Complete mitochondrial genome of Gomphocerus sibiricus (Orthoptera: Acrididae) and comparative analysis in four Gomphocerinae mitogenomes

Zoological Science

Volumn 30, Issue 3, 2013, Pages 192-204

  Zhang, Hong Li ^a   Zhao, Ling ^b,c   Zheng, Zhe Min ^a   Huang, Yuan ^a  

^a SHAANXI NORMAL UNIVERSITY   (China)

^b XINJIANG AGRICULTURAL UNIVERSITY   (China)

^c MIANYANG NORMAL UNIVERSITY   (China)

Author keywords

comparative analyses; Gomphocerinae; Gomphocerus sibiricus; mitochondrial genome; Orthoptera; phylogenetic analyses

Indexed keywords

INSECT PROTEIN; RNA;

ANIMAL; ARTICLE; CHEMISTRY; GENE EXPRESSION REGULATION; GENETICS; GENOME; METABOLISM; MITOCHONDRION; NUCLEOTIDE SEQUENCE; ORTHOPTERA; PHYLOGENY; SPECIES DIFFERENCE;

ANIMALS; BASE SEQUENCE; GENE EXPRESSION REGULATION; GENOME, INSECT; INSECT PROTEINS; MITOCHONDRIA; ORTHOPTERA; PHYLOGENY; RNA; SPECIES SPECIFICITY;

EID: 84874953516     PISSN: 02890003     EISSN: None     Source Type: Journal    
DOI: 10.2108/zsj.30.192     Document Type: Article

References (70)

