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Issue: Vol. 4732 No. 3: 13 Feb. 2020
Type: Article
Published: 2020-02-13
DOI: 10.11646/zootaxa.4732.3.8
Page range: 461–473
Abstract views: 65
PDF downloaded: 2

The complete mitochondrial genome of Amphinemura claviloba (Wu, 1973) (Plecoptera: Nemouridae)

Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan, 453003 China.
Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan, 453003 China.
Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan, 453003 China.
Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan, 453003 China.
Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan, 453003 China.
Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan, 453003 China.
Plecoptera Amphinemurinae Genome features Phylogenetic analyses

Abstract

We sequenced the complete mitochondrial genome (mitogenome) of a stonefly, Amphinemura claviloba (Wu, 1973), of the family Nemouridae (Insecta: Plecoptera). The mitogenome was 15,707 bp long and contained typical 37 genes with an A+T content of 68.5%. All protein-coding genes (PCGs) use standard initiation codons (methionine and isoleucine), except ND1 and ND5 which starts with TTG and GTG, respectively. Two of the 13 PCGs harbor the incomplete termination codon. All tRNA genes have typical clover secondary structures, except the dihydrouridine (DHU) arm of tRNASer(AGN) forms a simple loop. Secondary structure models of the ribosomal RNA genes of A. claviloba are similar to those proposed for other insects. We also found some structural elements in the control region, such as tandem repeats, poly-C stretch and microsatellite-like elements, etc. Phylogenetic analyses showed the clades for the Nemoura, Amphinemura, and (Mesonemoura + Sphaeronemoura + Indonemoura + Protonemura) are well supported in a polytomy.

 

References

  1. Abascal, F., Zardoya, R. & Telford, M.J. (2010) TranslatorX: multiple alignments of nucleotide sequences guided by amino acid translations. Nucleic Acids Research, 38, W7–W13.

    https://doi.org/10.1093/nar/gkq291

    Baumann, R.W. (1975) Revision of the stonefly family Nemouridae (Plecoptera): a study of the world fauna at the generic level. Smithsonian Contributions to Zoology, 40, 1–84.

    https://doi.org/10.5479/si.00810282.211

    Benson, G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research, 27, 573–580.

    https://doi.org/10.1093/nar/27.2.573

    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, 313–319.

    https://doi.org/10.1016/j.ympev.2012.08.023

    Boore, J.L. (1999) Animal mitochondrial genomes. Nucleic Acids Research, 27, 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, 112–123.

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

    Cannone, J.J., Subramainian, S., Schnar, M.N., Collett, J.R., D’Souza, L.M., Du, Y.S., Feng, B., Lin, N., Madabus, L.V., Müller, K.M., Pande, N., Shang, Z.D., Yu, N. & Gutell, R.R. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs: Correction. BMC Bioinformatics, 3, 15.

    https://doi.org/10.1186/1471-2105-3-15

    Cameron, S.L. (2014) Insect mitochondrial genomics: implications for evolution and phylogeny. Annual Review of Entomology, 59, 95–117.

    https://doi.org/10.1146/annurev-ento-011613-162007

    Cao, J.J., Wang, Y. & Li, W.H. (2019a) Comparative mitogenomic analysis of species in the subfamily Amphinemurinae (Plecoptera: Nemouridae) reveal conserved mitochondrial genome organization. International Journal of Biological Macromolecules, 138, 292–301.

    https://doi.org/10.1016/j.ijbiomac.2019.07.087

    Cao, J.J., Wang, Y., Huang, Y.R. & Li, W.H. (2019b) Mitochondrial genomes of the stoneflies Mesonemoura metafiligera and Mesonemoura tritaenia (Plecoptera, Nemouridae), with a phylogenetic analysis of Nemouroidea. ZooKeys, 835, 43–63.

    https://doi.org/10.3897/zookeys.835.32470

    Chen, Z.T. & Du, Y.Z. (2017a) First Mitochondrial genome from Nemouridae (Plecoptera) reveals novel features of the elongated control region and phylogenetic implications. International Journal of Molecular Sciences, 18, 996.

    https://doi.org/10.3390/ijms18050996

    Chen, Z.T. & Du, Y.Z, (2017b) Complete mitochondrial genome of Capnia zijinshana (Plecoptera: Capniidae) and phylogenetic analysis among stoneflies. Journal of Asia-Pacific Entomology, 20, 305–312.

    https://doi.org/10.1016/j.aspen.2017.01.013

    Chen, M.D., Wang, Y., Chen, J.J. & Cao, J.J. (2019) The complete mitochondrial genome of a stonefly species, Indonemoura auriformis (Plecoptera: Nemouridae). Mitochondrial DNA Part B, 4, 3392–3393.

    https://doi.org/10.1080/23802359.2019.1674723

    Chen, Z.T., Wu, H.Y. & Du, Y.Z. (2016) The nearly complete mitochondrial genome of a stonefly species, Styloperla sp. (Plecoptera: Styloperlidae). Mitochondrial DNA Part A, 27, 2728–2729.

