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Type: Articles
Published: 2012-03-19
Page range: 23–38
Abstract views: 45
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The complete mitochondrial genome of the flat bug Aradacanthia heissi (Hemiptera: Aradidae)

Department of Entomology, China Agricultural University, Yuanmingyuan West Road, Beijing 100193, China
Department of Entomology, China Agricultural University, Yuanmingyuan West Road, Beijing 100193, China
College of Life Sciences and Technology, Inner Mongolia Normal University, Zhaowudalu 81, Huhhot 010022, China
Research Center of Hongta Group, Yuxi, Yunnan 653100, China
Research Center of Hongta Group, Yuxi, Yunnan 653100, China
Département de Systématique et Evolution, Muséum national d'Histoire naturelle, UMR 7205, CP50, 45 rue Buffon, 75005 Paris, France
Department of Entomology, China Agricultural University, Yuanmingyuan West Road, Beijing 100193, China
Hemiptera Mitochondrial genome Aradacanthia heissi RNA secondary structure Gene arrangement Phylogenetic analyses

Abstract

The 15528 bp long complete mitochondrial genome (mt-genome) of a flat bug, Aradacanthia heissi Bai, Zhang & Cai,was determined. The entire genome contains typical 37 genes with an A+T content of 74.7%. The gene arrangement dif-fers from that of Drosophila yakuba Burla which is considered the representative ground pattern for insect mt-genomes,as the results of inversion of tRNAIle - tRNAGln and tRNACys - tRNATrp . All protein-coding genes (PCGs) use standard initia-tion codons (methionine and isoleucine), except COI which starts with TTG. Three of the 13 PCGs harbor the incompletetermination codon. Meanwhile, opposite CG-skew tendency occurs on the nucleotide composition and codon usage andthis tendency is also reflected on the J-strand and N-strand of PCGs. All tRNAs can fold into classic clover-leaf structure,whereas the dihydrouridine (DHU) arm of tRNASer(AGN) forms a simple loop. Secondary structure models of the ribosomalRNA genes of A. heissi are predicted and similar to those proposed for other insects. The control region is located betweensrRNA and tRNAGln with 81.5% A+T content, which was the most A+T-rich region of the mt-genome and four 68 bp tan-dem repeat units were found in this region. Phylogenetic analyses of available species of Pentatomomorpha showed Ara-doidea and the Trichophora are sister groups that bolstered the mainstream hypothesis, and provide the evidence for the feasibility of mt-genome data to resolve relationships at the subfamily level in Aradidae.

References

  1. Asakawa, S., Kumazawa, Y., Araki, T., Himeno, H., Miura, K. & Watanabe, K. (1991) Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes. Journal of Molecular Evolution, 32, 511–520.

    Avise, J.A., Aronold, 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.

    Bai, X.S., Zhang, W.J. & Cai, W. (2009) Aradacanthia, a first record of a Calisiinae genus (Hemiptera: Aradidae) from China, India, and Thailand with description of a new species. Zootaxa, 2137, 51–56.

    Boore, J.L. (1999) Animal mitochondrial genomes. Nucleic Acids Research, 27, 1767–1780.

    Boore, J.L. (2006) The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda). BMC Genomics, 7, 182.

    Boore, J.L. & Brown, W.M. (1998) Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Current Opinion in Genetics & Development, 8, 668–674.

    Buckley, T.R., Simon, C., Flook, P.K. & Misof, B. (2000) Secondary structure and conserved motifs of the frequently sequenced domains IV and V of the insect mitochondrial large subunit rRNA gene. Insect Molecular Biology, 9, 565–580.

    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.

    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.

    Carapelli, A., Comandi, S., Convey, P., Nardi, F. & Frati, F. (2008) The complete mitochondrial genome of the Antarctic springtail Cryptopygus antarcticus (Hexapoda: Collembola). BMC Genomics, 9, 315.

    Cassis, G. & Schuh, R.T. (2009) Systematic methods, fossils, and relationships within Heteroptera (Insecta). Cladistics, 25, 1–19.

    Clary, D.O. & Wolstenholme, D.R. (1985) The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization and genetic code. Journal of Molecular Evolution, 22, 252–271.

    Cook, C.E. (2005) The complete mitochondrial genome of the stomatopod crustacean Squilla mantis. BMC Genomics, 6, 105.

    Dotson, E.M. & Beard, C.B. (2001) Sequence and organization of the mitochondrial genome of the Chagas disease vector, Triatoma dimidiata. Insect Molecular Biology, 10, 205–215.

    Dowton, M., Castro, L.R. & Austin, A.D. (2002) Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome ‘morphology’. Invertebrate Systematics, 16, 345–356.

    Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783–791.

    Fenn, J.D., Cameron, S.L. & Whiting, M.F. (2007) The complete mitochondrial genome of the Mormon cricket (Anabrus simplex: Tettigoniidae: Orthoptera) and an analysis of control region variability. Insect Molecular Biology, 16, 239–252.

