메뉴 건너뛰기




Volumn 42, Issue 3, 2010, Pages 218-229

Secondary structure models of D2-D3 expansion segments of 28S rRNA for Hoplolaiminae species

Author keywords

28S; D2 D3; Hoplolaiminae; Hoplolaimus; Nematode

Indexed keywords

HOPLOLAIMINAE; HOPLOLAIMUS; HOPLOLAIMUS COLUMBUS; SCUTELLONEMA BRACHYURUM;

EID: 80051933166     PISSN: 0022300X     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (8)

References (44)
  • 1
    • 4444313986 scopus 로고    scopus 로고
    • Discrimination of six Pratylenchus species using PCR and species-specific primers
    • Al-Banna, L., Ploeg, A. T., Williamson, V. M., and Kaloshian, A. 2004. Discrimination of six Pratylenchus Species using PCR and Species-Specific Primers. Journal of Nematology 36:142-146. (Pubitemid 39160928)
    • (2004) Journal of Nematology , vol.36 , Issue.2 , pp. 142-146
    • Al-Banna, L.1    Ploeg, A.T.2    Williamson, V.M.3    Kaloshian, I.4
  • 2
    • 0031068278 scopus 로고    scopus 로고
    • Phylogenetic analysis of nematodes of the genus Pratylenchus using nuclear 26S rDNA
    • Al-Banna, L., Willamson, V. M., and Gardner, S. L. 1997. Phylogenetic analysis of nematodes of the genus Pratylenchus using nuclear 26S rDNA. Molecualr Phylogenetics and Evolution 7:94-102. (Pubitemid 127347167)
    • (1997) Molecular Phylogenetics and Evolution , vol.7 , Issue.1 , pp. 94-102
    • Al-Banna, L.1    Williamson, V.2    Gardner, S.L.3
  • 3
    • 0031253665 scopus 로고    scopus 로고
    • An Evolutionary Framework for the Study of Developmental Evolution in a Set of Nematodes Related toCaenorhabditis elegans
    • DOI 10.1006/mpev.1997.0433, PII S1055790397904334
    • Baldwin, J. G., Frisse, L. M., Vida, J. T., Eddleman, C. D., and Thomas, W. K. 1997. An evolutionary framework for the study of developmental evolution in a set of nematodes related to Caenorhabditis elegans. Molecular Phylogenetics and Evolution 8:249-259. (Pubitemid 127347519)
    • (1997) Molecular Phylogenetics and Evolution , vol.8 , Issue.2 , pp. 249-259
    • Baldwin, J.G.1    Frisse, L.M.2    Vida, J.T.3    Eddleman, C.D.4    Thomas, W.K.5
  • 4
    • 0029955186 scopus 로고    scopus 로고
    • Evidence that two types of 18S rDNA coexist in the genome of Dugesia (Schmidtea) mediterranea (Platyhelminthes, Turbellaria, Tricladida)
    • Carranza, S., Giribet, G., Ribera, C., Baugna, R., and Riutort, M. 1996. Evidence that two types of 18S rDNA coexist in the genome of Dugesia (Schmidtea) mediterranea (Platyhelminthes, Turbellaria, Tricladida). Molecular Biology and Evulution 13:824-832. (Pubitemid 26240087)
    • (1996) Molecular Biology and Evolution , vol.13 , Issue.6 , pp. 824-832
    • Carranza, S.1    Giribet, G.2    Ribera, C.3    Baguna, J.4    Riutort, M.5
  • 5
    • 0032211071 scopus 로고    scopus 로고
    • Common secondary structures for the second internal transcribed spacer pre-rRNA of two subfamilies of trichostrongylid nematodes
    • DOI 10.1016/S0020-7519(98)00129-5, PII S0020751998001295
    • Chilton, N. B., Hoste, H., Newton, L. A., Beveridge, I., and Gasser, R. B. 1998. Coomon secondary structures for the second internal transcribed spacer pre-rRNA of two subfamilies of trichostrongylid nematodes. International Journal of Parasitology 28:1765-1773. (Pubitemid 28522213)
