Molecular evolution and phylogenetic utility of the internal transcribed spacer 2 (ITS2) in calyptratae (Diptera: Brachycera)

Journal of Molecular Evolution

Volumn 67, Issue 5, 2008, Pages 448-464

  Song, Zhong Kui ^a,b   Wang, Xun Zhang ^b   Liang, Ge Qiu ^b  

^a SOUTHWEST FORESTRY UNIVERSITY   (China)

^b SUN YAT SEN UNIVERSITY   (China)

Author keywords

Calyptratae; Internal transcribed spacer 2; Phylogeny; Secondary structure

Indexed keywords

INTERNAL TRANSCRIBED SPACER 2;

ARTICLE; CALYPTRATAE; CONTROLLED STUDY; FLY; GENE SEQUENCE; INTRASPECIFIC VARIATION; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS; TANDEM REPEAT;

ALGORITHMS; ANIMALS; BASE SEQUENCE; BAYES THEOREM; CONSERVED SEQUENCE; DIPTERA; DNA, RIBOSOMAL SPACER; EVOLUTION, MOLECULAR; GENETIC SPECIATION; INTERSPERSED REPETITIVE SEQUENCES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, GENETIC; SEQUENCE ALIGNMENT; TANDEM REPEAT SEQUENCES;

BRACHYCERA; CALYPTRATAE; DIPTERA;

EID: 55949135461     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-008-9144-y     Document Type: Article

References (57)

