The multipartite mitochondrial genome of liposcelis bostrychophila: Insights into the evolution of mitochondrial genomes in bilateral animals

PLoS ONE

Volumn 7, Issue 3, 2012, Pages

  Wei, Dan Dan ^a   Shao, Renfu ^b,c   Yuan, Ming Long ^a   Dou, Wei ^a   Barker, Stephen C ^b   Wang, Jin Jun ^a  

^a SOUTHWEST UNIVERSITY   (China)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c UNIVERSITY OF THE SUNSHINE COAST   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CHROMOSOME SIZE; CONTROLLED STUDY; DNA EXTRACTION; GENE AMPLIFICATION; GENE SEQUENCE; LIPOSCELIS BOSTRYCHOPHILA; LOUSE; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ANALYSIS;

ANIMALS; BASE COMPOSITION; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENE ORDER; GENOME, MITOCHONDRIAL; INSECTS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA, TRANSFER; SEQUENCE ANALYSIS, DNA;

ANIMALIA; ISCHNOCERA; LIPOSCELIDAE; LIPOSCELIS; LIPOSCELIS BOSTRYCHOPHILA; PHTHIRAPTERA; PSOCOPTERA;

EID: 84859143923     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0033973     Document Type: Article

References (67)

1. Boore JL, (1999) Animal mitochondrial genomes. Nucleic Acids Res 27: 1767-1780.
2. Watanabe KI, Bessho Y, Kawasaki M, Hori H, (1999) Mitochondrial genes are found on minicircle DNA molecules in the mesozoan animal Dicyema. J Mol Biol 286: 645-650.
3. Armstrong MR, Blok VC, Phillips MS, (2000) A multipartite mitochondrial genome in the potato cyst nematode Globodera pallida. Genetics 154: 181-192.
4. Gibson T, Blok VC, Dowton M, (2007) Sequence and characterization of six mitochondrial subgenomes from Globodera rostochiensis: multipartite structure is conserved among close nematode relatives. J Mol Evol 65: 308-315.
5. Suga K, Welch DBM, Tanaka Y, Sakakura Y, Hagiwarak A, (2008) Two circular chromosomes of unequal copy number make up the mitochondrial genome of the rotifer Brachionus plicatilis. Mol Biol Evol 25: 1129-1137.
6. Shao R, Kirkness EF, Barker SC, (2009) The single mitochondrial chromosome typical of animals has evolved into 18 minichromosomes in the human body louse, Pediculus humanus. Genome Res 19: 904-912.
7. Cameron SL, Yoshizawa K, Mizukoshi A, Whiting MF, Johnson KP, (2011) Mitochondrial genome deletions and minicircles are common in lice (Insecta: Phthiraptera). BMC Genomics 12: 394.
8. Awata H, Noto T, Endoh H, (2005) Differentiation of somatic mitochondria and the structural changes in mtDNA during development of the dicyemid Dicyema japonicum (Mesozoa). Mol Genet Genomics 273: 441-449.
9. Sugiyama Y, Watase Y, Nagase M, Makita N, Yagura S, et al. (2005) The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants. Mol Genet Genomics 272: 603-615.
10. Burger G, Lang BF, (2003) Parallels in genome evolution in mitochondria and bacterial symbionts. IUBMB Life 55: 205-212.
11. Voigt O, Erpenbeck D, Wörheide G, (2008) A fragmented metazoan organellar genome: the two mitochondrial chromosomes of Hydra magnipapillata. BMC Genomics 9: 350.
12. Fan J, Lee RW, (2002) Mitochondrial genome of the colorless green alga Polytomella parva: two linear DNA molecules with homologous inverted repeat termini. Mol Biol Evol 19: 999-1007.
13. Nosek J, Tomaska L, Fukuhara H, Suyama Y, Kovac L, (1998) Linear mitochondrial genomes: 30 years down the line. Trends Genet 14: 184-188.
14. Marande W, Lukeš J, Burger G, (2005) Unique mitochondrial genome structure in diplonemids, the sister group of kinetoplastids. Eukaryot Cell 4: 1137-1146.
15. Burger G, Forget L, Zhu Y, Gray MW, Lang BF, (2003) Unique mitochondrial genome architecture in unicellular relatives of animals. Proc Natl Acad Sci USA 100: 892-897.
16. Smith DR, Kayal E, Yanagihara AA, Collins AG, Pirro S, et al. (2011) First complete mitochondrial genome sequence from a box jellyfish reveals a highly fragmented, linear architecture and insights into telomere evolution. Genome Biol Evol doi:10.1093/gbe/evr1127.
17. Marande W, Burger G, (2007) Mitochondrial DNA as a genomic jigsaw puzzle. Science 318: 415.
