Mitochondrial genomes of two Sinochlora species (Orthoptera): Novel genome rearrangements and recognition sequence of replication origin

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Liu, Chunxiang ^a   Chang, Jia ^b   Ma, Chuan ^c   Li, Ling ^c   Zhou, Shanyi ^b  

^a INSTITUTE OF ZOOLOGY   (China)

^b GUANGXI NORMAL UNIVERSITY   (China)

^c INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

Genome rearrangements; Mitochondrial genome; Recognition sequence; Sinochlora longifissa; Sinochlora retrolateralis

Indexed keywords

MITOCHONDRIAL DNA; RIBOSOME RNA; TRANSFER RNA;

ARTICLE; CONTROLLED STUDY; DNA REPLICATION ORIGIN; DNA STRAND; GC RICH SEQUENCE; GENE; GENE DOSAGE; GENE ORDER; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC VARIABILITY; MITOCHONDRIAL GENETICS; MITOCHONDRIAL GENOME; MOLECULAR RECOGNITION; NAD1 GENE; NAD2 GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOPTERA; RNA GENE; RRNS GENE; SINOCHLORA LONGIFISSA; SINOCHLORA RETROLATERALIS; TANDEM REPEAT; TRNL GENE; TRNM GENE; TRNQ GENE; TRNS GENE; TRNW GENE;

ANIMALS; GENE REARRANGEMENT; GENOME, INSECT; GENOME, MITOCHONDRIAL; NUCLEIC ACID CONFORMATION; ORTHOPTERA; PHYLOGENY; REPLICATION ORIGIN; SEQUENCE ANALYSIS, DNA;

ACRIDOMORPHA; HEXAPODA; ORTHOPTERA; SINOCHLORA;

EID: 84873956834     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-114     Document Type: Article

References (60)