1. BG Baldwin MJ Sanderson JM Porter MF Wo-Jciechowski CS Campbell MJ Donoghue 1995 The ITS regions of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny Ann Mo Bot Gard 82 241 217
2. NW Beebe JT Ellis RD Cooper A Saul 1999 DNA sequence analysis of the ribosomal DNA ITS2 region for the Anopheles punctulatus group of mosquitoes Insect Mol Biol 8 381 390
3. MV Bernasconi C Valsangiacomo JC Piffaretti PI Ward 2000 Phylogenetic relationships among Muscoidea (Diptera: Calyptratae) based on mitochondrial DNA sequences Insect Mol Biol 9 67 74
4. ES Buckler IV A Ippolito TP Holtsford 1997 The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications Genetics 145 821 832
5. AW Coleman 2003 ITS2 is a double-edged tool for eukaryote evolutionary comparisons Trends Genet 19 370 375
6. AW Coleman 2007 Pan-eukaryote ITS2 homologies revealed by RNA secondary structure Nucleic Acids Res 35 3322 3329
7. AW Coleman VD Vacquier 2002 Exploring the phylogenetic utility of ITS sequences for animals: a test case for abalone (Haliotis) J Mol Evol 54 246 257
8. CA Côte CL Greer BA Peculis 2002 Dynamic conformational model for the role of ITS2 in pre-rRNA processing in yeast RNA 8 786 797
9. GN Fritz J Conn A Cockburn J Seawright 1994 Sequence analysis of the ribosomal DNA internal transcribed spacer 2 from populations of Anopheles nuneztovari (Diptera: Culicidae) Mol Biol Evol 11 406 416
10. RB Gasser XQ Zhu I Beveridge N Chilton 2001 Mutation scanning analysis of sequence heterogeneity in the second internal transcribed spacer (rDNA) within some members of the Hypodontus macropi (Nematoda: Strongyloidea) complex Electrophoresis 22 1076 1085
11. Gerbi SA (1985) Evolution of ribosomal DNA. In: Macintype RJ (ed) Molecular evolutionary genetics. Plenum, New York, NY, pp 419-517
12. Gilbert DG (1992) loopDloop, a Macintosh program for visualizing RNA secondary structure. Available at: Anonymous ftp to ftp://iubio.bio.indiana.edu/ molbio/loopdloop/java/.
13. LR Goertzen JJ Cannone RR Gutell RK Jansen 2003 ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny Mol Phylogenet Evol 29 216 234
14. M Gottschling J Plötner 2004 Secondary structure models of the nuclear internal transcribed spacer regions and 5.8S rRNA in Calciodinelloideae (Peridiniaceae) and other dinoflagellates Nucleic Acids Res 32 307 315
15. J Gómez-Zurita C Juan E Petitpierre 2000 Sequence, secondary structure and phylogenetic analyses of the ribosomal internal transcribed spacer 2 (ITS2) in the Timarcha leaf beetles (Coleoptera: Chrysomelidae) Insect Mol Biol 9 591 604
16. RR Gutell N Larson CR Woese 1994 Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective Microbiol Rev 58 10 26
17. MA Hershkovitz LA Lewis 1996 Deep-level diagnostic value of rDNA-ITS region Mol Biol Evol 13 1276 1295
18. MA Hershkovitz EA Zimmer 1996 Conservation patterns in angiosperm rDNA ITS2 sequences Nucleic Acids Res 24 2857 2867
19. O Hlinka A Murrell SC Barker 2002 Evolution of the secondary structure of the rRNA internal transcribed spacer 2 (ITS2) in hard ticks (Ixodidae, Arthropoda) Heredity 88 275 279
20. YT Hung CA Chen WJ Wu CC Lin CJ Shih 2004 Phylogenetic utility of the ribosomal internal transcribed spacer 2 in Strumigenys spp. (Hymenoptera: Formicidae) Mol Phylogenet Evol 32 407 415
21. H Innan W Stephan 2001 Selection intensity against deleterious mutations in RNA secondary structures and rate of compensatory nucleotide substitutions Genetics 159 389 399
22. J Jobst K King V Hemleben 1998 Molecular evolution of the internal transcribed spacers (ITS1 and ITS2) and phylogenetic relationships among species of the Family Cucurbitaceae Mol Phylogenet Evol 9 204 219
23. N Joseph E Krauskopf MI Vera B Michot 1999 Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast Nucleic Acids Res 27 4533 4540
24. M Kimura 1985 The role of compensatory neutral mutations in molecular evolution J Genet 64 7 19
25. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis. Arizona State University, Tempe, AZ
26. WR Kuperus W Chapco 1994 Usefulness of internal transcribed spacer regions of ribosomal DNA in Melanopline (Orthoptera: Acrididae) systematics Annu Entomol Soc Am 87 751 754
27. JC Mai AW Coleman 1997 The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants J Mol Evol 44 258 271
28. DH Mathews J Sabina M Zuker DH Turner 1999 Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure J Mol Biol 288 911 940
29. McAlpine JF (1989) Phylogeny and classification of the Muscomorpha. In: McAlpine JF, Peterson BV, Shewell GE, Teskey HJ, Vockeroth JR, Wood DM (eds) Monograph 32, vol. 3: manual of nearctic diptera. Research Branch Agriculture Canada, Minister of Supply and Services Canada, pp 1397-1518