    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.

    Grozeva, S.M. & Kerzhner, I.M. (1992) On the phylogeny of aradid subfamilies (Heteroptera, Aradidae). Acta Zoologica Hungarica, 38 (3–4), 199–205.

    Guindon, S., Lethiec, F., Duroux, P. & Gascuel, O. (2005) PHYML online—a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Research, 33 (Web Server issue), W557–W559.

    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.

    Hassanin, A., Léger, N. & Deutsch, J. (2005) Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of metazoa, and consequences for phylogenetics inferences. Systematic Biology, 54, 277–298.

    Heiss, E. (2001) Superfamily Aradoidea Brullé 1836. In: Aukema, B. & Rieger, C. (Eds), Catalogue of the Heteroptera of the Palaearctic Region, vol 4. Amsterdam Netherlands Entomological Society, pp. 3–34.

    Henry, T.J. (1997) Phylogenetic analysis of family groups within the infraorder Pentatomomorpha (Hemiptera: Heteroptera), with emphasis on the Lygaeoidea. Annals of the Entomological Society of America, 90, 275–301.

    Hu, J., Zhang, D.X., Hao, J.S., Huang, D.Y., Stephen, C. & Zhu, C.D. (2010) The complete mitochondrial genome of the yellow coaster, Acraea issoria (Lepidoptera: Nymphalidae: Heliconiinae: Acraeini): sequence, gene organization and a unique tRNA translocation event. Molecular Biology Reports, 37, 3431–3438.

    Hua, J.M., Li, M., Dong, P.Z., Cui, Y., Xie, Q. & Bu, W. (2008) Comparative and phylogenomic studies on the mitochondrial genomes of Pentatomomorpha (Insecta: Hemiptera: Heteroptera). BMC Genomics, 9, 610.

    Hua, J.M., Li, M., Dong, P.Z., Cui, Y., Xie, Q. & Bu, W. (2009) Phylogenetic analysis of the true water bugs (Insecta: Hemiptera: Heteroptera: Nepomorpha): evidence from mitochondrial genomes. BMC Evolutionary Biology, 9, 134.

    Huelsenbeck, J.P. & Ronquist, F. (2001) MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics, 17, 754–755.

    Jermin, L.S., Graur, D. & Crozier, R.H. (1995) Evidence from analyses of intergenic regions for strand-specific directional mutation pressure in metazoan mitochondrial DNA. Molecular Biology and Evolution, 15, 558–563.

    Jia, W. & Higgs, P.G. (2008) Codon usage in mitochondrial genomes distinguishing context-dependent mutation from translational selection. Molecular Biology and Evolution, 25, 339–351.

    Kormilev, N.A. & Froeschner, R.C. (1987) Flat Bugs of the World: a Synonymic List (Heteroptera, Aradidae). Entomography, 5, 1–246.

    Kumar, R. (1967) Morphology of the reproductive and alimentary systems of the Aradoidea (Hemiptera), with comments on relationships within the superfamily. Annals of the Entomological Society of America, 60, 17–25.

    Kurabayashi, A., Sumida, M., Yonekawa, H., Glaw, F., Vences, M. & Hasegawa, M. (2008) Phylogeny, recombination, and mechanisms of stepwise mitochondrial genome reorganization in mantellid frogs from Madagascar. Molecular Biology and Evolution, 25, 874–891.

    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. Proceeding of the National Academy of Sciences of the United States of America, 97, 13738–13742.

    Leston, D. (1958) Chromosome number and the systematics of Pentatomomorpha (Hemiptera). In: Proceedings of the Tenth International Congress of Entomology. International Congress of Entomology, Montreal, 2, 911–918.

    Li, H., Gao, J.Y., Liu, H.Y., Liang, A.P., Zhou, X.G. & Cai, W. (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., Shi, A.M., Štys, P., Zhou, X.G. & Cai, W. (2012a) The complete mitochondrial genome and novel gene arrangement of the unique-headed bug Stenopirates sp. (Hemiptera: Enicocephalidae). PLoS ONE, 7, e29419.

    Li, H., Liu, H.Y., Cao, L.M., Shi, A.M, Yang, H.L. & Cai, W. (2012b) The complete mitochondrial genome of the damsel bug Alloeorhynchus bakeri (Hemiptera: Nabidae). International Journal of Biological Sciences, 8, 93–107.

    Li, H.M., Deng, R.Q., Wang, J.W., Chen, Z.Y., Jia, F.L. & Wang, X.Z. (2005) A preliminary phylogeny of the Pentatomomorpha (Hemiptera: Heteroptera) based on nuclear 18S rDNA and mitochondrial DNA sequences. Molecular Phylogenetics and Evolution, 37, 313–326.

    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.

