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Volumn 47, Issue 3, 2008, Pages 1090-1099

Large expansion segments in 18S rDNA support a new sponge clade (Class Demospongiae, Order Haplosclerida)

Author keywords

18S rRNA; GC content; Indels; Order Haplosclerida; Porifera; Secondary structure; Synapomorphies

Indexed keywords

RIBOSOME DNA; RNA 18S;

EID: 43949115163     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.02.018     Document Type: Article
Times cited : (16)

References (49)
  • 2
    • 0036080338 scopus 로고    scopus 로고
    • Detecting cryptcally simple protein sequences using the SIMPLE algorithm
    • Alba M.M., Laskowski R.A., and Hancock J.M. Detecting cryptcally simple protein sequences using the SIMPLE algorithm. Bioinformatics 18 5 (2002) 672-678
    • (2002) Bioinformatics , vol.18 , Issue.5 , pp. 672-678
    • Alba, M.M.1    Laskowski, R.A.2    Hancock, J.M.3
  • 3
    • 0034174416 scopus 로고    scopus 로고
    • Phylogenetic relationships of the family Axinellidae (Porifera: Demospongiae) using morphological and molecular data
    • Alvarez B., Crisp M.D., Driver F., Hooper J.N.A., and van Soest R.W.M. Phylogenetic relationships of the family Axinellidae (Porifera: Demospongiae) using morphological and molecular data. Zool. Scripta 29 2 (2000) 169-198
    • (2000) Zool. Scripta , vol.29 , Issue.2 , pp. 169-198
    • Alvarez, B.1    Crisp, M.D.2    Driver, F.3    Hooper, J.N.A.4    van Soest, R.W.M.5
  • 4
    • 0002215278 scopus 로고
    • The ordinal and subclass classification of the Demospongiae (Porifera): appraisal of the present arrangement, and proposal of a new order
    • Bergquist P.R. The ordinal and subclass classification of the Demospongiae (Porifera): appraisal of the present arrangement, and proposal of a new order. NZ J. Zool. 7 (1980) 1-16
    • (1980) NZ J. Zool. , vol.7 , pp. 1-16
    • Bergquist, P.R.1
  • 7
    • 0036892660 scopus 로고    scopus 로고
    • Unusually Expanded SSU Ribosomal DNA of Primary Osmotrophic Euglenids: Molecular Evolution and Phylogenetic Inference
    • Busse I., and Preisfeld A. Unusually Expanded SSU Ribosomal DNA of Primary Osmotrophic Euglenids: Molecular Evolution and Phylogenetic Inference. J. Mol. Evol. 55 (2002) 757-767
    • (2002) J. Mol. Evol. , vol.55 , pp. 757-767
    • Busse, I.1    Preisfeld, A.2
  • 8
    • 1842343465 scopus 로고
    • Strongly expanded 18S rRNA genes correlated with a peculiar morphology in the insect order Strepsiptera
    • Chalwatzis N., Baur A., Stetzer E., Kinzelbach R., and Zimmerman F.K. Strongly expanded 18S rRNA genes correlated with a peculiar morphology in the insect order Strepsiptera. Zoology 98 (1995) 115-126
    • (1995) Zoology , vol.98 , pp. 115-126
    • Chalwatzis, N.1    Baur, A.2    Stetzer, E.3    Kinzelbach, R.4    Zimmerman, F.K.5
  • 9
    • 0033281060 scopus 로고    scopus 로고
    • Analysis of the primary sequence and secondary structure of the unusually long SSU rRNA of the soil bug, Armadillium vulgare
    • Choe C.P., Hancock J.M., Hwang U.W., and Kim W. Analysis of the primary sequence and secondary structure of the unusually long SSU rRNA of the soil bug, Armadillium vulgare. J. Mol. Evol. 49 (1999) 798-805
    • (1999) J. Mol. Evol. , vol.49 , pp. 798-805
    • Choe, C.P.1    Hancock, J.M.2    Hwang, U.W.3    Kim, W.4
  • 10
    • 0032148625 scopus 로고    scopus 로고
    • Reassessment of homolgy of morphological characters in Tetractinellid sponges based on molecular data
    • Chombard C., Boury-Esnault N., and Tillier S. Reassessment of homolgy of morphological characters in Tetractinellid sponges based on molecular data. Syst. Biol. 47 3 (1998) 351-366
    • (1998) Syst. Biol. , vol.47 , Issue.3 , pp. 351-366