18. Rand DM, (2009) 'Why genomes in pieces?' revisited: Sucking lice do their own thing in mtDNA circle game. Genome Res 19: 700-702.
19. Burger G, Gray MW, Lang BF, (2003) Mitochondrial genomes: anything goes. Trends Genet 19: 709-716.
20. Fauron C, Casper M, Gao Y, Moore B, (1995) The maize mitochondrial genome: dynamic, yet functional. Trends Genet 11: 228-235.
21. Melov S, Lithgow GJ, Fischer DR, Tedesco PM, Johnson TE, (1995) Increased frequency of deletions in the mitochondrial genome with age of Caenorhabditis elegans. Nucleic Acids Res 23: 1419-1425.
22. Johnson KP, Yoshizawa K, Smith VS, (2004) Multiple origins of parasitism in lice. Proc R Soc Lond B 271: 1771-1776.
23. Yoshizawa K, Johnson KP, (2010) How stable is the "Polyphyly of Lice" hypothesis (Insecta: Psocodea)?: A comparison of phylogenetic signal in multiple genes. Mol Phylogenet Evol 55: 939-951.
24. Lyal CHC, (1985) Phylogeny and classification of the Psocodea, with particular reference to the lice (Psocodea: Phthiraptera). Syst Entomol 10: 145-165.
25. Grimaldi D, Engel MS, (2006) Fossil Liposcelididae and the lice ages (Insecta: Psocodea). Proc R Soc B 273: 625-633.
26. Murrell A, Barker SC, (2005) Multiple origins of parasitism in lice: phylogenetic analysis of SSU rDNA indicates that the Phthiraptera and Psocoptera are not monophyletic. Parasitol Res 97: 274-280.
27. Yoshizawa K, Johnson KP, (2003) Phylogenetic position of Phthiraptera (Insecta: Paraneoptera) and elevated rate of evolution in mitochondrial 12S and 16S rDNA. Mol Phylogenet Evol 29: 102-114.
28. Kim MJ, Kang AR, Jeong HC, Kim KG, Kim I, (2011) Reconstructing intraordinal relationships in Lepidoptera using mitochondrial genome data with the description of two newly sequenced lycaenids, Spindasis takanonis and Protantigius superans (Lepidoptera: Lycaenidae). Mol Phylogenet Evol 61: 436-445.
29. Cameron SL, Lambkin CL, Barker SC, Whiting MF, (2007) A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision. Syst Entomol 32: 40-59.
30. Wei SJ, Shi M, Sharkey MJ, Achterberg CV, Chen XX, (2010) Comparative mitogenomics of Braconidae (Insecta: Hymenoptera) and the phylogenetic utility of mitochondrial genomes with special reference to Holometabolous insects. BMC Genomics 11: 371.
31. Shao R, Dowton M, Murrell A, Barker SC, (2003) Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects. Mol Biol Evol 20: 1612-1619.
32. Li FS, (2002) Psocoptera of China Beijing Science press pp. 77-79.
33. Wei DD, Yuan ML, Wang ZY, Wang D, Wang BJ, et al. (2011) Sequence analysis of the ribosomal internal transcribed spacers region in psocids (Psocoptera: Liposcelididae) for phylogenetic inference and species discrimination. J Econ Entomol 104: 1720-1729.
34. Milligan BG, (1998) Total DNA isolation. In: Hoelzel AR, editors. Molecular Genetic Analysis of Population: A Practical Approach, 2nd Edition Oxford, New York, Tokyo Oxford University Press pp. 29-64.
35. Simon C, Frati F, Beckenbach A, Crespi B, Liu H, et al. (1994) Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann Entomol Soc Am 87: 651-701.
36. Hopp TP, Woods KR, (1981) Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci USA 78: 3824-3828.
37. 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.
38. Laslett D, Canbäck B, (2008) ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 24: 172-175.
39. Mathews DH, (2005) Predicting a set of minimal free energy RNA secondary structures common to two sequences. Bioinformatics 21: 2246-2253.
40. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using Maximum Likelihood, evolutionary distance, and Maximum Parsimony methods. Mol Biol Evol 28: 2731-2739.
41. Jiang HB, Liu YH, Tang PA, Zhou AW, Wang JJ, (2010) Validation of endogenous reference genes for insecticide-induced and developmental expression profiling of Liposcelis bostrychophila (Psocoptera: Liposcelididae). Mol Biol Rep 37: 1019-1029.
42. Pfaffl MW, (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29: e45.
