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Volumn 23, Issue 2, 2006, Pages 268-278

Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles)

Author keywords

Expressed sequence tag; Gene ontology; Phylogenomics; Shallow genomics

Indexed keywords

ACTIN; CHYMOTRYPSIN; MITOCHONDRIAL DNA; RIBOSOME PROTEIN; TROPONIN; TUBULIN;

EID: 30744435829     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msj041     Document Type: Article
Times cited : (80)

References (56)
  • 3
    • 0037022379 scopus 로고    scopus 로고
    • The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba
    • USA
    • Bapteste, E., H. Brinkmann, J. A. Lee et al. (11 co-authors). 2002. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc. Natl. Acad. Sci. USA 99:1414-1419.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 1414-1419
    • Bapteste, E.1    Brinkmann, H.2    Lee, J.A.3
  • 4
    • 0002844544 scopus 로고
    • Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees
    • Baum, B. R. 1992. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41:3-10.
    • (1992) Taxon , vol.41 , pp. 3-10
    • Baum, B.R.1
  • 5
    • 0034480303 scopus 로고    scopus 로고
    • Phylogenetic relationships of the suborders of Coleoptera (Insecta)
    • Beutel, R. G., and F. Haas. 2000. Phylogenetic relationships of the suborders of Coleoptera (Insecta). Cladistics 16:103-141.
    • (2000) Cladistics , vol.16 , pp. 103-141
    • Beutel, R.G.1    Haas, F.2
  • 7
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17:540-552.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 540-552
    • Castresana, J.1
  • 8
    • 0034072267 scopus 로고    scopus 로고
    • The current state of insect molecular systematics: A thriving Tower of Babel
    • Caterino, M. S., S. Cho, and F. A. Sperling. 2000. The current state of insect molecular systematics: a thriving Tower of Babel. Annu. Rev. Entomol. 45:1-54.
    • (2000) Annu. Rev. Entomol. , vol.45 , pp. 1-54
    • Caterino, M.S.1    Cho, S.2    Sperling, F.A.3
  • 9
    • 15944406867 scopus 로고    scopus 로고
    • On the constitution and phylogeny of Staphyliniformia (Insecta: Coleoptera)
    • Caterino, M. S., T. Hunt, and A. P. Vogler. 2005. On the constitution and phylogeny of Staphyliniformia (Insecta: Coleoptera). Mol. Phylogenet. Evol. 34:655-672.
    • (2005) Mol. Phylogenet. Evol. , vol.34 , pp. 655-672
    • Caterino, M.S.1    Hunt, T.2    Vogler, A.P.3
  • 10
    • 0036167319 scopus 로고    scopus 로고
    • Basal relationships of Coleoptera inferred from 18S rDNA sequences
    • Caterino, M. S., V. L. Shull, P. M. Hammond, and A. P. Vogler. 2002. Basal relationships of Coleoptera inferred from 18S rDNA sequences. Zool. Scr. 31:41-49.
    • (2002) Zool. Scr. , vol.31 , pp. 41-49
    • Caterino, M.S.1    Shull, V.L.2    Hammond, P.M.3    Vogler, A.P.4
  • 11
    • 13844250623 scopus 로고    scopus 로고
    • Clann: Investigating phylogenetic information through supertree analyses
    • Creevey, C. J., and J. O. McInerney. 2005. Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 21:390-392.
    • (2005) Bioinformatics , vol.21 , pp. 390-392
    • Creevey, C.J.1    McInerney, J.O.2
  • 13
    • 0000698003 scopus 로고
    • The phylogeny of Coleoptera
    • _. 1960. The phylogeny of Coleoptera. Annu. Rev. Entomol. 5:111-134.
    • (1960) Annu. Rev. Entomol. , vol.5 , pp. 111-134
  • 14
    • 27844438226 scopus 로고    scopus 로고
    • Genome-scale evidence of the nematode-arthropod clade
    • Dopazo, H., and J. Dopazo. 2005. Genome-scale evidence of the nematode-arthropod clade. Genome Biol. 6:R41.
    • (2005) Genome Biol. , vol.6
    • Dopazo, H.1    Dopazo, J.2
  • 16
    • 0141922184 scopus 로고    scopus 로고
    • Comparison of gene representation in midguts from two phytophagous insects, Bombyx mori and Ips pini, using expressed sequence tags
    • Eigenheer, A. L., C. I. Keeling, S. Young, and C. Tittiger. 2003. Comparison of gene representation in midguts from two phytophagous insects, Bombyx mori and Ips pini, using expressed sequence tags. Gene 316:127-136.
