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Volumn 7, Issue 1, 2012, Pages

Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data

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TRANSCRIPTOME;

EID: 84856025326     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0029843     Document Type: Article
Times cited : (25)

References (49)
  • 1
    • 18844435622 scopus 로고    scopus 로고
    • Myzostomida: A review of the phylogeny and ultrastructure
    • Eeckhaut I, Lanterbecq D, (2005) Myzostomida: A review of the phylogeny and ultrastructure. Hydrobiologia 535: 253-275.
    • (2005) Hydrobiologia , vol.535 , pp. 253-275
    • Eeckhaut, I.1    Lanterbecq, D.2
  • 2
    • 73149125552 scopus 로고    scopus 로고
    • Evidence for cospeciation events in the host-symbiont system involving crinoids (echinodermata) and their obligate associates, the myzostomids (myzostomida, annelida)
    • Lanterbecq D, Rouse GW, Eeckhaut I, (2010) Evidence for cospeciation events in the host-symbiont system involving crinoids (echinodermata) and their obligate associates, the myzostomids (myzostomida, annelida). Mol Phylogenet Evol 54: 357-71.
    • (2010) Mol Phylogenet Evol , vol.54 , pp. 357-371
    • Lanterbecq, D.1    Rouse, G.W.2    Eeckhaut, I.3
  • 3
    • 34547812067 scopus 로고    scopus 로고
    • Mitochondrial genome and nuclear sequence data support myzostomida as part of the annelid radiation
    • Bleidorn C, Eeckhaut I, Podsiadlowski L, Schult N, McHugh D, et al. (2007) Mitochondrial genome and nuclear sequence data support myzostomida as part of the annelid radiation. Mol Biol Evol 24: 1690-1701.
    • (2007) Mol Biol Evol , vol.24 , pp. 1690-1701
    • Bleidorn, C.1    Eeckhaut, I.2    Podsiadlowski, L.3    Schult, N.4    McHugh, D.5
  • 5
    • 67349117809 scopus 로고    scopus 로고
    • A pcr survey of hox genes in the myzostomid Myzostoma cirriferum
    • Bleidorn C, Lanterbecq D, Eeckhaut I, Tiedemann R, (2009) A pcr survey of hox genes in the myzostomid Myzostoma cirriferum. Dev Genes Evol 219: 211-216.
    • (2009) Dev Genes Evol , vol.219 , pp. 211-216
    • Bleidorn, C.1    Lanterbecq, D.2    Eeckhaut, I.3    Tiedemann, R.4
  • 7
    • 42149157760 scopus 로고    scopus 로고
    • Broad phylogenomic sampling improves resolution of the animal tree of life
    • Dunn C, Hejnol A, Matus D, Pang K, Browne W, et al. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452: 745-749.
    • (2008) Nature , vol.452 , pp. 745-749
    • Dunn, C.1    Hejnol, A.2    Matus, D.3    Pang, K.4    Browne, W.5
  • 8
    • 72749099971 scopus 로고    scopus 로고
    • Assessing the root of bilaterian animals with scalable phylogenomic methods
    • Hejnol A, Obst M, Stamatakis A, Ott M, Rouse GW, et al. (2009) Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc Biol Sci 276: 4261-70.
    • (2009) Proc Biol Sci , vol.276 , pp. 4261-4270
    • Hejnol, A.1    Obst, M.2    Stamatakis, A.3    Ott, M.4    Rouse, G.W.5
  • 9
    • 64849090758 scopus 로고    scopus 로고
    • Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes
    • Paps J, Baguñà J, Riutort M, (2009) Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes. Proc Biol Sci 276: 1245-54.
    • (2009) Proc Biol Sci , vol.276 , pp. 1245-1254
    • Paps, J.1    Baguñà, J.2    Riutort, M.3
  • 10
  • 11
    • 65249099546 scopus 로고    scopus 로고
    • Phylogenomics revives traditional views on deep animal relationships
    • Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, et al. (2009) Phylogenomics revives traditional views on deep animal relationships. Curr Biol 19: 706-12.
    • (2009) Curr Biol , vol.19 , pp. 706-712
    • Philippe, H.1    Derelle, R.2    Lopez, P.3    Pick, K.4    Borchiellini, C.5
  • 12
    • 0033692378 scopus 로고    scopus 로고
    • Notung: A program for dating gene duplications and optimizing gene family trees
    • Chen K, Durand D, Farach-Colton M, (2000) Notung: A program for dating gene duplications and optimizing gene family trees. Journal of Computational Biology 7: 429-447.
