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References

  • Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 33893402.
  • Ballard, J.W.O. (2000) Comparative genomics of mitochondrial DNA in members of the Drosophila melanogaster subgroup. Journal of Molecular Evolution, 51, 4863.
  • Beard, C.B., Hamm, D.M. & Collins, F.H. (1993) The mitochondrial genome of the mosquito Anopheles gambiae: DNA sequence, genome organization and comparisons with mitochondrial sequences of other insects. Insect Molecular Biology, 2, 103124.
  • Beckenbach, A.T. (2011) Mitochondrial genome sequences of Nematocera (Lower Diptera): evidence of rearrangement following a complete genome duplication in a winter crane fly. Genome Biology & Evolution, 4, 89101.
  • Beckenbach, A.T. & Joy, J.B. (2009) Evolution of the mitochondrial genomes of gall midges (Diptera: Cecidomyiidae): rearrangement and severe truncation of tRNA genes. Genome Biology & Evolution, 1, 278287.
  • Benasson, D., Zhang, D., Hartl, D.L. & Hewitt, G.M. (2001) Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends in Ecology & Evolution, 16, 314321.
  • Bernt, M., Bleidorn, C., Braband, A. et al.(2013a) A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny. Molecular Phylogenetics & Evolution, 69, 352364.
  • Bernt, M., Donath, A., Jühling, F. et al. (2013b) MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics & Evolution, 69, 313319.
  • Boore, J.L. (2006) Requirements and standards for organelle genome databases. OMICS, 10, 119126.
  • Boore, J.L., Lavrov, D.V. & Brown, W.M. (1998) Gene translocation links insects and crustaceans. Nature, 392, 667668.
  • Boore, J.L., Macey, J.R. & Medina, M. (2005) Sequencing and comparing whole mitochondrial genomes of animals. Methods in Enzymology, 395, 311348.
  • Braband, A., Cameron, S.L., Podsiadlowski, L., Daniels, S.R. & Mayer, G. (2010) The mitochondrial genome of the onychophoran Opisthopatus cinctipes (Peripatopsidae) reflects the ancestral mitochondrial gene arrangement of Panarthropoda and Ecdysozoa. Molecular Phylogenetics & Evolution, 57, 285292.
  • de Bruijn, M.H.L. (1983) Drosophila melanogaster mitochondrial DNA, a novel organization and genetic code. Nature, 304, 234241.
  • Burger, G., Gray, M.W. & Lang, B.F. (2003) Mitochondrial genomes: anything goes. Trends in Genetics, 19, 709716.
  • Cameron, S.L. (2014) Insect mitochondrial genomics: implications for evolution and phylogeny. Annual Review of Entomology, 59, 95117.
  • Cameron, S.L. & Whiting, M.F. (2007) Mitochondrial genomic comparisons of the subterranean termites from the Genus Reticulitermes (Insecta: Isoptera: Rhinotermitidae). Genome, 50, 188202.
  • 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, 112123.
  • Cameron, S.L., Lambkin, C.L., Barker, S.C. & Whiting, M.F. (2007) A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision. Systematic Entomology, 32, 4059.
  • Cameron, S.L., Dowton, M., Castro, L.R. et al. (2008) The sequence of the mitochondrial genomes of two vespid wasps reveals a number of derived tRNA gene rearrangements. Genome, 51, 800808.
  • 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, 575590.
  • Cameron, S.L., Yoshizawa, K., Mizukoshi, A., Whiting, M.F. & Johnson, K.P. (2011) Mitochondrial genome deletions and minicircles are common in lice (Insecta: Phthiraptera). BMC Genomics, 12, 394.
  • Cameron, S.L., Lo, N., Bourguignon, T., Svenson, G.J. & Evans, T.A. (2012) A mitochondrial genome phylogeny of termites (Blattodea: Termitoidae): Robust support for interfamilial relationships and molecular synapomorphies define major clades. Molecular Phylogenetics & Evolution, 65, 162173.
  • Clary, D.O. & Wolstenholme, D.R. (1983) Genes for cytochrome c oxidase subunit I, URF2 and three tRNAs in Drosophila mitochondrial DNA. Nucleic Acids Research, 11, 68596872.