    • (2003) Gene , vol.316 , pp. 127-136
    • Eigenheer, A.L.1    Keeling, C.I.2    Young, S.3    Tittiger, C.4
  • 17
    • 0003012443 scopus 로고
    • Tropical forests: Their richness in Coleoptera and other arthropod species
    • Erwin, T. L. 1982. Tropical forests: their richness in Coleoptera and other arthropod species. Coleopt. Bull. 36:74-75.
    • (1982) Coleopt. Bull. , vol.36 , pp. 74-75
    • Erwin, T.L.1
  • 18
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. Error probabilities
    • Ewing, B., and P. Green. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186-194.
    • (1998) Genome Res. , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 19
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185.
    • (1998) Genome Res. , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 20
    • 0033084945 scopus 로고    scopus 로고
    • Stability of cladistic relationships between Cetacea and higher-level artiodactyl taxa
    • Gatesy, J., M. Milinkovitch, V. Waddell, and M. Stanhope. 1999. Stability of cladistic relationships between Cetacea and higher-level artiodactyl taxa. Syst. Biol. 48:6-20.
    • (1999) Syst. Biol. , vol.48 , pp. 6-20
    • Gatesy, J.1    Milinkovitch, M.2    Waddell, V.3    Stanhope, M.4
  • 21
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
    • (2003) Syst. Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 23
    • 2942568227 scopus 로고    scopus 로고
    • A molecular timescale of eukaryote evolution and the rise of complex multicellular life
    • Hedges, S. B., J. E. Blair, M. L. Venturi, and J. L. Shoe. 2004. A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC Evol. Biol. 4:2.
    • (2004) BMC Evol. Biol. , vol.4 , pp. 2
    • Hedges, S.B.1    Blair, J.E.2    Venturi, M.L.3    Shoe, J.L.4
  • 25
    • 0029347201 scopus 로고
    • Phylogeny of the Coleoptera based on mitochondrial cytochrome oxidase I sequence data
    • Howland, D. E., and G. M. Hewitt. 1995. Phylogeny of the Coleoptera based on mitochondrial cytochrome oxidase I sequence data. Insect Mol. Biol. 4:203-215.
    • (1995) Insect Mol. Biol. , vol.4 , pp. 203-215
    • Howland, D.E.1    Hewitt, G.M.2
  • 26
    • 0035931072 scopus 로고    scopus 로고
    • A compendium of gene expression in normal human tissues
    • Hsiao, L. L., F. Dangond, T. Yoshida et al. (22 co-authors). 2001. A compendium of gene expression in normal human tissues. Physiol. Genomics 7:97-104.
    • (2001) Physiol. Genomics , vol.7 , pp. 97-104
    • Hsiao, L.L.1    Dangond, F.2    Yoshida, T.3
  • 27
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 28
    • 3042686787 scopus 로고    scopus 로고
    • The phylogeny of acorn weevils (genus Curculio) from mitochondrial and nuclear DNA sequences: The problem of incomplete data
    • Hughes, J., and A. P. Vogler. 2004. The phylogeny of acorn weevils (genus Curculio) from mitochondrial and nuclear DNA sequences: the problem of incomplete data. Mol. Phylogenet. Evol. 32:601-615.
    • (2004) Mol. Phylogenet. Evol. , vol.32 , pp. 601-615
    • Hughes, J.1    Vogler, A.P.2
  • 29
    • 9644284416 scopus 로고    scopus 로고
    • Interrelationships of Staphyliniform groups inferred from 18S and 28S rDNA sequences, with special emphasis on Hydrophiloidea (Coleoptera, Staphyliniformia)
    • Korte, A., I. Ribera, R. G. Beutal, and D. Bernhard. 2004. Interrelationships of Staphyliniform groups inferred from 18S and 28S rDNA sequences, with special emphasis on Hydrophiloidea (Coleoptera, Staphyliniformia). J. Zool. Syst. Evol. Res. 42:281-288.
    • (2004) J. Zool. Syst. Evol. Res. , vol.42 , pp. 281-288
    • Korte, A.1    Ribera, I.2    Beutal, R.G.3    Bernhard, D.4
  • 30
    • 84972047823 scopus 로고
    • Evolution of the hind wing in Coleoptera
    • Kukalova-Peck, J., and J. F. Lawrence. 1993. Evolution of the hind wing in Coleoptera. Can. Entomol. 125:181-258.
    • (1993) Can. Entomol. , vol.125 , pp. 181-258
