617.
  • Arriaga-Jimenez, A., Roy, L. 2015. CO1 DNA supports conspecificity of Geomyphilus pierai and G. barrerai (Coleoptera, Scarabaeidae, Aphodiinae) and is a good marker for their phylogeographic investigation in Mexican mountains. Zookeys, 512: 77-88.
  • Avise, J.C. 2004. Molecular Markers, Natural History and Evolution. Sinauer Associates, Sunderland. 684pp.
  • Avise, J.C., Arnold, J., Ball, R.M., Bermingham, E., Lamb, T., Neigel, J.E., Reeb, C.A., Saunders, N.C. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics, 18: 489-522.
  • Bernt, M., Donath, A., Juhling, F., Externbrink, F., Florentz, C., Fritzsch, G., Putz, J., Middendorf. M.,Stadler, P.F. 2013. Mitos: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics & Evolution, 69: 31-39.
  • Brandon-Mong, G.J., Gan, H.M., Sing, K.W., Lee, P.S., Lim, P.E., Wilson, J.J. 2015. DNA metabarcoding of insects and allies: an evaluation of primers and pipelines. Bulletin of Entomological Research, 105: 717-727.
  • Borsa, P., Durand, J.D., Chen, W.J., Hubert, N., Muths, D., Mou-Tham, G., Kulbicki, M. 2016. Comparative phylogeography of the western Indian Ocean reef fauna. Acta Oecologica, 72: 72-86.
  • Boore, J.L. 2006. The use of genome-level characters for phylogenetic reconstruction. Trends in Ecology & Evolution, 21: 439-446.
  • Brown, W.M., Prager, E.M., Wang, A., Wilson, A.C. 1982. Mitochondrial DNA sequences of primates: tempo and mode of evolution. Journal of Molecular Evolution, 18: 225-39.
  • Butcher, B.A., Smith, M.A., Sharkey, M.J., Quicke, D.L.J. 2012. A turbo-taxonomic study of Thai Aleiodes (Aleiodes) and Aleiodes (Arcaleiodes) (Hymenoptera: Braconidae: Rogadinae) based largely on COI barcoded specimens, with rapid descriptions of 179 new species. Zootaxa, 3457: 1-232.
  • Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., Madden, T.L. 2009. BLAST+: architecture and applications. BMC Bioinformatics, 10: 421.
  • Cameron, S.L. 2014a. Insect mitochondrial genomics: implications for evolution and phylogeny. Annual Review of Entomology, 59: 95- 117.
  • Cameron, S.L. 2014b. How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research. Systematic Entomology, 39: 400-411.
  • Chang, D., Knapp, M., Enk, J., Lippold, S., Kircher, M., Lister, A., MacPhee, R.D.E., Widga, C., Czechowski, P., Sommer, R., Hodges, E., Stumper, N., Barnes, I., Dalen, L., Derevianko, A., Germonpre, M., Hillebrand-Voiculescu, A., Constantin, S., Kuznetsova, T., Mol, D., Rathgeber, T., Rosendahl, W., Tikhonov, A.N., Willerslev, E., Hannon, G., Lalueza-Fox, C., Joger, U., Poinar, H., Hofreiter, M., Shapiro, B. 2017. The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis. Scientific Reports, 7: 44585.
  • Clary, D.O., Wolstenholme, D.R. 1985. The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. Journal of Molecular Evolution, 22: 252-271.
  • Crampton-Platt, A., Douglas, W.Y., Zhou, X., Vogler, A.P. 2016. Mitochondrial metagenomics: letting the genes out of the bottle. GigaScience, 5: 1.
  • Crooks, G.E., Hon, G., Chandonia, J.M., Brenner, S.E. 2004. WebLogo: A sequence logo generator. Genome Research, 14: 1188-1190.
  • Cui, Y., Dong, P.Z., Hua, J.M., Li, M., Xie, Q., Bu, W.J. 2012. The complete mitochondrial genome of Aquarius paludum (Fabricius) (Insecta, Hemiptera, Gerridae). Acta Zootaxonomica Sinica, 37: 255-262.
  • Evans, N.T., Olds, B.P., Renshaw, M.A., Turner, C.R., Li, Y.Y., Jerde, C.L., Mahon, A.R., Pfrender, M.E., Lamberti, G.A., Lodge, D.M. 2016. Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Molecular Ecology Resource, 16: 29.