1. Boore JL. Animal mitochondrial genomes. Nucleic Acids Res 1999, 27:1767-1780. 10.1093/nar/27.8.1767, 148383, 10101183.
2. Gissi C, Iannelli F, Pesole G. Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity 2008, 101:301-320. 10.1038/hdy.2008.62, 18612321.
3. Eades D, Otte D, Cigliano M, Braun H. Orthoptera Species File Online 2013, Version 2.0/4.1. http://Orthoptera.SpeciesFile.org.
4. Sheffield NC, Hiatt KD, Valentine MC, Song H, Whiting MF. Mitochondrial genomics in Orthoptera using MOSAS. Mitochondr DNA 2010, 21:87-104.
5. Flook P, Rowell H, Gellissen G. Homoplastic rearrangements of insect mitochondrial tRNA genes. Naturwissenschaften 1995, 82:336-337.
6. Ye W, Dang JP, Xie LD, Huang Y. Complete mitochondrial genome of Teleogryllus emma (Orthoptera: Gryllidae) with a new gene order in Orthoptera. Zool Res 2008, 29:236-244.
7. Ma C, Yang P, Jiang F, Chapuis MP, Shali Y, Sword GA, Kang L. Mitochondrial genomes reveal the global phylogeography and dispersal routes of the migratory locust. Mol Ecol 2012, 21:4344-4358. 10.1111/j.1365-294X.2012.05684.x, 22738353.
8. Saito S, Tamura K, Aotsuka T. Replication origin of mitochondrial DNA in insects. Genetics 2005, 171:1695-1705. 10.1534/genetics.105.046243, 1456096, 16118189.
9. Zhang DX, Hewitt GM. Insect mitochondrial control region: A review of its structure, evolution and usefulness in evolutionary studies. Biochem Syst Ecol 1997, 25:99-120.
10. Zhou Z, Huang Y, Shi F, Ye H. The complete mitochondrial genome of Deracantha onos (Orthoptera: Bradyporidae). Mol Biol Rep 2009, 36:7-12. 10.1007/s11033-007-9145-8, 17891510.
11. Fenn JD, Cameron SL, Whiting MF. The complete mitochondrial genome sequence of the Mormon cricket (Anabrus simplex: Tettigoniidae: Orthoptera) and an analysis of control region variability. Insect Mol Biol 2007, 16:239-252. 10.1111/j.1365-2583.2006.00721.x, 17316330.
12. Tinkham ER. Sinochlora, a new Tettigoniid genus from China with description of five new species (Orthoptera). Trans Amer Entomol Soc 1945, 70:235-246.
13. Liu CX, Kang L. Revision of the genus Sinochlora Tinkham (Orthoptera: Tettigoniidae, Phaneropterinae). J Nat Hist 2007, 41:1313-1341.
14. Wang G, Lu RS, Shi FM. Remarks on the genus Sinochlora Tinkham (Orthoptera: Tettigoniidae, Phaneropterinae). Zootaxa 2012, 3526:1-16.
15. Kimura M. The neutral theory of molecular evolution 1983, Cambridge: Cambridge University Press.
16. Bulmer M. The selection-mutation-drift theory of synonymous codon usage. Genetics 1991, 129:897-907. 1204756, 1752426.
17. Hassanin A, Leger N, Deutsch J. Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa, and consequences for phylogenetic inferences. Syst Biol 2005, 54:277-298. 10.1080/10635150590947843, 16021696.
18. Clary DO, Wolstenholme DR. The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. J Mol Evol 1985, 22:252-271. 10.1007/BF02099755, 3001325.
19. Satta Y, Ishiwa H, Chigusa SI. Analysis of nucleotide substitutions of mitochondrial DNAs in Drosophila melanogaster and its sibling species. Mol Biol Evol 1987, 4:638-650.
20. Stewart JB, Beckenbach AT. Characterization of mature mitochondrial transcripts in Drosophila, and the implications for the tRNA punctuation model in arthropods. Gene 2009, 445:49-57. 10.1016/j.gene.2009.06.006, 19540318.
21. Beard CB, Mills Hamm D, Collins FH. The mitochondrial genome of the mosquito Anopheles gambiae: DNA sequence, genome organization, and comparisons with mitochondrial sequences of other insects. Insect Mol Biol 1993, 2:103-124. 10.1111/j.1365-2583.1993.tb00131.x, 9087549.
22. Bae JS, Kim I, Sohn HD, Jin BR. The mitochondrial genome of the firefly, Pyrocoelia rufa: complete DNA sequence, genome organization, and phylogenetic analysis with other insects. Mol Phylogenet Evol 2004, 32:978-985. 10.1016/j.ympev.2004.03.009, 15288070.
23. Cameron SL, Johnson KP, Whiting MF. The mitochondrial genome of the screamer louse Bothriometopus (Phthiraptera: Ischnocera): Effects of extensive gene rearrangements on the evolution of the genome. J Mol Evol 2007, 65:589-604. 10.1007/s00239-007-9042-8, 17925995.
24. Ojala D, Montoya J, Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature 1981, 290:470-474. 10.1038/290470a0, 7219536.
25. Lessinger AC, Junqueira ACM, Conte FF, Espin A. Analysis of a conserved duplicated tRNA gene in the mitochondrial genome of blowflies. Gene 2004, 339:1-6.
26. Nelson LA, Lambkin CL, Batterham P, Wallman JF, Dowton M, Whiting MF, Yeates DK, Cameron SL. Beyond barcoding: A mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae). Gene 2012, 511:131-142. 10.1016/j.gene.2012.09.103, 23043935.
27. Cameron SL, Barker SC, Whiting MF. Mitochondrial genomics and the new insect order Mantophasmatodea. Mol Phylogenet Evol 2006, 38:274-279. 10.1016/j.ympev.2005.09.020, 16321547.
28. Shao RF, Barker SC. The highly rearranged mitochondrial genome of the plague thrips, Thrips imaginis (Insecta: thysanoptera): Convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes. Mol Biol Evol 2003, 20:362-370. 10.1093/molbev/msg045, 12644556.
29. Cameron SL, Yoshizawa K, Mizukoshi A, Whiting MF, Johnson KP. Mitochondrial genome deletions and minicircles are common in lice (Insecta: Phthiraptera). BMC Genomics 2011, 12:394. 10.1186/1471-2164-12-394, 3199782, 21813020.
30. Nardi F, Carapelli A, Fanciulli PP, Dallai R, Frati F. The complete mitochondrial DNA sequence of the basal Hexapod Tetrodontophora bielanensis: Evidence for heteroplasmy and tRNA translocations. Mol Biol Evol 2001, 18:1293-1304. 10.1093/oxfordjournals.molbev.a003914, 11420368.