    • (2000) Journal of Computational Biology , vol.7 , pp. 429-447
    • Chen, K.1    Durand, D.2    Farach-Colton, M.3
  • 13
    • 0034791426 scopus 로고    scopus 로고
    • A simple algorithm to infer gene duplication and speciation events on a gene tree
    • Zmasek C, Eddy S, (2001) A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17: 821-828.
    • (2001) Bioinformatics , vol.17 , pp. 821-828
    • Zmasek, C.1    Eddy, S.2
  • 14
    • 33746433923 scopus 로고    scopus 로고
    • Optimal gene trees from sequences and species trees using a soft interpretation of parsimony
    • Berglund-Sonnhammer A, Steffansson P, Betts M, Liberles D, (2006) Optimal gene trees from sequences and species trees using a soft interpretation of parsimony. J Mol Evol 63: 240-250.
    • (2006) J Mol Evol , vol.63 , pp. 240-250
    • Berglund-Sonnhammer, A.1    Steffansson, P.2    Betts, M.3    Liberles, D.4
  • 15
    • 84856030627 scopus 로고    scopus 로고
    • Chapter 5: Tangled tales from multiple markers
    • In: Bininda-Emonds ORP, editors, Combining information to reveal the Tree of Life, Kluwer Academic Publishers
    • Cotton JA, Page RDM, (2004) Chapter 5: Tangled tales from multiple markers. In: Bininda-Emonds ORP, editors. Phylogenetic Supertrees Combining information to reveal the Tree of Life, Kluwer Academic Publishers pp. 107-125.
    • (2004) Phylogenetic Supertrees , pp. 107-125
    • Cotton, J.A.1    Page, R.D.M.2
  • 16
    • 0000365320 scopus 로고
    • Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences
    • Goodman M, Czelusniak J, Moore GW, Romero-Herrera AE, Matsuda G, (1979) Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Systematic Zoology 28: 132-163.
    • (1979) Systematic Zoology , vol.28 , pp. 132-163
    • Goodman, M.1    Czelusniak, J.2    Moore, G.W.3    Romero-Herrera, A.E.4    Matsuda, G.5
  • 17
    • 79951569533 scopus 로고    scopus 로고
    • Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees
    • Burleigh JG, Bansal MS, Eulenstein O, Hartmann S, Wehe A, et al. (2011) Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees. Syst Biol 60: 117-25.
    • (2011) Syst Biol , vol.60 , pp. 117-125
    • Burleigh, J.G.1    Bansal, M.S.2    Eulenstein, O.3    Hartmann, S.4    Wehe, A.5
  • 18
    • 77958450862 scopus 로고    scopus 로고
    • Deep genomic-scale analyses of the metazoa reject coelomata: evidence from single- and multigene families analyzed under a supertree and supermatrix paradigm
    • Holton TA, Pisani D, (2010) Deep genomic-scale analyses of the metazoa reject coelomata: evidence from single- and multigene families analyzed under a supertree and supermatrix paradigm. Genome Biol Evol 2: 310-24.
    • (2010) Genome Biol Evol , vol.2 , pp. 310-324
    • Holton, T.A.1    Pisani, D.2
  • 19
    • 77956285690 scopus 로고    scopus 로고
    • Illumina sequencing library preparation for highly multiplexed target capture and sequencing
    • Meyer M, Kircher M, (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc 2010: pdb.prot5448.
    • (2010) Cold Spring Harb Protoc 2010: Pdb.prot5448
    • Meyer, M.1    Kircher, M.2
  • 20
    • 70350023532 scopus 로고    scopus 로고
    • Improved base calling for the illumina genome analyzer using machine learning strategies
    • Kircher M, Stenzel U, Kelso J, (2009) Improved base calling for the illumina genome analyzer using machine learning strategies. Genome Biol 10: R83.
    • (2009) Genome Biol , vol.10
    • Kircher, M.1    Stenzel, U.2    Kelso, J.3
  • 21
    • 79960852002 scopus 로고    scopus 로고
    • Addressing challenges in the production and analysis of illumina sequencing data
    • Kircher M, Heyn P, Kelso J, (2011) Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics 12: 382.
    • (2011) BMC Genomics , vol.12 , pp. 382
    • Kircher, M.1    Heyn, P.2    Kelso, J.3
  • 24
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright A, Van Dongen S, Ouzounis C, (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research 30: 1575-1584.
    • (2002) Nucleic Acids Research , vol.30 , pp. 1575-1584
    • Enright, A.1    Van Dongen, S.2    Ouzounis, C.3
  • 26
    • 40549098736 scopus 로고    scopus 로고
    • Uniprotkb/swiss-prot: The manually annotated section of the uniprot knowledgebase
    • Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A, (2007) Uniprotkb/swiss-prot: The manually annotated section of the uniprot knowledgebase. Methods Mol Biol 406: 89-112.