  • 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, 252271.
  • Covacin, C., Shao, R., Cameron, S.L. & Barker, S.C. (2006) Extraordinary amounts of gene rearrangement in the mitochondrial genomes of lice (Insecta: Phthiraptera). Insect Molecular Biology, 15, 6368.
  • Crozier, R.H. & Crozier, Y.C. (1993) The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization. Genetics, 133, 97117.
  • Domes, K., Maraun, M., Scheu, S. & Cameron, S.L. (2008) The complete mitochondrial genome of the sexual oribatid mite Steganacarus magnus: genome rearrangements and loss of tRNAs. BMC Genomics, 9, 532.
  • Dotson, E.M. & Beard, C.B. (2001) Sequence and organization of the mitochondrial genome of the Chagas disease vector, Triatoma dimidiate. Insect Molecular Biology, 10, 205215.
  • Dowton, M., Cameron, S.L., Austin, A.D. & Whiting, M.F. (2009) Phylogenetic approaches for the analysis of mitochondrial genome sequence data in the Hymenoptera – a lineage with both rapidly and slowly evolving mitochondrial genomes. Molecular Phylogenetics & Evolution, 52, 512519.
  • Dubrovsky, E.B., Dubrovskaya, V.A., Levinger, L., Schiffer, S. & Marchfelder, A. (2004) Drosophila RNase Z processes mitochondrial and nuclear pre-tRNA 3' ends in vivo. Nucleic Acids Research, 32, 255262.
  • Elbrecht, V., Poettker, L., John, U. & Leese, F. (2013) The complete mitochondrial genome of the stonefly Dinocras cephalotes (Plecoptera, Perlidae). Mitochondrial DNA, in press.
  • 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, 239252.
  • 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, 657686.
  • Glenn, T.C. (2011) Field guide to next-generation DNA sequencers. Molecular Ecology Resources, 11, 759769.
  • Gong, Y.-J., Shi, B.-C., Kang, Z.-J., Zhang, F. & Wei, S.-J. (2012) The complete mitochondrial genome of the oriental fruit moth Grapholita molesta (Busck) (Lepidoptera: Tortricidae). Molecular Biology Reports, 39, 28932900.
  • Groenenberg, D.S.J., Pirovano, W., Gittenberger, E. & Schilthuizen, M. (2012) The complete mitogenomne of Cylindrus obtusus (Helicidae, Ariantinae) using Illumina next generation sequencing. BMC Genomics, 13, 114.
  • Hahn, C., Bachmann, L. & Chevreux, B. (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads – a baiting and iterative mapping approach. Nucleic Acids Research, 41, e129.
  • Haran, J., Timmermans, M.J.T.N. & Vogler, A.P. (2013) Mitogenome sequences stabilize the phylogenetics of weevils (Curculionoidea) and establish the monophyly of larval ectophagy. Molecular Phylogenetics & Evolution, 67, 156166.
  • Hu, J., Zhang, D., Hao, J., Huang, D., Cameron, S.L. & 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, 34313438.
  • Hua, J., Li, M., Dong, P., Cui, Y., Xie, Q. & Bu, W. (2008) Comparative and phylogenomics studies on the mitochondrial genomes of Pentatomorpha (Insecta: Hemiptera: Heteroptera). BMC Genomics, 9, 610.
  • Hung, C.-M., Lin, R.-C., Chu, J.-H., Yeh, C.-F., Yao, C.-J. & Li, S.-H. (2013) The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing. PLoS One, 8, e56301.
  • International Aphid Genomics Consortium (2010) Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biology, 8, e1000313.
  • Jex, A.R., Hu, M., Littlewood, D.T.J., Waeschenbach, A. & Gasser, R.B. (2008) Using 454 technology for long-PCR base sequencing of the complete mitochondrial genome from single Haemonchus contortus (Nematoda). BMC Genomics, 9, 11.
  • Jühling, F., Putz, J., Bernt, M., Donath, A., Middendorf, M., Florentz, C. & Stadler, P.F. (2012) Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structues and into the mechanisms of mitochondrial genome rearrangements. Nucleic Acids Research, 40, 28332845.