43. Cameron SL, Johnson KP, Whiting MF, (2007) The mitochondrial genome of the screamer louse Bothriometopus (Phthiraptera: Ischnocera): effects of extensive gene rearrangements on the evolution of the genome. J Mol Evol 65: 589-604.
44. Covacin C, Shao R, Cameron S, Barker SC, (2006) Extraordinary number of gene rearrangements in the mitochondrial genomes of lice (Phthiraptera: Insecta). Insect Mol Biol 15: 63-68.
45. Shao R, Campbell NJH, Barker SC, (2001) Numerous gene rearrangements in the mitochondrial genome of the wallaby louse, Heterodoxus macropus (Phthiraptera). Mol Biol Evol 18: 858-865.
46. Thao ML, Baumann L, Baumann P, (2004) Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha). BMC Evol Biol 4: 25.
47. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG, (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24: 4876-4882.
48. Castresana J, (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17: 540-552.
49. Xia X, Xie Z, (2001) DAMBE: Software package for data analysis in molecular biology and evolution. J Hered 92: 371-373.
50. Posada D, (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25: 1253-1256.
51. Ronquist F, Huelsenbeck JP, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
52. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, et al. (2010) New algorithms and methods to estimate Maximum-Likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321.
53. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP, (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310-2314.
54. Lang BF, Gray MW, Burger G, (1999) Mitochondrial genome evolution and the origin of eukaryotes. Annu Rev Genet 33: 351-397.
55. Lavrov DV, (2007) Key transitions in animal evolution: a mitochondrial DNA perspective. Integr Comp Biol 47: 734-743.
56. Helfenbein KG, Fourcade HM, Vanjani RG, Boore JL, (2004) The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister group to protostomes. Proc Natl Acad Sci USA 101: 10639-10643.
57. Domes K, Maraun M, Scheu S, Cameron SL, (2008) The complete mitochondrial genome of the sexual oribatid mite Steganacarus magnus: genome rearrangements and loss of tRNAs. BMC Genomics 9: 532.
58. Yuan ML, Wei DD, Wang BJ, Dou W, Wang JJ, (2010) The complete mitochondrial genome of the citrus red mite Panonychus citri (Acari: Tetranychidae): high genome rearrangement and extremely truncated tRNAs. BMC Genomics 11: 597.
59. Hayashi JL, Ohta S, Kikuchi A, Takemitsu M, Goto Y, et al. (1991) Introduction of disease-related mitochondrial DNA deletions into HeLa cells lacking mitochondrial DNA results in mitochondrial dysfunction. Proc Natl Acad Sci USA 88: 10614-10618.
60. Kajander OA, Rovio AT, Majamaa K, Poulton J, Spelbrink JN, et al. (2000) Human mtDNA sublimons resemble rearranged mitochondrial genoms found in pathological states. Hum Mol Genet 9: 2821-2835.
61. Melov S, Hinerfeld D, Esposito L, Wallace DC, (1997) Multi-organ characterization of mitochondrial genomic rearrangements in ad libitum and caloric restricted mice show striking somatic mitochondrial DNA rearrangements with age. Nucleic Acids Res 25: 974-982.
62. Palmer JD, Shields CR, (1984) Tripartite structure of the Brassica campestris mitochondrial genome. Nature 307: 437-440.
63. Liu B, Liu Y, Motyka SA, Agbo EEC, Englund PT, (2005) Fellowship of the rings: the replication of kinetoplast DNA. Trends Parasitol 21: 363-369.
64. Klingbeil MM, Drew ME, Yanan Liu, Morris JC, Motyka SA, et al. (2001) Unlocking the secrets of trypanosome kinetoplast DNA network replication. Protist 152: 255-262.
65. Bogenhagen DF, (2011) Mitochondrial DNA nucleoid structure. Biochim Biophys Acta doi:10.1016/j.bbagrm.2011.1011.1005.
66. Price RD, Hellenthal RA, Palma RL, (2003) World checklist of chewing lice with host associations and keys to families and genera. In: Price RD, Hellenthal RA, Palma RL, Johnson KP, Clayton DH, editors. The Chewing Lice: World Checklist and Biological Overview Illinois Natural History Survey Special Publication pp. 1-448.
67. Johnson KP, Whiting MF, (2002) Multiple genes and the monophyly of Ischnocera. Mol Phylogenet Evol 22: 101-110.