  • Grant, J.R., Stothard, P. 2008. The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Research, 36: W181-W184.
  • Hall, T.A. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41: 95-98.
  • Hebert, P.D.N., Cywinska, A., Ball, S.L. 2003a. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B: Biological Sciences, 270: 313-321.
  • Hebert, P.D.N, Ratnasingham, S., Dewaard, J.R. 2003b. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings Biological Sciences, 270: S96.
  • Hendrich, L., Balke, M. 2011. A simultaneous journal/wiki publication and dissemination of a new species description: Neobidessodes darwiniensis sp. n. from northern Australia (Coleoptera, Dytiscidae, Bidessini). ZooKeys, 79: 11-20.
  • Jung, S., Duwal, R.K., Lee, S. 2011. COI barcoding of true bugs (Insecta, Heteroptera). Molecular Ecology Resources, 11: 266-270.
  • 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: 1647-1649.
  • Kartzinel, T.R., Chen, P.A., Coverdale, T.C., Erickson, D.L., Kress, W.J., Kuzmina, M.L., Rubenstein, D.I., Wang, W., Pringle, R.M. 2015. DNA metabarcoding illuminates dietary niche partitioning by African large herbivores. PNAS, 112: 8019-8024.
  • Kastally, C., Mardulyn, P. 2017. Widespread co-occurrence of two distantly related mitochondrial genomes in individuals of the leaf beetle gonioctena intermedia. Biology Letters, 13: 20170570.
  • Kayal, E., Roure, B., Philippe, H., Collins, A.G., Lavrov, D.V. 2013. Cnidarian phylogenetic relationships as revealed by mitogenomics. BMC Evolutionary Biology, 13: 5.
  • Keis, M., Remm, J., Ho, S.Y., Davison, J., Tammeleht, E., Tumanov, I.L., Saveljev, A., Mannil, P., Kojola, I., Abramov, A., Margus, T., Saarma, U. 2013. Complete mitochondrial genomes and a novel spatial genetic method reveal cryptic phylogeographical structure and migration patterns among brown bears in north-western Eurasia. Journal of Biogeography, 40: 915-927.
  • Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16: 111-120.
  • Kumar, S., Stecher, G., Tamura, K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33: 1870-1874.
  • Leray, M., Knowlton, N. 2015. DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. PNAS, 112: 2076-2081.
  • Li, H., Gao, J.Y., Liu, H.Y., Liu, H., Liang, A.P., Zhou, X.G., Cai, W.Z. 2011. The architecture and complete sequence of mitochondrial genome of an assassin bug Agriosphodrus dohrni (Hemiptera: Reduviidae). International Journal of Biological Sciences, 7: 792- 804.
  • Li, H., Liu, H.Y., Cao, L.M., Shi, A.M., Yang, H.L., Cai, W.Z. 2012a. The complete mitochondrial genome of the damsel bug Alloeorhynchus bakeri (Hemiptera: Nabidae). International Journal of Biological Sciences, 8: 93-107.
  • Li, H., Liu, H., Shi, A., Stys, P., Zhou, X., Cai, W.Z. 2012b. The complete mitochondrial genome and novel gene arrangement of the unique-headed bug Stenopirates sp. (Hemiptera: Enicocephalidae). PLoS One, 7: e29419.
  • 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: 955-964.
  • Ma, C., Yang, P.C., Jiang, F., Chapuis, M.P., Shali, Y., Sword, G.A., Kang, L. 2012. Mitochondrial genomes reveal the global phylogeography and dispersal routes of the migratory locust. Molecular Ecology, 21: 4344-4358.
  • Magalhaes, M.G.P., Moreira, D.A., Furtado, C., Parente, T.E. 2016. The mitochondrial genome of Hypancistrus zebra, (Isbrucker & Nijssen, 1991) (Siluriformes: Loricariidae), an endangered ornamental fish from the Brazilian Amazon. Conservation Genetics Resources, 9(2): 1-6. doi: 10.1007/s12686-016-0645-5.
  • Mao, M., Austin, A.D., Johnson, N.F., Dowton, M. 2013. Coexistence of minicircular and a highly rearranged mtDNA molecule suggests that recombination shapes mitochondrial genome organization. Molecular Biology and Evolution, 31: 36-644.