    • (2007) Methods Mol Biol , vol.406 , pp. 89-112
    • Boutet, E.1    Lieberherr, D.2    Tognolli, M.3    Schneider, M.4    Bairoch, A.5
  • 27
    • 38549097071 scopus 로고    scopus 로고
    • The universal protein resource (uniprot)
    • UniProtConsortium
    • UniProtConsortium (2008) The universal protein resource (uniprot). Nucleic Acids Res 36: D190-5.
    • (2008) Nucleic Acids Res , vol.36
  • 28
    • 13744252890 scopus 로고    scopus 로고
    • Mafft version 5: improvement in accuracy of multiple sequence alignment
    • Katoh K, Kuma K, Toh H, Miyata T, (2005) Mafft version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33: 511-518.
    • (2005) Nucleic Acids Research , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 29
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • Remm M, Storm CE, Sonnhammer EL, (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314: 1041-52.
    • (2001) J Mol Biol , vol.314 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.2    Sonnhammer, E.L.3
  • 30
    • 14644397888 scopus 로고    scopus 로고
    • Raxml-iii: a fast program for maximum likelihood-based inference of large phylogenetic trees
    • Stamatakis A, Ludwig T, Meier H, (2005) Raxml-iii: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21: 456-463.
    • (2005) Bioinformatics , vol.21 , pp. 456-463
    • Stamatakis, A.1    Ludwig, T.2    Meier, H.3
  • 31
    • 40049112246 scopus 로고    scopus 로고
    • Phyutility: a phyloinformatics tool for trees, alignments and molecular data
    • Smith SA, Dunn CW, (2008) Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 24: 715-6.
    • (2008) Bioinformatics , vol.24 , pp. 715-716
    • Smith, S.A.1    Dunn, C.W.2
  • 32
    • 43249090276 scopus 로고    scopus 로고
    • Using ests for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?
    • Hartmann S, Vision T, (2008) Using ests for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evol Biol 8: 95.
    • (2008) BMC Evol Biol , vol.8 , pp. 95
    • Hartmann, S.1    Vision, T.2
  • 33
    • 0031296691 scopus 로고    scopus 로고
    • Inferring species trees from gene trees: A phylogenetic analysis of the elapidae (serpentes) based on the amino acid sequences of venom proteins
    • Slowinski JB, Knight A, Rooney AP, (1997) Inferring species trees from gene trees: A phylogenetic analysis of the elapidae (serpentes) based on the amino acid sequences of venom proteins. Molecular Phylogenetics and Evolution 8: 349-362.
    • (1997) Molecular Phylogenetics and Evolution , vol.8 , pp. 349-362
    • Slowinski, J.B.1    Knight, A.2    Rooney, A.P.3
  • 34
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • Maddison WP, (1997) Gene trees in species trees. Systematic Biology 46: 523-536.
    • (1997) Systematic Biology , vol.46 , pp. 523-536
    • Maddison, W.P.1
  • 35
    • 46249126320 scopus 로고    scopus 로고
    • Duptree: a program for large-scale phylogenetic analyses using gene tree parsimony
    • Wehe A, Bansal M, Burleigh J, Eulenstein O, (2008) Duptree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 24: 1540-1541.
    • (2008) Bioinformatics , vol.24 , pp. 1540-1541
    • Wehe, A.1    Bansal, M.2    Burleigh, J.3    Eulenstein, O.4
  • 36
    • 0027846270 scopus 로고
    • Life cycle and mode of infestation of Myzostoma cirriferum (annelida), a symbiotic myzostomid of the comatulid crinoid Antedon bifida (echinodermata)
    • Eeckhaut I, Jangoux M, (1993) Life cycle and mode of infestation of Myzostoma cirriferum (annelida), a symbiotic myzostomid of the comatulid crinoid Antedon bifida (echinodermata). Diseases of Aquatic Organisms 15: 207-217.
    • (1993) Diseases of Aquatic Organisms , vol.15 , pp. 207-217
    • Eeckhaut, I.1    Jangoux, M.2
  • 37
    • 0242365676 scopus 로고    scopus 로고
    • Genome-scale approaches to resolving incongruence in molecular phylogenies
    • Rokas A, Williams B, King N, Carroll S, (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
    • (2003) Nature , vol.425 , pp. 798-804
    • Rokas, A.1    Williams, B.2    King, N.3    Carroll, S.4
  • 38
    • 3242703950 scopus 로고    scopus 로고
    • A molecular supermatrix of the rabbits and hares (leporidae) allows for the identification of five intercontinental exchanges during the miocene
    • Matthee CA, van Vuuren BJ, Bell D, Robinson TJ, (2004) A molecular supermatrix of the rabbits and hares (leporidae) allows for the identification of five intercontinental exchanges during the miocene. Syst Biol 53: 433-47.