    DeWalt, R.E., Maehr, M.D., Neu-Becker, U. & Stueber, G. (2019) Plecoptera Species File Online. Version 5.0/5.0. Available from: http://Plecoptera.Species.File.org (accessed 16 August 2019)

    Elbrecht, V., Poettker, L., John, U. & Leese, F. (2015) The complete mitochondrial genome of the stonefly, Dinocras cephalotes, (Plecoptera, Perlidae). Mitochondrial DNA, 26, 469–470.

    https://doi.org/10.3109/19401736.2013.830301

    Elbrecht, V. & Leese, F. (2016) The mitochondrial genome of the Arizona Snowfly Mesocapnia arizonensis (Plecoptera, Capniidae). Mitochondrial DNA Part A, 27, 3365–3366.

    https://doi.org/10.3109/19401736.2015.1018223

    Gamboa, M., Muranyi, D., Kanmori, S. & Watanabe, K. (2019) Molecular phylogeny and diversification timing of the Nemouridae family (Insecta, Plecoptera) in the Japanese archipelago. PLoS ONE, 14, e0210269.

    https://doi.org/10.1371/journal.pone.0210269

    Gillespie, J.J., Johnston, J.S., Cannone, J.J. & Gutell, R.R. (2006) Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): Structure, organization and retrotransposable elements. Insect Molecular Biology, 15, 657–686.

    https://doi.org/10.1111/j.1365-2583.2006.00689.x

    Huang, M.C., Wang, Y.Y., Liu, X.Y., Li, W.H., Kang, Z.H., Wang, K., Li, X.K. & Yang, D. (2015) The complete mitochondrial genome and its remarkable secondary structure for a stonefly Acroneuria hainana Wu (Insecta: Plecoptera, Perlidae). Gene, 557, 52–60.

    https://doi.org/10.1016/j.gene.2014.12.009

    James, B.S. & Andrew, T.B. (2006) Insect mitochondrial genomics 2: the complete mitochondrial genome sequence of a giant stonefly, Pteronarcys princeps, asymmetric directional mutation bias, and conserved plecopteran A + T-region elements. Genome, 49, 815–824.

    https://doi.org/10.1139/g06-037

    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.

    https://doi.org/10.1093/bioinformatics/bts199

    Lavrov, D.V., Brown, W.M. & Boore, J.L. (2000) A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. Proceedings of the National Academy of Sciences of the United States of America, 97, 13738–13742.

    https://doi.org/10.1073/pnas.250402997

    Li, H., Leavengood, Jr. J.M., Chapman, E.G., Burkhardt, D., Song, F., Jiang, P., Liu, J., Zhou, X.G. & Cai, W.Z. (2017) Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs. Proceedings of the Royal Society B: Biological Sciences, 284, 1862.

    https://doi.org/10.1098/rspb.2017.1223

    Meikejohn, K.A., Danielson, M.J., Faircloth, B.C., Glenn, T.C., Braun, E.L. & Kimball, R.T. (2014) Incongruence among different mitochondrial regions: A case study using complete mitogenomes. Molecular Phylogenetics and Evolution, 78, 314–323.

    https://doi.org/10.1016/j.ympev.2014.06.003

    Nguyen, L.T., Schmidt, H.A., von Haeseler, A. & Minh, B.Q. (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32, 268–274.

    https://doi.org/10.1093/molbev/msu300

    Ojala, D., Montoya, J. & Attardi, G. (1981) tRNA punctuation model of RNA processing in human mitochondria. Nature, 290, 470–474.

    https://doi.org/10.1038/290470a0

    Perna, N.T. & Kocher, T.D. (1995) Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. Journal of Molecular Evolution, 41, 353–358.

    https://doi.org/10.1007/BF01215182

    Posada, D. (2008) jModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253–1256.

    https://doi.org/10.1093/molbev/msn083

    Ronquist, F., Teslenko, M., van der 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, 539–542.