    Min, X.J. & Hickey, D.A. (2007) DNA asymmetric strand bias affects the amino acid composition of. DNA Research, 14, 201–206.

    Misof, B. & Fleck, G. (2003) Comparative analysis of mt LSU rRNA secondary structures of Odonates: structural variability and phylogenetic signal. Insect Molecular Biology, 12, 535–548.

    Nylander, JAA. (2004) MrModeltest v2. Program Distributed by the Author. Evolutionary Biology Centre, Uppsala University.

    Ojala, D., Merkel, C., Gelfand, R. & Attardi, G. (1980) The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell, 2, 393–403.

    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.

    Posada, D. & Crandall, K.A. (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics, 14, 817–818.

    Reineke, A., Karlovsky, P. & Zebitz, C.P. (1998) Preparation and purification of DNA from insects for AFLP analysis. Insect Molecular Biology, 7, 95–99.

    Salvato, P., Simonato, M., Battisti, A. & Negrisolo, E. (2008) The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae). BMC Genomics, 9, 331.

    Segawa, R.D. & Aotsuka, T. (2005) The mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Crustacea: Brachyura): Evidence for its evolution via gene duplication. Gene, 355, 28–39.

    Sharp, P.M., Bailes, E., Grocock, R.J., Peden, J.F. & Sockett, R.E. (2005) Variation in the strength of selected codon usage bias among Bacteria. Nucleic Acids Research, 33, 1141–1153.

    Sheffield, N.C., Song, H., Cameron, S.L. & Whiting, M.F. (2008) A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles. Molecular Biology and Evolution, 25, 2499–2509.

    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, and Systematics, 37, 545–579.

    Simon, C., Frati, F., Beckenbach, A., Cresp, B., Liu, H. & Flook, P. (1994) Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chainreaction primers. Annals of the Entomological Society of America, 87, 651–701.

    Sweet, M.H. (1996) Comparative external morphology of the pregenital abdomen of the Hemiptera. In: Schaefer, C.W. (Ed.), Studies on Hemipteran Phylogeny. Thomas Say Publications in Entomology. Entomological Society of America, Lanham, MD, pp. 119–158.

    Sweet, M.H. (2006) Justification for the Aradimorpha as an infraorder of the suborder Heteroptera (Hemiptera, Prosorrhyncha) with special reference to the pregenital abdominal structure. Denisia, 19, 225–248.

    Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596–1599.

    Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. (1997) The CLUSTAL_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25, 4876–4882.

    Tomita, K., Yokobori, S., Oshima, T., Ueda, T. & Watanabe, K. (2001) The cephalopod Loligo bleekeri mitochondrial genome: multiplied noncoding regions and transposition of tRNA genes. Journal of Molecular Evolution, 54, 486−500.

    Vásárhelyi, T. (1987) On the relationships of the eight aradid subfamilies (Heteroptera). Acta Zoologica Hungarica, 33, 263–267.

    Wei, S.J., Shi, M., He, J.H., Sharkey, M. & Chen, X.X. (2009) The complete mitochondrial genome of Diadegma semiclausum (Hymenoptera: Ichneumonidae) indicates extensive independent evolutionary events. Genome, 52, 308–319.

    Wei, S.J., Tang, P., Zheng, L.H., Shi, M. & Chen, X.X. (2010) The complete mitochondrial genome of Evania appendigaster (Hymenoptera: Evaniidae) has low A+T content and a long intergenic spacer between atp8 and atp6. Molecular Biology Reports, 37, 1931–1942.

    Wilson, K., Cahill, V., Ballment, E. & Benzie, J. (2000) The complete sequence of the mitochondrial genome of the crustacean Penaeus mondon: are malacostracan crustaceans more closely related to insects than to branchiopods? Molecular Biology and Evolution, 17, 863–874.

    Wolstenholme, D.R. (1992) Genetic novelties in mitochondrial genomes of multicellular animals. Current Opinion in Genetics & Development, 2, 918–925.

    Xie, Q., Bu, W. & Zheng, L. (2005) The Bayesian phylogenetic analysis of the 18S rRNA sequences from the main lineages of Trichophora (Insecta: Heteroptera: Pentatomomorpha). Molecular Phylogenetics and Evolution, 34, 448–451.

    Zhang, C.Y. & Huang, Y. (2008) Complete mitochondrial genome of Oxya chinensis (Orthoptera, Acridoidea). Acta Biochimica et Biophysica Sinica, 40, 7–18.

    Zhang, D.X. & Hewitt, F.M. (1997) Insect mitochondrial control region: A review of its structure, evolution and usefulness in evolutionary studies. Biochemical Systematics and Ecology, 25, 99–120.

    Zhou, Z., Huang, Y. & Shi, F. (2007) The mitochondrial genome of Ruspolia dubia (Orthoptera: Conocephalidae) contains a short A+T-rich region of 70 bp in length. Genome, 50, 855–866.

    Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research, 31, 3406–3415.