1. Abascal F, Zardoya R, Posada D (2009) Genetic code prediction for metazoan mitochondria with GenDecoder. Methods Mol Biol 537: 233-242
2. Abascal F, Zardoya R, Posada D (2012) The evolution of the mitochondrial genetic code in arthropods revisited. Mitochondr DNA 23(2): 84-91
3. Albu M, Min XJ, Golding GB, Hickey D (2009) Nucleotide substitution bias within the genus Drosophila affects the pattern of proteome evolution. Genome Biol Evol 1: 288-293
4. Asakawa S, Kumazawa Y, Araki T, Himeno H, Miura K, Watanabe K (1991) Strand specific nucleotide composition bias in Echinoderm and vertebrate mitochondrial genome. J Mol Evol 32: 511-520
5. Boore JL (2006) The use of genome-level characters for phylogenetic reconstruction. Trends Ecol Evol 21: 39-446
6. Boore JL, Lavrov DV, Brown WM (1998) Gene translocation links insects and crustaceans. Nature 392: 667-668
7. Buckley TR, Simon C, Flook PK, 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 Mol Biol 9: 565-580
8. Cameron SL, Lambkin CL, Barker SC, whiting MF (2007) A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationship over broad timescales with high precision. Syst Entomol 32: 40-59
9. Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, et al. (2002) The Comparative RNA Web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3(2): 1-31
10. Cheng KC, Cahill DS, Kasai H, Nishimura S, Loeb LA (1992) 8- Hydroxyguanine, an abundant form of oxidative DNA damage, causes G-T and A-C substitutions. J Biol Chem 267: 166- 172
11. Clayton DA (1982) Replication of animal mitochondrial DNA. Cell 28: 693-705
12. Corneli PS, Ward RH (2000) Mitochondrial genes and mammalian phylogenies: increasing the reliability of branch length estimation. Mol Biol Evol 17: 224-234
13. Dsouli N, Delsuc F, Michaux J, Stordeur ED, Couloux A, Veuille M, Duvallet G (2011) Phylogenetic analyses of mitochondrial and nuclear data in haematophagous flies support the paraphyly of the genus Stomoxys (Diptera: Muscidae). Infect Genet Evol 11: 663-670
14. Eades DC, Otte D (2010) Orthoptera species file 2.0/3.5 [accessed 26 January 2010]. Available from: http://orthoptera.speciesfile.org
15. Fernandez-Silva P, Enriquez JA, Montoya J (2003) Replication and transcription of mammalian mitochondrial DNA. Exp Physiol 88: 41-56
16. Fenn JD, Cameron SL, Whiting MF (2007) The complete mitochondrial genome sequence of the Mormon cricket (Anabrus simplex: Tettigoniidae: Orthoptera) and an analysis of control region variability. Insect Mol Biol 16: 239-252
17. Fenn JD, Song H, Cameron SL, Whiting MF (2008) A preliminary mitochondrial genome phylogeny of Orthoptera (Insecta) and approaches to maximizing phylogenetic signal found within mitochondrial genome data. Mol Phylogenet Evol 49(1): 59-68
18. Flook P, Rowell H, Gellissen G (1995a) Homoplastic rearrangements of insect mitochondrial transfer-RNA genes. Naturwissenschaften 82: 336-337
19. Flook PK, Rowell CHF, Gellissen G (1995b) The sequence, organization, and evolution of the Locusta migratoria mitochondrial genome. J Mol Evol 41: 928-941
20. Francino MP, Ochman H (1997) Strand asymmetries in DNA evolution. Trends Genet 13: 240-245
21. Gillespie JJ, Johnston JS, Cannone JJ, Gutell RR (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 retro-transposable elements. Insect Mol Biol 15: 657-686
22. Gissi C, Iannelli F, Pesole G (2008) Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity 101: 301-320
23. Gotzek D, Clarke J, Shoemaker D (2010) Mitochondrial genome evolution in fire ants (Hymenoptera: Formicidae). BMC Evol Biol 10(300): 1-13
24. Gutell RR, Larsen N, Woese CR (1994) Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev 58(1): 10-26
25. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp 41: 95-98
26. Hickson RE, Simon C, Cooper A, Spicer GS, Sullivan J, Penny D (1996) Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. Mol Biol Evol 13: 150-169
27. Kim I, Cha SY, Hwang JS, Lee SM, Sohn HD, Jin BR (2005) The complete nucleotide sequence and gene organization of the mitochondrial genome of the oriental mole cricket, Gryllotalpa orientalis (Orthoptera: Gryllotalpidae). Gene 353: 155-168
28. Kjer KM (1995) Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. Mol Phylogenet Evol 4: 314-330
29. Krzywinski J, Grushko OG, Besansky NJ (2006) Analysis of the complete mitochondrial DNA from Anopheles funestus: an improved dipteran mitochondrial genome annotation and a temporal dimension of mosquito evolution. Mol Phylogenet Evol 39: 417-423
30. Li H, Liu HY, Cao LM, Shi AM, Yang HL, Cai WZ (2012) The complete mitochondrial genome of the damsel bug Alloeorhynchus bakeri (Hemiptera: Nabidae). Int J Biol Sci 8(1): 93-107
31. Lin CP, Danforth BN (2004) How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets. Mol Phylogenet Evol 30: 686- 702
32. Liu N, Hu J, Huang Y (2006) Amplification of grasshoppers complete mitochondrial genomes using long PCR. Chin J Zool 41: 61-65
33. Liu N, Huang Y (2010) Complete Mitochondrial Genome Sequence of Acrida cinerea (Acrididae: Orthoptera) and Comparative Analysis of Mitochondrial Genomes in Orthoptera. Comp Funct Genom ID 319486, 16 pages
34. Liu Y, Huang Y (2008) Sequencing and analysis of complete mitochondrial genome of Chorthippus chinensis Tarb. Chinese Journal of Biochemistr 24: 329-335
35. Lowe TM, Eddy SR (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964
36. Ma C, Liu C, Yang P, Kang L (2009) The complete mitochondrial genomes of two band-winged grasshoppers, Gastrimargus marmoratus and Oedaleus asiaticus. BMC Genomics 10(156): 1-12