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

    Song, F., Li, H., Jiang, P., Zhou, X.G., Liu, J., Sun, C., Vogler, A.P. & Cai, W.Z. (2016) Capturing the phylogeny of Holometabola with mitochondrial genome data and bayesian site-heterogeneous mixture models. Genome Biology and Evolution, 8, 1411.

    https://doi.org/10.1093/gbe/evw086

    Sproul, J.S., Houston, D.D., Nelson, C.R., Evans, R.P., Crandall, K.A. & Shiozawa, D.K. (2015) Climate oscillations, glacial refugia, and dispersal ability: factors influencing the genetic structure of the least salmonfly, Pteronarcella badia, (Plecoptera), in Western North America. BMC Evolutionary Biology, 15, 279.

    https://doi.org/10.1186/s12862-015-0553-4

    Stewart, J.B. & Beckenbach, A.T. (2005) Insect mitochondrial genomics: the complete mitochondrial genome sequence of the meadow spittlebug Philaenus spumarius (Hemiptera: Auchenorrhyncha: Cercopoidae). Genome, 48, 46–54.

    https://doi.org/10.1139/g04-090

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

    https://doi.org/10.1016/S0005-2728(98)00161-3

    Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30, 2725–2729.

    https://doi.org/10.1093/molbev/mst197

    Terry, M.D. & Whiting, M.F. (2003) Phylogeny of Plecoptera: molecular evidence and evolutionary trends. Entomologische Abhandlungen, 61, 130–131.

    Wang, Y., Cao, J.J. & Li, W.H. (2017a) The complete mitochondrial genome of the styloperlid stonefly species Styloperla spinicercia Wu (Insecta: Plecoptera) with family-level phylogenetic analyses of the Pteronarcyoidea. Zootaxa, 4243 (1), 125–138.

    https://doi.org/10.11646/zootaxa.4243.1.5

    Wang, Y., Cao, J.J. & Li, W.H. (2018a) Complete Mitochondrial genome of Suwallia teleckojensis (Plecoptera: Chloroperlidae) and implications for the higher phylogeny of stoneflies. International Journal of Molecular Sciences, 19, 680.

    https://doi.org/10.3390/ijms19030680

    Wang, Y., Cao, J.J., Li, W.H. & Chen, X.L. (2017b) The mitochondrial genome of Mesocapina daxingana (Plecoptera: Capniidae). Conservation Genetics Resources, 9, 639–642.

    https://doi.org/10.1007/s12686-017-0745-x

    Wang, Y., Cao, J.J., Murányi, D. & Li, W.H. (2018b) Comparison of two complete mitochondrial genomes from Perlodidae (Plecoptera: Perloidea) and the family-level phylogenetic implications of Perloidea. Gene, 675, 254–264.

    https://doi.org/10.1016/j.gene.2018.06.093

    Wang, Y., Cao, J.J., Li, N., Ma, G.Y. & Li, W.H. (2019) The first mitochondrial genome from Scopuridae (Insecta: Plecoptera) reveals structural features and phylogenetic implications. International Journal of Biological Macromolecules, 122, 893–902.

    https://doi.org/10.1016/j.ijbiomac.2018.11.019

    Wei, S.J., Shi, M., Chen, X.X., Sharkey, M.J., Achterberg, C.V., Ye, G.Y. & He, J.H. (2010). New views on strand asymmetry in insect mitochondrial genomes. PLoS ONE, 5, e12708.

    https://doi.org/10.1371/journal.pone.0012708

    Wu, H.Y., Ji, X.Y., Yu, W.W. & Du, Y.Z. (2014) Complete mitochondrial genome of the stonefly Cryptoperla stilifera sivec (Plecoptera: Peltoperlidae) and the phylogeny of polyneopteran insects. Gene, 537, 177–183.

    https://doi.org/10.1016/j.gene.2013.12.044

    Zhang, D.X., Szymura, J.M. & Hewitt, G.M. (1995) Evolution and structural conservation of the control region of insect mitochondrial DNA. Journal of Molecular Evolution, 40, 382–391.

    https://doi.org/10.1007/BF00164024

    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, 99–120.

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

    Zwick, P. (2000) Phylogenetic system and zoogeography of the Plecoptera. Annual Review of Entomology, 45, 709–746.

    https://doi.org/10.1146/annurev.ento.45.1.709