  • Kim, I., Lee, E.M., Seol, K.Y., Yun, E.Y., Lee, Y.B., Hwang, J.S. & Jin, B.R. (2006) The mitochondrial genome of the Korean hairstreak, Coreana raphaelis (Lepidoptera: Lycaenidae). Insect Molecular Biology, 15, 217225.
  • Kirkness, E.F., Haas, B.J., Sun, W. et al. (2010) Genome sequences of the human body louse and its primary endosymbiont: insights into the permanent parasitic lifestyle. Proceedings of the National Academy of Sciences of the United States of America, 107, 12 16812 173.
  • Laslett, D. & Canback, B. (2008) ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics, 24, 172175.
  • Lee, E.-S., Shin, K.S., Kim, M.-S., Park, H., Cho, S. & Kim, C.-B. (2006) The mitochondrial genome of the smaller tea tortrix Adoxophyes honmai (Lepidoptera: Tortricidae). Gene, 373, 5257.
  • Levinger, L., Vasisht, V., Greene, V., Bourne, R., Birk, A. & Kolla, S. (1998) Sequence and structure requirements for Drosophila tRNA 5'- and 3'- end processing. Journal of Biological Chemistry, 270, 1890318909.
  • Lorenzo-Carballa, M.O., Thompson, D.J., Cordero-Rivera, A. & Watts, P.C. (2013) Next generation sequencing yields the complete mitochondrial genome of the scarce blue-tailed damselfly, Ischnura pumilio. Mitochondrial DNA, in press.
  • 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, 955964.
  • Luo, R., Liu, B., Xie, Y. et al. (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience, 1, 18.
  • Lupi, R., D'Onorio de Meo, P., Picardi, E., D'Antonio, M., Paoletti, D., Castignano, T., Pesole, G. & Gissi, C. (2010) MitoZoa: a curated mitochondrial genome database of metazoans for comparative genomics studies. Mitochondrion, 10, 192199.
  • Ma, C., Yang, P.C., Jiang, F., Chapuis, M.-P., Shall, Y., Sword, G.A. & Kang, L. (2012) Mitochondrial genomes reveal the global phylogeography and dispersal routes of the migratory locust. Molecular Ecology, 21, 43444358.
  • Margam, V.M., Coates, B.S., Hellmich, R.L. et al. (2011) Mitochondrial genome sequences and expression profiling for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae). PLoS One, 6, e16444.
  • Nabholz, B., Jarvis, E.D. & Ellegren, H. (2010) Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny. Molecular Phylogenetics & Evolution, 57, 466470.
  • Nawrocki, E.P., Kolbem, D.L. & Eddy, S.R. (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics, 25, 13351337.
  • Neira-Oviedo, M., Tsyganov-Bodounov, A., Lycett, G.J., Kokoza, V., Raikhel, A.S. & Krzywinski, J. (2011) The RNA-seq approach to studying the expression of mosquito mitochondrial genes. Insect Molecular Biology, 20, 141152.
  • Nelson, L.A., Lambkin, C.L., Batterham, P. et al. (2012) Beyond barcoding: genomic approaches to molecular diagnostics in blowflies (Diptera: Calliphoridae). Gene, 511, 131142.
  • Niehuis, O., Naumann, C.M. & Misof, B. (2006) Identification of evolutionary conserved structural elements in the mt SSU Rrna of Zygaenoidea (Lepidoptera): a comparative sequence analysis. Organisms, Diversity & Evolution, 6, 1732.
  • Ojala, D., Montoyo, J. & Attardi, G. (1981) Trna punctuation model of RNA processing in human mitochondria. Nature, 290, 470474.
  • Oliveira, D.C.S.G., Raychoudhury, R., Lavrov, D.V. & Werren, J.H. (2008) Rapidly evolving mitochondrial genome and directional selection in mitochondrial genes in the parasitic wasp Nasonia (Hymenoptera: Pteromalidae). Molecular Biology & Evolution, 25, 21672180.