    • (1998) International Journal for Parasitology , vol.28 , Issue.11 , pp. 1765-1773
    • Chilton, N.B.1    Hoste, H.2    Newton, L.A.3    Beveridge, I.4    Gasser, R.B.5
  • 6
    • 0034983487 scopus 로고    scopus 로고
    • Evolutionary relationships of trichostrongyloid nematodes (Strongylida) inferred from ribosomal DNA sequence data
    • DOI 10.1006/mpev.2001.0938
    • Chilton, N. B., Hoste, H., Newton, L. A., Beveridge, I., and Gasser, R. B. 2001. Evolutionary relationships of Trichostrongyloid nematodes (Strongylid) inferred from Ribosomal DNA sequence Data. Molecular phylogenetics and Evolution 19:367-386. (Pubitemid 32566642)
    • (2001) Molecular Phylogenetics and Evolution , vol.19 , Issue.3 , pp. 367-386
    • Chilton, N.B.1    Newton, L.A.2    Beveridge, I.3    Gasser, R.B.4
  • 7
    • 0037291508 scopus 로고    scopus 로고
    • First complete large subunit ribosomal RNA sequence and secondary structure for a parasitic nematode: Phylogenetic and diagnostic implications
    • DOI 10.1016/S0890-8508(02)00107-X
    • Chilton, N. B., Huby-Chilton, F., and Gasser, R. B. 2003. First complete large subunit ribosomal RNA sequence and secondary structure for parasitic nematode; phylogenic and diagnostic implications. Molecular and Cellular Probes 17:33-39. (Pubitemid 36287308)
    • (2003) Molecular and Cellular Probes , vol.17 , Issue.1 , pp. 33-39
    • Chilton, N.B.1    Huby-Chilton, F.2    Gasser, R.B.3
  • 9
    • 4444327187 scopus 로고    scopus 로고
    • Characterization and sequence variation in the rDNA region of six nematode species of the genus Longidorus (Nematoda)
    • De Luca, F., Reyes, A., Grander, J., Kunz, P., Agostinelli, A., De Giorgi, C., and Lamberti, F. 2004. Characterization and sequence variation in the rDNA region of six nematode species of the Genus Longidorus (Nematoda). Journal of Nematology 36:147-152. (Pubitemid 39160929)
    • (2004) Journal of Nematology , vol.36 , Issue.2 , pp. 147-152
    • De Luca, F.1    Reyes, A.2    Grunder, J.3    Kunz, P.4    Agostinelli, A.5    De Giorgi, C.6    Lamberti, F.7
  • 11
    • 0027500136 scopus 로고
    • Ribosomal RNA secondary structure: Compensatory mutations and implications for phylogenetic analysis
    • Dixon, M. T., and Hillis, D. M. 1993. Ribosomal secondary structure: compensatory mutations and implications for phylogenetic analysis. Molecular Biology and Evolution 10:256-267. (Pubitemid 23040235)
    • (1993) Molecular Biology and Evolution , vol.10 , Issue.1 , pp. 256-267
    • Dixon, M.T.1    Hillis, D.M.2
  • 13
    • 0022649450 scopus 로고
    • The rDNA of C. elegans: Sequence and structure
    • Ellis, R. E., Sulston, J. E., and Coulson, A. R. 1986. Xhe rDNA of C. elegans; Sequence and structure. Nucleic Acids Research 14:2345-2364. (Pubitemid 16154959)
    • (1986) Nucleic Acids Research , vol.14 , Issue.5 , pp. 2345-2364
    • Ellis, R.E.1    Sulston, J.E.2    Coulson, A.R.3
  • 14
    • 0010382287 scopus 로고
    • A reappraisal of Tylenchina (Nemata) 8. The family Hoplolaimidae Filip'ev, 1934
    • Fortuner, R. 1987. A reappraisal of Tylenchina (Nemata) 8. The family Hoplolaimidae Filip'ev, 1934. Revue Nématol 10:219-232.