    • Chombard, C.1    Boury-Esnault, N.2    Tillier, S.3
  • 11
    • 0001798122 scopus 로고    scopus 로고
    • Good congruence between morphology and molecular phylogeny of Hadromerida or how to bother sponge taxonomists
    • Chombard C., and Boury-Esnault N. Good congruence between morphology and molecular phylogeny of Hadromerida or how to bother sponge taxonomists. Mem. Queensl. Mus. 44 (1999) 100
    • (1999) Mem. Queensl. Mus. , vol.44 , pp. 100
    • Chombard, C.1    Boury-Esnault, N.2
  • 12
    • 0031937306 scopus 로고    scopus 로고
    • The unusually long small-subunit ribosomal RNA of the crustacean, Daphnia pulex: sequence and predicted secondary structure
    • Crease T.J., and Colbourne J.K. The unusually long small-subunit ribosomal RNA of the crustacean, Daphnia pulex: sequence and predicted secondary structure. J. Mol. Evol. 46 (1998) 307-313
    • (1998) J. Mol. Evol. , vol.46 , pp. 307-313
    • Crease, T.J.1    Colbourne, J.K.2
  • 13
    • 0037314114 scopus 로고    scopus 로고
    • RnaViz2: an improved representation of RNA secondary structure
    • De Rijk P., Wuyts J., and De Watcher R. RnaViz2: an improved representation of RNA secondary structure. Bioinformatics 19 2 (2003) 299-300
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 299-300
    • De Rijk, P.1    Wuyts, J.2    De Watcher, R.3
  • 14
    • 0037133957 scopus 로고    scopus 로고
    • Structure and function of the eukaryotic ribosome: the next frontier
    • Doudna J.A., and Rath V.L. Structure and function of the eukaryotic ribosome: the next frontier. Cell 109 (2002) 153-156
    • (2002) Cell , vol.109 , pp. 153-156
    • Doudna, J.A.1    Rath, V.L.2
  • 15
    • 3042701600 scopus 로고    scopus 로고
    • Order level differences in the structure of partial LSU across demosponges (Porifera): new insights into an old taxon
    • Erpenbeck D., McCormack G.P., Breeuwer J.A.J., and van Soest R.W.M. Order level differences in the structure of partial LSU across demosponges (Porifera): new insights into an old taxon. Mol. Phylogenet. Evol. 32 (2004) 388-395
    • (2004) Mol. Phylogenet. Evol. , vol.32 , pp. 388-395
    • Erpenbeck, D.1    McCormack, G.P.2    Breeuwer, J.A.J.3    van Soest, R.W.M.4
  • 17
    • 0030590363 scopus 로고    scopus 로고
    • Secondary structures and features of the 18S, 5.8S and 26S ribosomal RNAs from the Apicomplexan parasite Toxoplasma gondii
    • Gagnon S., Bourbeau D., and Levesque R.C. Secondary structures and features of the 18S, 5.8S and 26S ribosomal RNAs from the Apicomplexan parasite Toxoplasma gondii. Gene 173 (1996) 129-135
    • (1996) Gene , vol.173 , pp. 129-135
    • Gagnon, S.1    Bourbeau, D.2    Levesque, R.C.3
  • 18
    • 0002127932 scopus 로고    scopus 로고
    • Expansion segments: regions of variable size that interrupt the universal core secondary structure of ribosomal RNA
    • Zimmerman R.A., and Dahlberg A.E. (Eds), CRC Press
    • Gerbi S.A. Expansion segments: regions of variable size that interrupt the universal core secondary structure of ribosomal RNA. In: Zimmerman R.A., and Dahlberg A.E. (Eds). Ribosomal RNA-Structure, Processing, and Function in Protein Biosynthesis (1996), CRC Press 71-87
    • (1996) Ribosomal RNA-Structure, Processing, and Function in Protein Biosynthesis , pp. 71-87
    • Gerbi, S.A.1
  • 19
    • 33645263708 scopus 로고    scopus 로고
    • Assessing the odd secondary structural properties of nuclear small subunit ribosomal RNA sequences (18S) of the twisted-wing parasites (Insecta: Strepsiptera)
    • Gillespie J.J., McKenna C.H., Yoder M.J., Gutell R.R., Johnston J.S., Kathirithamby J., and Cognato A.I. Assessing the odd secondary structural properties of nuclear small subunit ribosomal RNA sequences (18S) of the twisted-wing parasites (Insecta: Strepsiptera). Insect Mol. Biol. 14 6 (2005) 625-643