31. Navajas M, Le Conte Y, Solignac M, Cros-Arteil S, Cornuet JM. The complete sequence of the mitochondrial genome of the honeybee ectoparasite mite Varroa destructor (Acari: Mesostigmata). Mol Biol Evol 2002, 19:2313-2317. 10.1093/oxfordjournals.molbev.a004055, 12446822.
32. Shao RF, Barker SC, Mitani H, Aoki Y, Fukunaga M. Evolution of duplicate control regions in the mitochondrial genomes of Metazoa: A case study with Australasian Ixodes ticks. Mol Biol Evol 2005, 22:620-629.
33. Fenn JD, Song H, Cameron SL, Whiting MF. A preliminary mitochondrial genome phylogeny of Orthoptera (Insecta) and approaches to maximizing phylogenetic signal found within mitochondrial genome data. Mol Phylogenet Evol 2008, 49:59-68. 10.1016/j.ympev.2008.07.004, 18672078.
34. Boore JL. The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals. Comparative genomics, computational biology series 2000, 133-147. Netherlands: Dordrecht, Sankoff D, Nadeau J, 1.
35. Levinson G, Gutman GA. Slipped-strand mispairing: A major mechanism for DNA sequence evolution. Mol Biol Evol 1987, 4:203-221.
36. Broughton RE, Dowling TE. Length variation in mitochondrial DNA of the minnow Cyprinella spiloptera. Genetics 1994, 138:179-190. 1206129, 8001785.
37. Cameron SL, Lo N, Bourguignon T, Svenson GJ, Evans TA. A mitochondrial genome phylogeny of termites (Blattodea: Termitoidae): Robust support for interfamilial relationships and molecular synapomorphies define major clades. Mol Phylogenet Evol 2012, 65:163-173. 10.1016/j.ympev.2012.05.034, 22683563.
38. Cameron SL, Whiting MF. Mitochondrial genomic comparisons of the subterranean termites from the Genus Reticulitermes (Insecta: Isoptera: Rhinotermitidae). Genome 2007, 50:188-202. 10.1139/g06-148, 17546084.
39. Cameron SL, Whiting MF. 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 2008, 408:112-123. 10.1016/j.gene.2007.10.023, 18065166.
40. Sheffield NC, Song H, Cameron L, Whiting MF. A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles. Mol Biol Evol 2008, 25:2499-2509. 10.1093/molbev/msn198, 2568038, 18779259.
41. Roberti M, Bruni F, Polosa PL, Gadaleta MN, Cantatore P. The Drosophila termination factor DmTTF regulates in vivo mitochondrial transcription. Nucleic Acids Res 2006, 34:2109-2116. 10.1093/nar/gkl181, 1450328, 16648357.
42. Roberti M, Polosa PL, Bruni F, Musicco C, Gadaleta MN, Cantatore P. DmTTF, a novel mitochondrial transcription termination factor that recognises two sequences of Drosophila melanogaster mitochondrial DNA. Nucleic Acids Res 2003, 31:1597-1604. 10.1093/nar/gkg272, 152874, 12626700.
43. Dowton M, Cameron SL, Dowavic JI, Austin AD, Whiting MF. Characterization of 67 mitochondrial tRNA gene rearrangements in the Hymenoptera suggests that mitochondrial tRNA gene position is selectively neutral. Mol Biol Evol 2009, 26:1607-1617. 10.1093/molbev/msp072, 19359443.
44. Macey JR, Larson A, Ananjeva NB, Fang ZL, Papenfuss TJ. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol Biol Evol 1997, 14:91-104. 10.1093/oxfordjournals.molbev.a025706, 9000757.
45. Lavrov DV, Boore JL, Brown WM. Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: Duplication and nonrandom loss. Mol Biol Evol 2002, 19:163-169. 10.1093/oxfordjournals.molbev.a004068, 11801744.
46. Hixson JE, Wong TW, Clayton DA. Both the conserved stem-loop and divergent 5'-flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication. J Biol Chem 1986, 261:2384-2390.
47. Sheffield NC, Song H, Cameron SL, Whiting MF. Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics. Syst Biol 2009, 58:381-394. 10.1093/sysbio/syp037, 20525592.
48. Song H, Sheffield NC, Cameron SL, Miller KB, Whiting MF. When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics. Syst Entomol 2010, 35:429-448.
49. Ma C, Liu C, Yang P, Kang L. The complete mitochondrial genomes of two band-winged grasshoppers, Gastrimargus marmoratus and Oedaleus asiaticus. BMC Genomics 2009, 10:156. 10.1186/1471-2164-10-156, 2674460, 19361334.
50. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 1999, 27:573-580. 10.1093/nar/27.2.573, 148217, 9862982.
51. Lowe TM, Eddy SR. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25:955-964. 146525, 9023104.
52. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
53. Feijao PC, Neiva LS, de Azeredo-Espin AML, Lessinger AC. AMiGA: the arthropodan mitochondrial genomes accessible database. Bioinformatics 2006, 22:902-903. 10.1093/bioinformatics/btl021, 16446277.
54. Lobry JR. Properties of a general model of DNA evolution under no-strand-bias conditions. J Mol Evol 1995, 40:326-330. 10.1007/BF00163237, 7723059.
55. Stothard P. The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 2000, 28:1102-1104.
56. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31:3406-3415. 10.1093/nar/gkg595, 169194, 12824337.
57. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28:2731-2739. 10.1093/molbev/msr121, 3203626, 21546353.
58. Jukes TH, Cantor CR. Evolution of protein molecules. Mammalian protein metabolism 1969, 21-132. New York: Academic Press, Munro H.
59. Robinson M, Gouy M, Gautier C, Mouchiroud D. Sensitivity of the relative-rate test to taxonomic sampling. Mol Biol Evol 1998, 15:1091-1098. 10.1093/oxfordjournals.molbev.a026016, 9729873.
60. Robinson-Rechavi M, Huchon D. RRTree: Relative-Rate Tests between groups of sequences on a phylogenetic tree. Bioinformatics 2000, 16:296-297. 10.1093/bioinformatics/16.3.296, 10869026.