    • (1987) Revue Nématol , vol.10 , pp. 219-232
    • Fortuner, R.1
  • 15
    • 80051923446 scopus 로고
    • Manual of agricultural nematology; the Hoplolainae
    • Fortuner, 1991. Manual of agricultural nematology; the Hoplolainae. Marcel Dekker 619-719.
    • (1991) Marcel Dekker , pp. 619-719
    • Fortuner1
  • 16
    • 0010381112 scopus 로고
    • Description de Dolichorhynchus elegans n. sp. et Aphasmatylenchus variubilis n. sp. (Nematoda: Tylenchida)
    • Germani, G., and Luc. M. 1984. Description de Dolichorhynchus elegans n. sp. et Aphasmatylenchus variubilis n. sp. (Nematoda: Tylenchida). Revue Nématol 7:81-86.
    • (1984) Revue Nématol , vol.7 , pp. 81-86
    • Germani, G.1    Luc, M.2
  • 17
    • 5044230709 scopus 로고    scopus 로고
    • A secondary structural model of the 28S rRNA expansion segments D2 and D3 from rootworms and related leaf beetles (Coleoptera: Chrysomelidae; Galerucinae)
    • DOI 10.1111/j.0962-1075.2004.00509.x
    • Gillespie, J., Cannone, J., Gutell, R., and Cognato, A. 2004. A secondary structural model of the 28S rRNA expansion segments D2 and D3 from rootworms and related leaf beetles. Insect Molecular Biology 13:495-518. (Pubitemid 39333192)
    • (2004) Insect Molecular Biology , vol.13 , Issue.5 , pp. 495-518
    • Gillespie, J.1    Cannone, J.2    Gutell, R.3    Cognato, A.4
  • 18
    • 20444379556 scopus 로고    scopus 로고
    • A secondary structural model of the 28S rRNA expansion segments D2 and D3 for chalcidoid wasps (Hymenoptera: Chalcidoidea)
    • DOI 10.1093/molbev/msi152
    • Gillespie, J. J., Munro, J. B., Heraty, J. M., Yoder, M. J., Owen, A. K., and Carmichael, A. E. 2005. A secondary structural model of the 28S rRNA expansion segments D2 and D3 for Chalcidoid Wasps. Molecular Biology and Evolution 22:1593-1608. (Pubitemid 40800688)
    • (2005) Molecular Biology and Evolution , vol.22 , Issue.7 , pp. 1593-1608
    • Gillespie, J.J.1    Munro, J.B.2    Heraty, J.M.3    Yoder, M.J.4    Owen, A.K.5    Carmichael, A.E.6
  • 19
    • 0346971259 scopus 로고    scopus 로고
    • ITS secondary structure derived from comparative analysis: Implications for sequence alignment and phylogeny of the Asteraceae
    • DOI 10.1016/S1055-7903(03)00094-0
    • Goertzen, L. R., Cannone. J. J., Gutell, R. R., and Jansen, R. K. 2003. ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae. Molecular Phylogenetics and Evolution 29:216-234. (Pubitemid 38370212)
    • (2003) Molecular Phylogenetics and Evolution , vol.29 , Issue.2 , pp. 216-234
    • Goertzen, L.R.1    Cannone, J.J.2    Gutell, R.R.3    Jansen, R.K.4
  • 20
    • 0034520029 scopus 로고    scopus 로고
    • Sequence, secondary structure and phylogenetic analyses of the ribosomal internal transcribed spacer 2 (ITS2) in the Timarcha leaf beetles (Coleoptera: Chrysomelidae)
    • DOI 10.1046/j.1365-2583.2000.00223.x
    • Gomez-Zurita, J., Juan, C., and Petitpierre, E. 2000. Sequence, secondary structure and phylogenetic analyses of the ribosomal internal transcribed spacer 2 (ITS2) in the Timarcha leaf beetles. Insect Molecular Biology 9:591-604. (Pubitemid 32040048)
    • (2000) Insect Molecular Biology , vol.9 , Issue.6 , pp. 591-604
    • Gomez-Zurita, J.1    Juan, C.2    Petitpierre, E.3
  • 22
    • 0021770476 scopus 로고
    • The complete nucleotide sequence of mouse 28S rRNA gene: Implications for the process of size increase of the large subunit rRNA in higher eukaryotes
    • Hassouna, N., Michot, B., and Bachellerie, J. P. 1984. The complete nucleotide sequence of mouse 28S rRNA gene: implications for the process of size increase of the large subunit rRNA in higher eukaryotes. Nucleic Acids Research 12:3563-3583.