    • (2005) Insect Mol. Biol. , vol.14 , Issue.6 , pp. 625-643
    • Gillespie, J.J.1    McKenna, C.H.2    Yoder, M.J.3    Gutell, R.R.4    Johnston, J.S.5    Kathirithamby, J.6    Cognato, A.I.7
  • 20
    • 0012014083 scopus 로고    scopus 로고
    • Some unusual small-subunit ribosomal RNA sequences of metazoans
    • Giribet G., and Wheeler W.C. Some unusual small-subunit ribosomal RNA sequences of metazoans. Am. Mus. Novit. 3337 (2001) 14
    • (2001) Am. Mus. Novit. , vol.3337 , pp. 14
    • Giribet, G.1    Wheeler, W.C.2
  • 21
    • 0029268667 scopus 로고
    • The phylogenetic position of the pterobranch hemichordates revealed by 18S rDNA sequence data
    • Halanych K.M. The phylogenetic position of the pterobranch hemichordates revealed by 18S rDNA sequence data. Mol. Phylogenet. Evol. 4 (1995) 72-76
    • (1995) Mol. Phylogenet. Evol. , vol.4 , pp. 72-76
    • Halanych, K.M.1
  • 22
    • 0026300584 scopus 로고
    • Ribosomal RNA: molecular evolution and phylogenetic inference
    • Hillis D.M., and Dixon M.T. Ribosomal RNA: molecular evolution and phylogenetic inference. Q. Rev. Biol. 66 (1991) 411-453
    • (1991) Q. Rev. Biol. , vol.66 , pp. 411-453
    • Hillis, D.M.1    Dixon, M.T.2
  • 23
    • 43949135578 scopus 로고    scopus 로고
    • Hooper, J.N.A., 2000. Sponguide: Guide to Sponge Collection and Identification (Version August 2000). pp 71. .
    • Hooper, J.N.A., 2000. Sponguide: Guide to Sponge Collection and Identification (Version August 2000). pp 71. .
  • 24
    • 0031436890 scopus 로고    scopus 로고
    • Phylogeny estimation and hypothesis testing using maximum likelihood
    • Huelsenbeck J.P., and Crandall K.A. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28 (1997) 437-466
    • (1997) Annu. Rev. Ecol. Syst. , vol.28 , pp. 437-466
    • Huelsenbeck, J.P.1    Crandall, K.A.2
  • 25
    • 0031022860 scopus 로고    scopus 로고
    • The nucleotide sequence and predicted secondary structure of small (18S) ribosomal RNA from Spirometra erinaceieuropaei
    • Liu D.W., Kato H., and Sugane K. The nucleotide sequence and predicted secondary structure of small (18S) ribosomal RNA from Spirometra erinaceieuropaei. Gene 184 (1997) 221-227
    • (1997) Gene , vol.184 , pp. 221-227
    • Liu, D.W.1    Kato, H.2    Sugane, K.3
  • 26
    • 0038487295 scopus 로고    scopus 로고
    • Phylogeny and evolution of Calcareous sponges: monophyly of Calcinea and Calcaronea, high level of morphological homoplasy, and the primitive nature of axial symmetry
    • Manuel M., Borchiellini C., Alivon E., Le Parco Y., Vacelet J., and Boury-Esnault N. Phylogeny and evolution of Calcareous sponges: monophyly of Calcinea and Calcaronea, high level of morphological homoplasy, and the primitive nature of axial symmetry. Syst. Biol. 52 3 (2003) 311-333
    • (2003) Syst. Biol. , vol.52 , Issue.3 , pp. 311-333
    • Manuel, M.1    Borchiellini, C.2    Alivon, E.3    Le Parco, Y.4    Vacelet, J.5    Boury-Esnault, N.6
  • 27
    • 0036944445 scopus 로고    scopus 로고
    • Major discrepancies between phylogenetic hypotheses based on molecular and morphological criteria within the Order Haplosclerida (Phylum Porifera: Class Demospongiae)
    • McCormack G.P., Erpenbeck D., and van Soest R.W.M. Major discrepancies between phylogenetic hypotheses based on molecular and morphological criteria within the Order Haplosclerida (Phylum Porifera: Class Demospongiae). J. Zool. Syst. Evol. Research 40 (2002) 237-240
    • (2002) J. Zool. Syst. Evol. Research , vol.40 , pp. 237-240
    • McCormack, G.P.1    Erpenbeck, D.2    van Soest, R.W.M.3