  • Osigus, H.-J., Eitel, M., Bernt, M., Donath, A. & Schierwater, B. (2013) Mitogenomics at the base of Metazoa. Molecular Phylogenetics & Evolution, 69, 339351.
  • Ovchinnikov, S. & Masta, S.E. (2012) Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias. BMC Evolutionary Biology, 12, 31.
  • Parameswaran, P., Jalili, R., Tao, L., Shokralla, S., Gharizadeh, B., Ronaghi, M. & Fire, A.Z. (2007) A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Research, 35, e130.
  • Park, J.S., Cho, Y., Kim, M.J., Nam, S.-H. & Kim, I. (2012) Description of the complete mitochondrial genome of the black-veined white, Aporia crataegi (Lepidoptera: Papilionoidea), and a comparison to papilionoid species. Journal of Asia-Pacific Entomology, 15, 331341.
  • Reyes, A., Gissi, C., Pesole, G. & Saccone, C. (1998) Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Molecular Biology & Evolution, 15, 957966.
  • Roberti, M., Polosa, P.L., Bruni, F., Musicco, C., Gadaleta, M.N. & Cantatore, P. (2003) DmTTF, a novel mitochondrial transcription factor that recognizes two sequences of Drosophila melanogaster mitochondrial DNA. Nucleic Acids Research, 31, 15971604.
  • Roehrdanz, R.L. (1995) Amplification of complete insect mitochondrial genomes in two easy pieces. Insect Molecular Biology, 4, 169172.
  • Saccone, C., Arrimonelli, M. & Sbisa, E. (1987) Structural elements highly preserved during the evolution of the D-Loop containing region in vertebrate mitochondrial DNA. Journal of Molecular Evolution, 26, 205211.
  • Saito, S., Tamura, K. & Aotsuka, T. (2005) Replication origin of mitochondrial DNA in insects. Genetics, 171, 16951705.
  • Shao, R., Kirkness, E.F. & Barker, S.C. (2009) The single mitochondrial chromosome typical of animals has evolved into 18 minichromosomes in the human body louse, Pediculus humanus. Genome Research, 19, 904912.
  • 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 & Evolution, 25, 24992509.
  • Sheffield, N.C., Hiatt, K.D., Valentine, M.C., Song, H. & Whiting, M.F. (2010) Mitochondrial genomics in Orthoptera using MOSAS. Mitochondrial DNA, 21, 87104.
  • 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, 545579.
  • Song, H., Buhay, J.E., Whiting, M.F. & Crandall, K.A. (2008) Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are co-amplified. Proceedings of the National Academy of Sciences of the United States of America, 105, 13 48613 491.
  • Song, H., Sheffield, N.C., Cameron, S.L., Miller, K.B. & Whiting, M.F. (2010) What happens when the phylogenetic assumptions are violated?: The effect of base compositional heterogeneity and among-site rate heterogeneity in beetle mitochondrial phylogenomics. Systematic Entomology, 35, 429448.
  • Stewart, J.B. & Beckenbach, A.T. (2009) Characterization of mature mitochondrial transcripts in Drosophila and the implications for the tRNA punctuation model in arthropods. Gene, 445, 4957.
  • Sun, Q.-Q., Sun, X.-Y., Wang, X.-C., Gai, Y.-H., Hu, J., Zhu, C.D. & Hao, J.-S. (2012) Complete sequence of the mitochondrial genome of the Japanese buff-tip moth, Phalera flavescens (Lepidoptera: Notodontidae). Genetics & Molecular Research, 11, 42134225.
  • Taanman, J.-W. (1999) The mitochondrial genome: structure, transcription, translation and replication. Biochimica et Biophysica Acta, 1410, 103123.
  • Tamura, K. & Aotsuka, T. (1988) Rapid isolation method of animal mitochondrial DNA by the alkaline lysis procedure. Biochemical Genetics, 26, 815819.
  • Timmermans, M.J.T.N. & Vogler, A.P. (2012) Phylogenetically informative rearrangements in mitochondrial genomes of Coleoptera, and monophyly of aquatic elateriform beetles (Dryopoidea). Molecular Phylogenetics & Evolution, 63, 299304.