  • Morin, P.A., Archer, F.I., Foote, A.D., Vilstrup, J., Allen, E.E., Wade, P., Durban, J., Parsons, K., Pitnam, R., Li, L., Bouffard, P., Nielsen, S.C.A., Rasmussen, M., Willerslev, E., Gilbert, M.T.P., Harkins, T. 2010. Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Research, 20: 908-916.
  • Ratnasingham, S, Hebert, P.D. 2013. A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS One, 8: e66213.
  • Raupach, M.J., Hendrich, L., Kuchler, S.M., Deister, F., Moriniere, J., Gossner, M.M. 2014. Building-up of a DNA barcode library for true bugs (Insecta: Hemiptera: Heteroptera) of Germany reveals taxonomic uncertainties and surprises. PLoS One, 9: e106940.
  • Reineke, A., Karlovsky, P., Zebitz, C.P.W. 1998. Preparation and purification of DNA from insects for AFLP analysis. Insect Molecular Biology, 7: 95-99.
  • Reiner, J.E., Kishore, R.B., Levin, B.C., Albanetti, T., Boire, N., Knipe, A., Helmerson, K., Deckman, K.H. 2010. Detection of heteroplasmic mitochondrial DNA in single mitochondria. PLoS One, 5: e14359.
  • Riedel, A., Sagata, K., Surbakti, S., Tanzler, R., Balke, M. 2013. One hundred and one new species of Trigonopterus weevils from New Guinea. ZooKeys, 280: 1-150.
  • Sanger, F., Nicklen, S., Coulson, A.R. 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, 74: 5463-5467.
  • Simon, C., Buckley, T.R., Frati, F., Stewart, J.B., Beckenbach, A.T. 2006. Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annual Review of Ecology, Evolution, Systematics, 37: 545-579.
  • Stoev, P., Akkari, N., Zapparoli, M., Porco, D., Enghoff, H., Edgecombe, G.D., Georgiev, T., Penev, L. 2010. The centipede genus Eupolybothrus verhoef, 1907 (Chilopoda: Lithobiomorpha: Lithobiidae) in North Africa, a cybertaxonomic revision, with a key to all species in the genus and the first use of DNA barcoding for the group. ZooKeys, 50: 29-77.
  • Sun, X.J., Xiao, J.H., Cook, J.M., Feng, G., Huang, D.W. 2011. Comparisons of host mitochondrial, nuclear and endosymbiont bacterial genes reveal cryptic fig wasp species and the effects of Wolbachia on host mtDNA evolution and diversity. BMC Evolutionary Biology, 11: 86.
  • Tang, M., Hardman, C.J., Ji, Y.Q., Meng, G.L., Liu, S.L., Tan, M.H., Yang, S.Z., Moss, E.D., Wang, J.X., Yang, C.X., Bruce, C., Nevard, T., Potts, S.G., Zhou, X., Yu, D.W. 2015. High-throughput monitoring of wild bee diversity and abundance via mitogenomics. Methods in Ecology and Evolution, 6: 1034-1043.
  • Tang, M., Tan, M., Meng, G.L., Yang, S.Z., Su, X., Liu, S.L., Song, W.H., Li, Y.Y., Wu, Q., Zhang, A.B.. Zhou, X. 2014. Multiplex sequencing of pooled mitochondrial genomes - a crucial step toward biodiversity analysis using mito-metagenomics. Nucleic Acids Research, 42: e166-e166.
  • Timbo, R.V., Togawa, R.C., Costa, M.M.C., Andow, D.A., Paula, D.P. 2017. Mitogenome sequence accuracy using different elucidation methods. PloS one, 12: e0179971.
  • Tonione, M.A., Fisher, R.N., Zhu,C., Moritz, C. 2016. Deep divergence and structure in the Tropical Oceanic Pacific: A multilocus phylogeography of a widespread gekkonid lizard (Squamata: Gekkonidae: Gehyra oceanica). Journal of Biogeography, 43: 268- 278.
  • Ward, R., Zemlak, T., Innes, B., Last, P.P. 2005. DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society of London, 360: 1847-1857.
  • Xie, Y., Wu, G., Tang, J., Luo, R., Patterson, J., Liu, S., Huang, W., He, G., Gu, S., Li, S., Zhou, X., Lam, T., Li, Y., Xu, X., Wong, G., Wang, J. 2014. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics, 30: 1660-1666.
  • Zhou, X., Li, Y., Liu, S., Yang, Q., Su, X., Zhou, L., Tang, M., Fu, R., Li, J., Huang, Q. 2013. Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. Gigascience, 2: 4.