  • 28
    • 9744239617 scopus 로고    scopus 로고
    • An evaluation of support for order-level monophyly and interrelationships within the class Demospongiae using partial data from the large subunit rDNA and cytochrome oxidase subunit I
    • Nichols S.A. An evaluation of support for order-level monophyly and interrelationships within the class Demospongiae using partial data from the large subunit rDNA and cytochrome oxidase subunit I. Mol. Phylogenet. Evol. 34 (2005) 81-96
    • (2005) Mol. Phylogenet. Evol. , vol.34 , pp. 81-96
    • Nichols, S.A.1
  • 29
    • 0029923819 scopus 로고    scopus 로고
    • Simplicity-correlated size growth of the nuclear 28S ribosomal RNA D3 expansion segment in the Crustacean Order Isopoda
    • Nunn G.B., Theisen B.F., Christensen B., and Actander P. Simplicity-correlated size growth of the nuclear 28S ribosomal RNA D3 expansion segment in the Crustacean Order Isopoda. J. Mol. Evol. 42 (1996) 211-223
    • (1996) J. Mol. Evol. , vol.42 , pp. 211-223
    • Nunn, G.B.1    Theisen, B.F.2    Christensen, B.3    Actander, P.4
  • 30
    • 0029883267 scopus 로고    scopus 로고
    • Characterization of a flatworm ribosomal RNA-encoding gene: promoter sequence and small subunit rRNA secondary structure
    • Picón M., Gutell R.R., Ehrlich R., and Zaha A. Characterization of a flatworm ribosomal RNA-encoding gene: promoter sequence and small subunit rRNA secondary structure. Gene 171 (1996) 215-220
    • (1996) Gene , vol.171 , pp. 215-220
    • Picón, M.1    Gutell, R.R.2    Ehrlich, R.3    Zaha, A.4
  • 31
    • 0031773680 scopus 로고    scopus 로고
    • Modeltest: testing the model of DNA substitution
    • Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 33
    • 0141882050 scopus 로고    scopus 로고
    • Class Hexactinellida Schmidt, 1870
    • Hooper J.N.A., and van Soest R.W.M. (Eds), Kluwer Academic/Plenum Publishers
    • Reiswig H.M. Class Hexactinellida Schmidt, 1870. In: Hooper J.N.A., and van Soest R.W.M. (Eds). Systema Porifera. A Guide to the Classification of Sponges (2002), Kluwer Academic/Plenum Publishers 1201-1202
    • (2002) Systema Porifera. A Guide to the Classification of Sponges , pp. 1201-1202
    • Reiswig, H.M.1
  • 34
    • 33947594935 scopus 로고    scopus 로고
    • Reassessment of the classification of the Order Haplosclerida (Class Demospongiae, Phylum Porifera) using 18S rRNA gene sequence data
    • Redmond N.E., van Soest R.W.M., Kelly M., Raleigh J., Travers S.A.A., and Raleigh J. Reassessment of the classification of the Order Haplosclerida (Class Demospongiae, Phylum Porifera) using 18S rRNA gene sequence data. Mol. Phylogenet. Evol. 43 (2007) 344-352
    • (2007) Mol. Phylogenet. Evol. , vol.43 , pp. 344-352
    • Redmond, N.E.1    van Soest, R.W.M.2    Kelly, M.3    Raleigh, J.4    Travers, S.A.A.5    Raleigh, J.6
  • 35
    • 43949138665 scopus 로고    scopus 로고
    • Schmidt, O., 1870. Grundzüge einer Spongien-Fauna des atlantischen Gebietes. (Wilheim Engelman: Leipzig): iii-iv, 1-88, pls I-VI.
    • Schmidt, O., 1870. Grundzüge einer Spongien-Fauna des atlantischen Gebietes. (Wilheim Engelman: Leipzig): iii-iv, 1-88, pls I-VI.
  • 36
    • 18844451805 scopus 로고    scopus 로고
    • ITS-2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae)
    • Schmitt S., Hentschel U., Zea S., Dandekar T., and Wolf M. ITS-2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae). J. Mol. Evol. 60 (2005) 327-336
    • (2005) J. Mol. Evol. , vol.60 , pp. 327-336
    • Schmitt, S.1    Hentschel, U.2    Zea, S.3    Dandekar, T.4    Wolf, M.5
  • 37
    • 43949123890 scopus 로고    scopus 로고
    • Swofford, D.L., 1998. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, MA.