    • Kukalova-Peck, J.1    Lawrence, J.F.2
  • 31
    • 0242291313 scopus 로고    scopus 로고
    • Annotation pattern of ESTs from Spodoptera frugiperda Sf9 cells and analysis of the ribosomal protein genes reveal insect-specific features and unexpectedly low codon usage bias
    • Landais, I., M. Ogliastro, K. Mita, J. Nohata, M. Lopez-Ferber, M. Duonor-Cerutti, T. Shimada, P. Fournier, and G. Devauchelle. 2003. Annotation pattern of ESTs from Spodoptera frugiperda Sf9 cells and analysis of the ribosomal protein genes reveal insect-specific features and unexpectedly low codon usage bias. Bioinformatics 19:2343-2350.
    • (2003) Bioinformatics , vol.19 , pp. 2343-2350
    • Landais, I.1    Ogliastro, M.2    Mita, K.3    Nohata, J.4    Lopez-Ferber, M.5    Duonor-Cerutti, M.6    Shimada, T.7    Fournier, P.8    Devauchelle, G.9
  • 32
    • 0000240541 scopus 로고
    • Families and subfamilies of Coleoptera (with selected genera, notes, references and data on family-group names)
    • J. Palaluk and S. A. Slipinski, eds. Papers celebrating the 80th birthday of Roy A. Crowson. Muzeum I Instytut Zoologii PAN, Warsaw, Poland
    • Lawrence, J. F., and A. F. Newton Jr. 1995. Families and subfamilies of Coleoptera (with selected genera, notes, references and data on family-group names). Pp. 779-913 in J. Palaluk and S. A. Slipinski, eds. Biology, phylogeny and classification of Coleoptera. Papers celebrating the 80th birthday of Roy A. Crowson. Muzeum I Instytut Zoologii PAN, Warsaw, Poland.
    • (1995) Biology, Phylogeny and Classification of Coleoptera , pp. 779-913
    • Lawrence, J.F.1    Newton Jr., A.F.2
  • 33
    • 0037348716 scopus 로고    scopus 로고
    • Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database
    • Li, L., B. P. Brunk, J. C. Kissinger et al. (20 co-authors). 2003. Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database. Genome Res. 13:443-454.
    • (2003) Genome Res. , vol.13 , pp. 443-454
    • Li, L.1    Brunk, B.P.2    Kissinger, J.C.3
  • 34
    • 10744228286 scopus 로고    scopus 로고
    • The construction of an EST database for Bombyx mori and its application
    • USA
    • Mita, K., M. Morimyo, K. Okano et al. (12 co-authors). 2003. The construction of an EST database for Bombyx mori and its application. Proc. Natl. Acad. Sci. USA 100:14121-14126.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 14121-14126
    • Mita, K.1    Morimyo, M.2    Okano, K.3
  • 35
    • 0035861441 scopus 로고    scopus 로고
    • Resolution of the early placental mammal radiation using Bayesian phylogenetics
    • Murphy, W. J., E. Eizirik, S. J. O'Brien et al. (11 co-authors). 2001. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348-2351.
    • (2001) Science , vol.294 , pp. 2348-2351
    • Murphy, W.J.1    Eizirik, E.2    O'Brien, S.J.3
  • 36
    • 0028255725 scopus 로고
    • Combining data in phylogenetic systematics - An empirical approach using 3 molecular data sets in the Solanaceae
    • Olmstead, R. G., and J. A. Sweere. 1994. Combining data in phylogenetic systematics - an empirical approach using 3 molecular data sets in the Solanaceae. Syst. Biol. 43:467-481.
    • (1994) Syst. Biol. , vol.43 , pp. 467-481
    • Olmstead, R.G.1    Sweere, J.A.2
  • 38
    • 0037433041 scopus 로고    scopus 로고
    • SimiTri - Visualizing similarity relationships for groups of sequences
    • Parkinson, J., and M. Blaxter. 2003. SimiTri - visualizing similarity relationships for groups of sequences. Bioinformatics 19:390-395.
    • (2003) Bioinformatics , vol.19 , pp. 390-395
    • Parkinson, J.1    Blaxter, M.2
  • 39
    • 3242674571 scopus 로고    scopus 로고
    • Expressed sequence tags: Analysis and annotation
    • _. 2004. Expressed sequence tags: analysis and annotation. Methods Mol. Biol. 270:93-126.
    • (2004) Methods Mol. Biol. , vol.270 , pp. 93-126
  • 41
    • 9644260489 scopus 로고    scopus 로고
    • A transcriptomic analysis of the phylum Nematoda