    • (1984) Nucleic Acids Research , vol.12 , pp. 3563-3583
    • Hassouna, N.1    Michot, B.2    Bachellerie, J.P.3
  • 24
    • 0030034071 scopus 로고    scopus 로고
    • Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA
    • Hickson, R. E., Simon, C., Cooper, A., Spicer, G. S., Sullivan, J., and Penny, D. 1996. Conserved sequence motifs, Alignment, and secondary structure for the third domain of Animal 12S rRNA. Molecular Biology and Evolution 13:150-169. (Pubitemid 26012462)
    • (1996) Molecular Biology and Evolution , vol.13 , Issue.1 , pp. 150-169
    • Hickson, R.E.1    Simon, C.2    Cooper, A.3    Spicer, G.S.4    Sullivan, J.5    Penny, D.6
  • 25
    • 0026300584 scopus 로고
    • Ribosomal DNA: Molecular evolution and phylogenetic inference
    • Hillis, D. M., and Dixon, M. 1991. Ribosomal DNA: molecular evolution and phylogenetic inference. The Quarterly Review of Biology 66:411-446. (Pubitemid 21916771)
    • (1991) Quarterly Review of Biology , vol.66 , Issue.4 , pp. 411-446
    • Hillis, D.M.1    Dixon, M.T.2
  • 26
    • 0033534774 scopus 로고    scopus 로고
    • RDNA units are highly polymorphic in Scutellospora castanea (Glomales, Zygomycetes)
    • DOI 10.1016/S0378-1119(98)00562-9, PII S0378111998005629
    • Hosny, M., Hijri, M., Passerieux, E., and Hubert Dulieu. 1999. rDNA units are highly polymorphic in Scutellospora castanea (Glomales, Zygomycetes). Gene 226:61-71. (Pubitemid 29049441)
    • (1999) Gene , vol.226 , Issue.1 , pp. 61-71
    • Hosny, M.1    Hijri, M.2    Passerieux, E.3    Dulieu, H.4
  • 27
    • 0000045446 scopus 로고    scopus 로고
    • Secondary structure model for the ITS-2 precursor rRNA of strongyloid nematodes of equids: Implification for phylogenetic inference
    • Hung, G. C., Chilton, N. B., Beveridge, I., and Gasser, R. B. 1999. Secondary structure model for the ITS-2 precursor rRNA of strongyloid nematodes of equids: implification for phylogenetic inference. Internaltional Journal of Parasitology 29:1949-1964.
    • (1999) Internaltional Journal of Parasitology , vol.29 , pp. 1949-1964
    • Hung, G.C.1    Chilton, N.B.2    Beveridge, I.3    Gasser, R.B.4
  • 29
    • 0029365329 scopus 로고
    • Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: An example of alignment and data presentation from the frogs
    • Kjer, K. M. 1995. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: An example of alignment and data presentation from the frogs. Molecular Phylogenetics and Evolution 4:314-330.