  • Timmermans, M.J.T.N., Dodsworth, S., Culverwell, C.L. et al. (2010) Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics. Nucleic Acids Research, 38, e197.
  • Torres, T.T., Dolezal, M., Schlotterer, C. & Ottenwalder, B. (2009) Expression profiling of Drosophila mitochondrial genes via deep mRNA sequencing. Nucleic Acids Research, 37, 75097518.
  • Wan, X., Kim, M.I., Kim, M.J. & Kim, I. (2012) Complete mitochondrial genome of the free-living earwig, Challia fletcheri (Dermaptera: Pygidicranidae) and phylogeny of Polyneoptera. PLoS One, 7, e42056.
  • Wang, Y., Liu, X., Winterton, S.L. & Yang, D. (2012) The first mitochondrial genome for the fishfly subfamily Chauliodinae and implications for the higher phylogeny of Megaloptera. PLoS One, 7, e47302.
  • Wang, H.-L., Yang, J., Boykin, L.M., Zhao, Q.-Y., Wang, X.-W. & Liu, S.-S. (2013) The characteristics and expression profile of the mitochondrial genome for the Mediterranean species of Bemisia tabaci complex. BMC Genomics, 14, 401.
  • Wei, D.D., Shao, R., Yuan, M.-L., Dou, W., Barker, S.C. & Wang, J.-J. (2012) The multipartite mitochondrial genome of Liposcelis bostrychophila: insights into the evolution of mitochondrial genome in bilaterian animals. PLoS One, 7, e33973.
  • Williams, S.T., Foster, P.G. & Littlewood, D.T.J. (2014) The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny. Gene, 533, 3847.
  • Wolff, J.N., Shearman, D.C.A., Brooks, R.C. & Ballard, J.W.O. (2012) Selective enrichment and sequencing of whole mitochondrial genomes in the presence of nuclear encoded mitochondrial pseudogenes (Numts). PLoS One, 7, e37142.
  • Wyman, S.K., Jensen, R.K. & Boore, J.L. (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 20, 32523255.
  • Yamauchi, M.M., Miya, M. & Nishida, M. (2004) Use of a PCR-based approach for sequencing whole mitochondrial genomes of insects: two examples (cockroach and dragonfly) based on the method developed for decapod crustaceans. Insect Molecular Biology, 13, 435442.
  • Yin, J., Hong, G.-Y., Wang, A.-M., Cao, Y.-Z. & Wei, Z.-J. (2010) Mitochondrial genome of the cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) and comparison with other Lepidoptera. Mitochondrial DNA, 21, 160169.
  • Yukuhiro, K., Sezutsu, H., Itoh, H., Shimizu, K. & Banno, Y. (2002) Significant levels of sequence divergence and gene rearrangements have occurred between the mitochondrial genomes of the wild mulberry silkmoth, Bombyx mandarina, and its close relative, the domesticated silkmoth, Bombyx mori. Molecular Biology & Evolution, 19, 13851389.
  • Zhang, D.X. & Hewitt, G.M. (1997) Insect mitochondrial control region: a review of its structure, evolution and usefulness in evolutionary studies. Biochemical Systematics & Ecology, 25, 99120.
  • Zhao, J.-L., Zhang, Y.-Y., Luo, A.-R., Jiang, G.-F., Cameron, S.L. & Zhu, C.-D. (2011) The complete mitochondrial genome of Spilonota lechriaspis Meyrick (Lepidoptera: Tortricidae). Molecular Biology Reports, 38, 37573764.
  • Zhao, J., Winterton, S.L. & Liu, Z. (2013a) Ancestral gene organization in the mitochondrial genome of Thyridosmylus langii (McLachlan, 1970) (Neuroptera: Osmylidae) and implications for lacewing evolution. PLoS One, 8, e62943.
  • Zhao, F., Huang, D.-Y., Sun, X.-Y., Shi, Q.-H., Hao, J.-S., Zhang, L.-L. & Yang, Q. (2013b) The first mitochondrial genome for the butterfly family Riodinidae (Abisara fylloides) and its systematic implications. Zoological Research, 34, E109E119.
  • Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research, 31, 34063415.