    • Swofford, D.L., 1998. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, MA.
  • 38
    • 0000661401 scopus 로고
    • Spongiaires de l'Atlantique et de la Méditerranée proveenant des croisiéres de Prince Albert ler de Monaco
    • Topsent E. Spongiaires de l'Atlantique et de la Méditerranée proveenant des croisiéres de Prince Albert ler de Monaco. Rés Camp Sci. Prince Albert ler Monaco 74 (1928) 1-376
    • (1928) Rés Camp Sci. Prince Albert ler Monaco , vol.74 , pp. 1-376
    • Topsent, E.1
  • 39
    • 0000393614 scopus 로고
    • Electron microscope study of the association between some sponges and bacteria
    • Vacelet J., and Donadey C. Electron microscope study of the association between some sponges and bacteria. J. Exp. Mar. Ecol. 30 (1977) 301-314
    • (1977) J. Exp. Mar. Ecol. , vol.30 , pp. 301-314
    • Vacelet, J.1    Donadey, C.2
  • 41
    • 33845911389 scopus 로고    scopus 로고
    • Order Haplosclerida Topsent, 1928
    • Hooper J.N.A., and van Soest R.W.M. (Eds), Kluwer Academic/Plenum Publishers
    • van Soest R.W.M., and Hooper J. Order Haplosclerida Topsent, 1928. In: Hooper J.N.A., and van Soest R.W.M. (Eds). Systema Porifera. A Guide to the Classification of Sponges (2002), Kluwer Academic/Plenum Publishers 831-832
    • (2002) Systema Porifera. A Guide to the Classification of Sponges , pp. 831-832
    • van Soest, R.W.M.1    Hooper, J.2
  • 43
    • 0031012071 scopus 로고    scopus 로고
    • Phylogenetic analysis of slippage-like sequence variation in the V4 rRNA expansion segment in Tiget Beetles (Cicindelidae)
    • Vogler A.P., Welsh A., and Hancock J.M. Phylogenetic analysis of slippage-like sequence variation in the V4 rRNA expansion segment in Tiget Beetles (Cicindelidae). Mol. Biol. Evol. 14 1 (1997) 6-19
    • (1997) Mol. Biol. Evol. , vol.14 , Issue.1 , pp. 6-19
    • Vogler, A.P.1    Welsh, A.2    Hancock, J.M.3
  • 45
    • 7444222362 scopus 로고    scopus 로고
    • Intragenomic variation of the rDNA intertranscribed spacers in sponges (Phylum Porifera): implications for phylogenetics studies
    • Wörheide G., Nichols S.A., and Goldberg J. Intragenomic variation of the rDNA intertranscribed spacers in sponges (Phylum Porifera): implications for phylogenetics studies. Mol. Phylogenet. Evol. 33 (2004) 816-830
    • (2004) Mol. Phylogenet. Evol. , vol.33 , pp. 816-830
    • Wörheide, G.1    Nichols, S.A.2    Goldberg, J.3
  • 46
    • 0034554835 scopus 로고    scopus 로고
    • Comparative analysis of more than 3000 seqeunces reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA
    • Wuyts J., De Rijk P., Van de Peer Y., Pison G., Rousseeuw P., and De Watcher R. Comparative analysis of more than 3000 seqeunces reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA. Nucleic Acids Res. 28 23 (2000) 4698-4708
    • (2000) Nucleic Acids Res. , vol.28 , Issue.23 , pp. 4698-4708
    • Wuyts, J.1    De Rijk, P.2    Van de Peer, Y.3    Pison, G.4    Rousseeuw, P.5    De Watcher, R.6
  • 47
    • 0035945246 scopus 로고    scopus 로고
    • Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA
    • Wuyts J., Van de Peer Y., and De Watcher R. Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. Nucleic Acids Res. 29 24 (2001) 5017-5028
    • (2001) Nucleic Acids Res. , vol.29 , Issue.24 , pp. 5017-5028
    • Wuyts, J.1    Van de Peer, Y.2    De Watcher, R.3
  • 49
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 13 (2003) 3406-3415
    • (2003) Nucleic Acids Res. , vol.31 , Issue.13 , pp. 3406-3415
    • Zuker, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.