    • (1995) Molecular Phylogenetics and Evolution , vol.4 , pp. 314-330
    • Kjer, K.M.1
  • 30
    • 0031020581 scopus 로고    scopus 로고
    • The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants
    • Mai, J. C., and Coleman, A. W. 1997. The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants. Journal of Molecular Evolution 44:258-231.
    • (1997) Journal of Molecular Evolution , vol.44 , pp. 258-231
    • Mai, J.C.1    Coleman, A.W.2
  • 31
    • 0030934592 scopus 로고    scopus 로고
    • Effects of nucleotide sequence alignment on phylogeny estimation
    • Morrison, D. A., and Ellis, J. T. 1997. Effects of nucleotide sequence alignment on phylogeny estimation. Molecular Biology and Evolution 14:428-441.
    • (1997) Molecular Biology and Evolution , vol.14 , pp. 428-441
    • Morrison, D.A.1    Ellis, J.T.2
  • 33
    • 0040790546 scopus 로고
    • Antarctylus humus n. gen., n. sp. from the Subantarctic Nematoda: Tylenchoidea
    • Sher, S. A. 1973. Antarctylus humus n. gen., n. sp. from the Subantarctic Nematoda: Tylenchoidea). Journal of nematology 15:19-21.
    • (1973) Journal of Nematology , vol.15 , pp. 19-21
    • Sher, S.A.1
  • 34
    • 0033062206 scopus 로고    scopus 로고
    • Comparison of ribosomal DNA ITS regions among geographical isolates of Cenococcum geophilum
    • Shinohara, M. L., LoBuglio, K. F., and Rogers, S. O. 1999. Comparison of ribosomal DNA ITS regions among geographical isolates of Cenococcum geophilum. Current Genetics 35:527-537.
    • (1999) Current Genetics , vol.35 , pp. 527-537
    • Shinohara, M.L.1    LoBuglio, K.F.2    Rogers, S.O.3
  • 35
    • 0029815120 scopus 로고    scopus 로고
    • Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules
    • Springer, M. S., and Douzery, E. 1996. Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules. 1996. Journal of Molecular Evolution 43:357-373. (Pubitemid 26337545)
    • (1996) Journal of Molecular Evolution , vol.43 , Issue.4 , pp. 357-373
    • Springer, M.S.1    Douzery, E.2
  • 36
    • 33749649260 scopus 로고    scopus 로고
    • Phylogeny of Criconematina Siddiqi, 1980 (nematode: Tylenchida) based on morphology and D2-D3 expansion segments of the 28S-rRNA gene sequences with application of a secondary structure model
    • Subbotin, S. A., Vovlas, N., Crozzoli, R., Sturhan, D., Lamberti, F., Moens, M., and Baldwin, J. G. 2005. Phylogeny of Criconematina Siddiqi, 1980 (nematode: Tylenchida) based on morphology and D2-D3 expansion segments of the 28S-rRNA gene sequences with application of a secondary structure model. Nematology 7:927-944.
    • (2005) Nematology , vol.7 , pp. 927-944
    • Subbotin, S.A.1    Vovlas, N.2    Crozzoli, R.3    Sturhan, D.4    Lamberti, F.5    Moens, M.6    Baldwin, J.G.7
  • 37
    • 34248666090 scopus 로고    scopus 로고
    • Application of the secondary structure model of rRNA for phylogeny: D2-D3 expansion segments of the LSU gene of plant-parasitic nematodes from the family Hoplolaimidae Filipjev, 1934
    • DOI 10.1016/j.ympev.2006.09.019, PII S1055790306003782
    • Subbotin, S. A., Sturhan, D., Vovlas, N., Castillo, P., Tanyi Tambe, J., Moens, M., and Baldwin, J. G. 2007. Application of secondary structure model of rRNA for phylogeny: D2-D3 expansion segments of the LSU gene of plant-parasitic nematodes from the family Hoplolaimidae Filipjev, 1934. Molecular Phylogenetics and Evolution 43:881-890. (Pubitemid 46777381)
    • (2007) Molecular Phylogenetics and Evolution , vol.43 , Issue.3 , pp. 881-890
    • Subbotin, S.A.1    Sturhan, D.2    Vovlas, N.3    Castillo, P.4    Tambe, J.T.5    Moens, M.6    Baldwin, J.G.7
  • 38
    • 47749123440 scopus 로고    scopus 로고
    • A phylogenetic framework for root lesion nematodes of the genus Pratylenchus (Nematoda): Evidence from 18S and D2-D3 expansion segments of 28S ribosomal RNA genes and morphological characters
    • Subbotin, S. A., Ragsdale, E. J., Mullens, T., Roberts, P. A., Mundo-Ocampo, M., and Baldwin, J. G. 2008. A phylogenetic framework for root lesion nematodes of the genus Pratylenchus (Nematoda): evidence from 18S and D2-D3 expansion segments of 28S ribosomal RNA genes and morphological characters. Molecular Phylogenetics and Evolution 48:491-505.