30. JAT Morgan D Blair 1998 Trematode and monogenean rRNA ITS2 secondary structures support a four-domain model J Mol Evol 47 406 419
31. TD Muccio M Marinucci L Frusteri M Maroli B Pesson M Gramiccia 2000 Phylogenetic analysis of Phlebotomus species belonging to the subgenus Larroussius (Diptera, Psychodidae) by ITS2 rDNA sequences Insect Biochem Mol Biol 30 387 393
32. X Nirmala V Hypsa M Zurovec 2001 Molecular phylogeny of Calyptratae (Diptera: Brachycera): The evolution of 18S and 16S ribosomal rDNAs in higher dipterans and their use in phylogenetic inference Insect Mol Biol 10 475 485
33. T Pape 1992 Phylogeny of the Tachinidae family group (Diptera: Calyptratae) Tijdschr Entomol 135 43 86
34. K Rognes 1991 Blowflies (Diptera, Calliphoridae) of Fennoscandia and Denmark Fauna Entomol Scandinavica 24 1 272
35. K Rognes 1997 The Calliphoridae (blowflies) (Diptera: Oestroidea) are not a monophyletic group Cladistics 13 27 66
36. F Rousset M Pélandakis M Solignac 1991 Evolution of compensatory substitutions through a G • U intermediate state in Drosophila rRNA Proc Natl Acad Sci U S A 88 10032 10036
37. NJ Savill DC Hoyle PG Higgs 2001 RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods Genetics 157 399 411
38. C Schlötterer MT Hauser A von Haeseler D Tautz 1994 Comparative evolutionary analysis of rDNA ITS regions in Drosophila Mol Biol Evol 11 513 522
39. J Schultz S Maisel D Gerlach T Muller M Wolf 2005 A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota RNA 11 361 364
40. T Shimada 1992 Distribution of split 5.8S ribosomal RNA in Diptera Insect Mol Biol 1 45 49
41. SM Smith P Fuerst KL Mecklenburg 1996 Mitochondrial DNA sequences of cytochrome oxidase II from Calliphora erythrocephala: Evolution of blowflies (Diptera: Calliphoridae) Ann Entomol Soc Am 89 28 36
42. JR Stevens 2003 The evolution of myiasis in blowflies (Calliphoridae) Int J Parasitol 33 1105 1113
43. Swofford DL (2002) PAUP*phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sinauer Associates, Sunderland, MA
44. D Tautz C Tautz D Webb GA Dover 1987 Evolutionary divergence of promoters and spacers in the rDNA family of four Drosophila species J Mol Biol 195 525 542
45. CAFM van der Sande M Kwa RW van Nues H van Heerikhuizen HA Raué RJ Planta 1992 Functional analysis of internal transcribed spacer 2 of Saccharomyces cerevisiae ribosomal DNA J Mol Biol 223 899 910
46. RW van Nues JMJ Rientjes CAFM van der Sande SF Zerp C Sluiter J Venema RJ Planta HA Raué 1994 Separate structural elements within internal transcribed spacer 1 of Saccharomyces cerevisiae precursor ribosomal RNA direct the formation of 17S and 26SrRNA Nucleic Acids Res 22 912 919
47. RW van Nues JMJ Rientjes SA Morré E Mollee RJ Planta J Venema HA Raué 1995 Evolutionarily conserved structural elements are critical for processing of internal transcribed spacer 2 from Saccharomyces cerevisiae precursor ribosomal RNA J Mol Biol 250 24 36
48. JHG von der Schulenburg JM Hancock A Pagnamenta JJ Sloggett MEN Majerus GDD Hurst 2001 Extreme length and length variation in the first ribosomal internal transcribed spacer of ladybird beetles (Coleoptera: Coccinellidae) Mol Biol Evol 18 648 660
49. CR Vossbrinck S Friedman 1989 A 28 s ribosomal RNA phylogeny of certain cyclorrhaphous Diptera based upon a hypervariable region Syst Entomol 14 417 431
50. DM Wesson CH Porter FH Collins 1992 Sequence and secondary structure comparisons of ITS rDNA in mosquitoes (Diptera: Culicidae) Mol Phylogenet Evol 1 253 269
51. M Wolf M Achtziger J Schultz T Dandekar T Müller 2005 Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures RNA 11 1616 1623
52. H Won SS Renner 2005 The internal transcribed spacer of nuclear ribosomal DNA in the gymnosperm Gnetum Mol Phylogenet Evol 36 581 597
53. G Wörheide SA Nichols J Goldberg 2004 Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies Mol Phylogenet Evol 33 816 830
54. DK Yeates BM Wiegmann 1999 Congruence and controversy: towards a higher-level phylogeny of Diptera Ann Rev Entomol 44 397 428
55. I Young AW Coleman 2004 The advantages of the ITS2 region of the nuclear rDNA cistron for analysis of phylogenetic relationships of insects: a Drosophila example Mol Phylogenet Evol 30 236 242
56. M Zuker 2003 Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res 31 3406 3415
57. Zuker M, Mathews DH, Turner DH (1999) Algorithms and thermodynamics for RNA secondary-structure prediction: a practical guide. In: Barciszewski J, Clark BFC (eds) RNA biochemistry and biotechnology. NATO ASI Series. Kluwer Academic, Dordrecht, The Netherlands, pp 11-43