    • (2004) Syst Biol , vol.53 , pp. 433-447
    • Matthee, C.A.1    van Vuuren, B.J.2    Bell, D.3    Robinson, T.J.4
  • 41
    • 0033278654 scopus 로고    scopus 로고
    • How should species phylogenies be inferred from sequence data?
    • Slowinski JB, Page RD, (1999) How should species phylogenies be inferred from sequence data? Syst Biol 48: 814-25.
    • (1999) Syst Biol , vol.48 , pp. 814-825
    • Slowinski, J.B.1    Page, R.D.2
  • 42
    • 0031296691 scopus 로고    scopus 로고
    • Inferring species trees from gene trees: A phylogenetic analysis of the elapidae (serpentes) based on the amino acid sequences of venom proteins
    • Slowinski JB, Knight A, Rooney AP, (1997) Inferring species trees from gene trees: A phylogenetic analysis of the elapidae (serpentes) based on the amino acid sequences of venom proteins. Molecular Phylogenetics and Evolution 8: 349-362.
    • (1997) Molecular Phylogenetics and Evolution , vol.8 , pp. 349-362
    • Slowinski, J.B.1    Knight, A.2    Rooney, A.P.3
  • 43
    • 0037036630 scopus 로고    scopus 로고
    • Going nuclear: gene family evolution and vertebrate phylogeny reconciled
    • Cotton JA, Page RDM, (2002) Going nuclear: gene family evolution and vertebrate phylogeny reconciled. Proc Biol Sci 269: 1555-61.
    • (2002) Proc Biol Sci , vol.269 , pp. 1555-1561
    • Cotton, J.A.1    Page, R.D.M.2
  • 44
    • 84856030627 scopus 로고    scopus 로고
    • Chapter 5: Tangled tales from multiple markers
    • In: Bininda-Emonds ORP, editors, Combining information to reveal the Tree of Life, Kluwer Academic Publishers
    • Cotton JA, Page RDM, (2004) Chapter 5: Tangled tales from multiple markers. In: Bininda-Emonds ORP, editors. Phylogenetic Supertrees Combining information to reveal the Tree of Life, Kluwer Academic Publishers pp. 107-125.
    • (2004) Phylogenetic Supertrees , pp. 107-125
    • Cotton, J.A.1    Page, R.D.M.2
  • 45
    • 0036365666 scopus 로고    scopus 로고
    • Vertebrate phylogenomics: reconciled trees and gene duplications
    • Page RDM, Cotton JA, (2002) Vertebrate phylogenomics: reconciled trees and gene duplications. Pac Symp Biocomput pp. 536-47.
    • (2002) Pac Symp Biocomput , pp. 536-547
    • Page, R.D.M.1    Cotton, J.A.2
  • 46
    • 1642274782 scopus 로고    scopus 로고
    • Gene tree parsimony vs uninode coding for phylogenetic reconstruction
    • Cotton JA, Page RDM, (2003) Gene tree parsimony vs uninode coding for phylogenetic reconstruction. Mol Phylogenet Evol 29: 298-308.
    • (2003) Mol Phylogenet Evol , vol.29 , pp. 298-308
    • Cotton, J.A.1    Page, R.D.M.2
  • 47
    • 34248217100 scopus 로고    scopus 로고
    • Inferring angiosperm phylogeny from est data with widespread gene duplication
    • Sanderson M, McMahon M, (2007) Inferring angiosperm phylogeny from est data with widespread gene duplication. BMC Evol Biol 7 (Suppl 1): S3.
    • (2007) BMC Evol Biol , vol.7 , Issue.SUPPL. 1
    • Sanderson, M.1    McMahon, M.2
  • 48
    • 78650722451 scopus 로고    scopus 로고
    • A.: Heuristics for the gene duplication problem: A θ (n) speed-up for the local search
    • Bansal MS, Burleigh JG, Eulenstein O, Wehe A, (2007) A.: Heuristics for the gene duplication problem: A θ (n) speed-up for the local search. RECOMB 2007: 238-252.
    • (2007) RECOMB , vol.2007 , pp. 238-252
    • Bansal, M.S.1    Burleigh, J.G.2    Eulenstein, O.3    Wehe, A.4
  • 49
    • 75149135738 scopus 로고    scopus 로고
    • Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models
    • Bansal MS, Burleigh JG, Eulenstein O, (2010) Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models. BMC Bioinformatics 11 (Suppl 1): S42.
    • (2010) BMC Bioinformatics , vol.11 , Issue.SUPPL. 1
    • Bansal, M.S.1    Burleigh, J.G.2    Eulenstein, O.3


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