    • (2008) Molecular Phylogenetics and Evolution , vol.48 , pp. 491-505
    • Subbotin, S.A.1    Ragsdale, E.J.2    Mullens, T.3    Roberts, P.A.4    Mundo-Ocampo, M.5    Baldwin, J.G.6
  • 40
    • 0027309533 scopus 로고
    • Rates and patterns of base change in the small subunit ribosomal RNA gene
    • Vawter, L., and Brown, W. M. 1993. Rates and Patterns of base change in the Small Subunit Ribosomal RNA gene. Genetics 134:597-608. (Pubitemid 23156954)
    • (1993) Genetics , vol.134 , Issue.2 , pp. 597-608
    • Vawter, L.1    Brown, W.M.2
  • 41
    • 49749108983 scopus 로고    scopus 로고
    • Molecular phylogeny of the genus Rolylenchus (Nematoda, Tylenchida) and description of a new species
    • Vovlas, N., Subbotin, S. A., Troccoli, A., Liebanas, G., and Castillo, P. 2008. Molecular phylogeny of the genus Rolylenchus (Nematoda, Tylenchida) and description of a new species. Zoologica Scripta 37:521-537.
    • (2008) Zoologica Scripta , vol.37 , pp. 521-537
    • Vovlas, N.1    Subbotin, S.A.2    Troccoli, A.3    Liebanas, G.4    Castillo, P.5
  • 42
    • 0036148235 scopus 로고    scopus 로고
    • Secondary structure of mitochondrial 12S rRNA among Fish and its phylogenetic applications. 2002
    • Wang, H. Y., and Lee, S. C. 2002. Secondary structure of mitochondrial 12S rRNA among Fish and its phylogenetic applications. 2002. Molecular Biology and Evolution 19:138-148.
    • (2002) Molecular Biology and Evolution , vol.19 , pp. 138-148
    • Wang, H.Y.1    Lee, S.C.2
  • 43
    • 0021012648 scopus 로고
    • Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids
    • Woese, C. R., Gutell, R. R., Gupta, R., and Noller, H. F. 1983. Detailed analysis of the high order structure of 16S-like ribosomal ribonucleic acids. Microbiological Reviews 47:621-669. (Pubitemid 14210914)
    • (1983) Microbiological Reviews , vol.47 , Issue.4 , pp. 621-669
    • Woese, C.R.1    Gutell, R.2    Gupta, R.3    Noller, H.F.4
  • 44
    • 0002287019 scopus 로고    scopus 로고
    • Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide in RNA biochemistry and biotechnology
    • J. Barciszewski and B. F. C. Clark, eds, Kluwer Academic Publishers
    • Zuker, M., Mathews, D. H., and Turner, D. H. 1999. Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide in RNA Biochemistry and Biotechnology, J. Barciszewski and B. F. C. Clark, eds. NATO ASI Series. Kluwer Academic Publishers.
    • (1999) NATO ASI Series
    • Zuker, M.1    Mathews, D.H.2    Turner, D.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.