37. Montooth KL, Abt DN, Hofmann JW, Rand DM (2009) Comparative genomics of Drosophila mtDNA: novel features of conservation and change across functional domains and lineages. J Mol Evol 69: 94-114
38. Morlais I, Severson DW (2002) Complete mitochondrial DNA sequence and aminoacid analysis of the cytochrome coxidase subunit I (COI) from Aedesaegypti. DNA Seq 13: 123-127
39. Negrisolo E, Babbucci M, Patarnello T (2011) The mitochondrial genome of the ascalaphid owlfly Libelloides maius and comparative evolutionary mitochondriomics of neuropterid insects. BMC Genomics 12(221): 1-26
40. Neira-Oviedo M, Tsyganov-Bodounov A, Lycett GJ, Kokoza V, Raikhel AS, Krzywinski J (2011) The RNA-Seq approach to studying the expression of mosquito mitochondrial genes. Insect Mol Biol 20: 141-152
41. Perna NT, Kocher TD (1995) Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol 41: 353-358
42. Plazzi F, Ricci A, Passamonti M (2011) The mitochondrial genome of Bacillus stick insects (Phasmatodea) and the phylogeny of orthopteroid insects. Mol Phylogenet Evol 58: 304-316
43. Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817-818
44. Randall SK, Eritja R, Kaplan BE, Petruska J, Goodman MF (1987) Nucleotide insertion kinetics opposite abasic lesions in DNA. J Biol Chem 262: 6864-6870
45. Reyes A, Gissi C, Pesole G, Saccone C (1998) Asymmetrical Directional Mutation Pressure in the Mitochondrial Genome of Mammals. Mol Biol Evol 15(8): 957-966
46. Roberti M, Polosa PL, Bruni F, Musicco C, Gadaleta MN, Cantatore P (2003) DmTTF, a novel mitochondrial transcription terminating factor that recognises two sequences of Drosophila melanogaster mitochondrial DNA. Nucleic Acids Res 31: 1597- 1604
47. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572- 1574
48. Salvato P, Simonato M, Battisti A, Negrisolo E (2008) The complete mitochondrial genome of the bagshelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae). BMC Genomics 9(331): 1- 15
49. Sheffield NC, Hiatt KD, Valentine MC, Song H, Whiting MF (2010) Mitochondrial genomics in Orthoptera using MOSAS. Mitochondr DNA 21(3-4): 87-104
50. Simon C, Buckley TR, Frati F, Stewart JB, Beckenbach AT (2006) Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annu Rev Ecol Evol Syst 37: 545- 579
51. Soon V, Saarma U (2011) Mitochondrial phylogeny of the Chrysis ignita (Hymenoptera: Chrysididae) species group based on simultaneous Bayesian alignment and phylogeny reconstruction. Mol Phylogenet Evol 60: 13-20
52. Staden R, Beal KF, Bonfield JK (2000) The Staden package, 1998. Methods Mol Biol 132: 115-130
53. Stewart JB, Beckenbach AT (2009) Characterization of mature mitochondrial transcripts in Drosophila, and the implications for the tRNA punctuation model in arthropods. Gene 445: 49-57
54. Sun HM, Zheng ZM, Huang Y (2010) Sequence and phylogenetic analysis of complete mitochondrial DNA of two grasshopper species Gomphocerus rufus (Linnaeus, 1758) and Primnoa arctica (Zhang & Jin, 1985) (Orthoptera: Acridoidea). Mitochondr DNA 21: 115-131
55. Swofford DL (2001) PAUP: Phylogenetic analysis using parsimony (and other methods) 4.0 Beta. Sunderland, MA: Sinauer Associates
56. Taanman JW (1999) The mitochondrial genome: Structure, transcription, translation and replication. Biochim Biophys Acta Bioenerg 1410: 103-123
57. Talavera G, Vila R (2011) What is the phylogenetic signal limit from mitogenomes? The reconciliation between mitochondrial and nuclear data in the Insecta class phylogeny. BMC Evol Biol 11(315): 1-15
58. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24(8): 1596-1599
59. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by qualityanalysis tools. Nucleic Acids Res 25(24): 4876-4882
60. Torres TT, Dolezal M, Schlötterer C, Ottenwälder B (2009) Expression profiling of Drosophila mitochondrial genes via deep mRNA sequencing. Nucleic Acids Res 37: 7509-7518
61. Ugelvig LV, Vila R, Pierce NE, Nash DR (2011) A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. Mol Phylogenet Evol 61: 237-243
62. Xia KL (1958) Classification Summary of Grasshoppers in China, Science Press, Beijing, China
63. Xia KL (1994) Fauna Sinica Insecta Vol. 4. Science Press, Beijing, China
64. Yang F, Du YZ, Wang LP, Cao JM, Yu WW (2011) The complete mitochondrial genome of the leafminer Liriomyza sativae (Diptera: Agromyzidae): Great difference in the A+T-rich region compared to Liriomyza trifolii. Gene 485: 7-15
65. Yin H, Zhi YC, Jiang HD, Wang PX, Yin XC, Zhang DC (2011) The complete mitochondrial genome of Gomphocerus tibetanus Uvarov, 1935 (Orthoptera: Acrididae: Gomphocerinae). Gene doi:10.1016/j.gene.2011.12.020
66. Zhang DX, Szymura JM, Hewitt GM (1995) Evolution and structural conservation of the control region of insect mitochondrial DNA. J Mol Evol 40: 382-391
67. Zhang DX, Hewitt FM (1997) Insect mitochondrial control region: a review of its structure, evolution and usefulness in evolutionary studies. Biochem Syst Ecol 25: 99-120
68. Zhao L, Zheng ZM, Huang Y, Sun HM (2010) A Comparative Analysis of Mitochondrial Genomes in Orthoptera (Arthropoda: Insecta) and Genome Descriptions of Three Grasshopper Species. Zool Sci 27: 662-672
69. Zhou ZJ, Huang Y, Shi FM (2007) The mitochondrial genome of Ruspolia dubia (Orthoptera: Conocephalidae) contains a short A+T-rich region of 70bp in length. Genome 50: 855-866
70. Zhou ZJ, Ye HY, Huang Y, Shi FM (2010) The phylogeny of Orthoptera inferred from mtDNA and description of Elimaea cheni (Tettigoniidae: Phaneropterinae) mitogenome. J Genet Genomics 37: 315-324