    • Parkinson, J., M. Mitreva, C. Whitton et al. (12 co-authors). 2004b. A transcriptomic analysis of the phylum Nematoda. Nat. Genet. 36:1259-1267.
    • (2004) Nat. Genet. , vol.36 , pp. 1259-1267
    • Parkinson, J.1    Mitreva, M.2    Whitton, C.3
  • 42
    • 17744379783 scopus 로고    scopus 로고
    • The Opisthokonta and the Ecdysozoa may not be clades: Stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa
    • Philip, G. K., C. J. Creevey, and J. O. McInerney. 2005. The Opisthokonta and the Ecdysozoa may not be clades: stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa. Mol. Biol. Evol. 22:1175-1184.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1175-1184
    • Philip, G.K.1    Creevey, C.J.2    McInerney, J.O.3
  • 43
    • 17744386162 scopus 로고    scopus 로고
    • Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia
    • Philippe, H., N. Lartillot, and H. Brinkmann. 2005. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol. Biol. Evol. 22:1246-1253.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1246-1253
    • Philippe, H.1    Lartillot, N.2    Brinkmann, H.3
  • 45
    • 4644298067 scopus 로고    scopus 로고
    • Using exon and intron sequences of the gene Mp20 to resolve basal relationships in Cicindela (Coleoptera: Cicindelidae)
    • Pons, J., T. Barraclough, K. Theodorides, A. Cardoso, and A. Vogler. 2004. Using exon and intron sequences of the gene Mp20 to resolve basal relationships in Cicindela (Coleoptera: Cicindelidae). Syst. Biol. 53:554-570.
    • (2004) Syst. Biol. , vol.53 , pp. 554-570
    • Pons, J.1    Barraclough, T.2    Theodorides, K.3    Cardoso, A.4    Vogler, A.5
  • 46
    • 0027104018 scopus 로고
    • Matrix representation in reconstructing phylogenetic relationships among the eukaryotes
    • Ragan, M. A. 1992. Matrix representation in reconstructing phylogenetic relationships among the eukaryotes. Biosystems 28:47-55.
    • (1992) Biosystems , vol.28 , pp. 47-55
    • Ragan, M.A.1
  • 49
    • 0042232552 scopus 로고    scopus 로고
    • Expressed sequence tags: Alternative or complement to whole genome sequences?
    • Rudd, S. 2003. Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci. 8:321-329.
    • (2003) Trends Plant Sci. , vol.8 , pp. 321-329
    • Rudd, S.1
  • 51
    • 12844251802 scopus 로고    scopus 로고
    • A molecular phylogeny for bats illuminates biogeography and the fossil record
    • Teeling, E. C., M. S. Springer, O. Madsen, P. Bates, J. O'Brien S, and W. J. Murphy. 2005. A molecular phylogeny for bats illuminates biogeography and the fossil record. Science 307:580-584.
    • (2005) Science , vol.307 , pp. 580-584
    • Teeling, E.C.1    Springer, M.S.2    Madsen, O.3    Bates, P.4    O'Brien S, J.5    Murphy, W.J.6
  • 52
    • 0036788174 scopus 로고    scopus 로고
    • Comparison of EST libraries from seven beetle species: Towards a framework for phylogenomics of the Coleoptera
    • Theodorides, K., A. De Riva, J. Gomez-Zurita, P. G. Foster, and A. P. Vogler. 2002. Comparison of EST libraries from seven beetle species: towards a framework for phylogenomics of the Coleoptera. Insect Mol. Biol. 11:467-475.
    • (2002) Insect Mol. Biol. , vol.11 , pp. 467-475
    • Theodorides, K.1    De Riva, A.2    Gomez-Zurita, J.3    Foster, P.G.4    Vogler, A.P.5
  • 53
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 55
    • 0042905752 scopus 로고    scopus 로고
    • Missing data, incomplete taxa, and phylogenetic accuracy
    • Wiens, J. J. 2003. Missing data, incomplete taxa, and phylogenetic accuracy. Syst. Biol. 52:528-538.
    • (2003) Syst. Biol. , vol.52 , pp. 528-538
    • Wiens, J.J.1
  • 56
    • 0037020194 scopus 로고    scopus 로고
    • Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster
    • Zdobnov, E. M., C. von Mering, I. Letunic et al. (36 co-authors). 2002. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 298:149-159.
    • (2002) Science , vol.298 , pp. 149-159
    • Zdobnov, E.M.1    Von Mering, C.2    Letunic, I.3


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