Phylogenetic analyses of Meloidogyne small subunit rDNA

Journal of Nematology

Volumn 34, Issue 4, 2002, Pages 319-327

  De Ley, Irma Tandingan ^a   De Ley, Paul ^a   Vierstraete, Andy ^b   Karssen, Gerrit ^c   Moens, Maurice ^d   Vanfleteren, Jacques ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b GHENT UNIVERSITY   (Belgium)

^c WAGENINGEN UNIVERSITY   (Netherlands)

^d Centrum voor Landbouwkundig Onderzoek Gent CLO / Centre de Recherches Agronomiques Gand   (Belgium)

Author keywords

18S; Globodera; Meloidogyne spp.; Nacobbus; Nematode; Phylogeny; rDNA; Root knot nematode; SSU; Subanguina; Zygotylenchus

Indexed keywords

GLOBODERA; GLOBODERA PALLIDA; GRAMINICOLA; INVERTEBRATA; MELOIDOGYNE; MELOIDOGYNE ARENARIA; MELOIDOGYNE ARTIELLIA; MELOIDOGYNE CHITWOODI; MELOIDOGYNE DUYTSI; MELOIDOGYNE EXIGUA; MELOIDOGYNE GRAMINICOLA; MELOIDOGYNE HAPLA; MELOIDOGYNE ICHINOHEI; MELOIDOGYNE INCOGNITA; MELOIDOGYNE JAVANICA; MELOIDOGYNE MARITIMA; MELOIDOGYNE MICROTYLA; NACOBBUS; NACOBBUS ABERRANS; SUBANGUINA; SUBANGUINA RADICICOLA; ZYGOTYLENCHUS; ZYGOTYLENCHUS GUEVARAI;

EID: 0036967774     PISSN: 0022300X     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (54)

1. Baldwin, J. G. 1992. Evolution of the cyst and noncyst-forming Heteroderinae. Annual Review of Phytopathology 30:271-290.
2. Baum, T. J., P. M. Gresshoff, S. A. Lewis, and R. A. Dean. 1994. Characterization and phylogenetic analysis of four root-knot nematode species using DNA amplification fingerprinting and automated polyacrylamide gel electrophoresis. Molecular Plant-Microbe Interactions, 7:39-47.
3. Bert, W., G. Karssen, R. Van Driessche, and E. Geraert. 2002. The cellular structure of the female reproductive system within the Heteroderinae and Meloidogyninae (Nematoda). Nematology, in press.
4. Blaxter, M. L., P. De Ley, J. R. Garey, L. X. Liu, P. Scheldeman, A. Vierstraete, J. R. Vanfleteren, L. Y. Mackey, M. Dorris, L. M. Frisse, J. T. Vida, and W. K. Thomas. 1998. A molecular evolutionary framework for the phylum Nematoda. Nature 392:71-75.
5. Castagnone-Sereno, P., C. Piotte, J. Uijthof, P. Abad, E. Wajnberg, F. Vanlerberghe-Masutti, M. Bongiovanni, and A. Dalmasso. 1993. Phylogenetic relationships between amphimictic and parthenogenetic nematodes of the genus Meloidogyne as inferred from repetitive DNA analysis. Heredity 70:195-204.
6. Dalmasso, A., and J. G. Bergé. 1978. Molecular polymorphism and phylogenetic relationship in some Meloidogyne spp.: Application to the taxonomy of Meloidogyne. Journal of Nematology 10:323-332.
7. De Ley, I. T., G. Karssen, P. De Ley, A. Vierstraete, L. Waeyenberge, M. Moens, and J. Vanfleteren. 1999. Phylogenetic analyses of internal transcribed spacer region sequences within Meloidogyne. Journal of Nematology 31:530-531 (Abstr.).
8. De Ley, I. T., P. De Ley, A. Vierstraete, G. Karssen, M. Moens, and J. Vanfleteren. 2001. Phylogenetic analyses of Meloidogyne SSU rDNA. Phytopathology 91 (Supplement): S133 (Abstr.).
9. De Rijk, P., and R. De Wachter. 1993. DCSE, an interactive tool for sequence alignment and secondary structure research. Computer Applications in the Biosciences 9:735-740.
10. Dickson, D. W., D. Huisingh, and J. N. Sasser. 1971. Dehydrogenases, acid and alkaline phosphatases, and esterases for chemotaxonomy of selected Meloidogyne, Ditylenchus, Heterodera, and Aphelenchus spp. Journal of Nematology 3:1-16.
11. Eisenback, J. D. 1982. Description of the blueberry root-knot nematode, Meloidogyne carolinensis n. sp.Journal of Nematology 14:303-317.
12. Eisenback, J. D. 1997. Root-knot nematode taxonomic database. Wallingford, UK: CAB International.
13. Esbenshade, P. R., and A. C. Triantaphyllou. 1985. Use of enzyme phenotypes for identification of Meloidogyne species. Journal of Nematology 17:6-20.
14. Esbenshade, P. R., and A. C. Triantaphyllou. 1987. Enzymatic relationships and evolution in the genus Meloidogyne (Nematoda: Tylenchida). Journal of Nematology 19:8-18.
15. Farris, J. S. 1989. The retention index and the rescaled consistency index. Cladistics 5:417-419.
16. Files, J. G., and D. Hirsh. 1981. Ribosomal DNA of Caenorhabditis elegans. Journal of Molecular Biology 149:223.
17. Geraert, E. 1997. Comparison of head patterns in the Tylenchoidea (Nematoda). Nematologica 43:283-294.
18. Hasegawa, M., H. Kishino, and T-A. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22:160-174.
19. Hein, J. 1989. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when phylogeny is given. Molecular Biology and Evolution 6:649-668.
20. Hickson, R. E., C. Simon, A. Cooper, G. S. Spicer, J. Sullivan, and D. Penny. 1996. Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. Molecular Biology and Evolution 13:150-169.
21. Hillis, D. M., and M. T. Dixon. 1991. Ribosomal DNA: Molecular evolution and phylogenetic inference. The Quarterly Review of Biology 66:411-453.
22. Hillis, D. M., and J. P. Huelsenbeck. 1992. Signal, noise, and reliability in molecular phylogenetic analysis. Journal of Heredity 83:189-195.
23. Hugall, A., J. Stanton, and C. Moritz. 1999. Reticulate evolution and the origins of ribosomal internal transcribed spacer diversity in apomictic Meloidogyne. Molecular Biology and Evolution 16:157-164.
24. Hyman, B. C., and T. O. Powers. 1991. Integration of molecular data with systematics of plant parasitic nematodes. Annual Review of Phytopathology 29:89-107.
25. Jeanmougin, F., J. D. Thompson, M. Gouy, D. G. Higgins, and T. J. Gibson. 1998. Multiple sequence alignment with ClustalX. Trends in Biochemical Science 23:403-405.
26. Karssen, G., A. van Aelst, and W. H. van der Putten. 1998. Meloidogyne duytsi n. sp. (Nematoda: Heteroderidae), a root-knot nematode from Dutch coastal foredunes. Fundamental and Applied Nematology 21:299-306.
27. Karssen, G., and T. van Hoenselaar. 1998. Revision of the genus Meloidogyne Göldi, 1892 (Nematoda: Heteroderidae) in Europe. Nematologica 44:713-788.
28. Karssen, G., T. van Hoenselaar, B. Verkerk, and R. Janssen. 1995. Species identification of cyst and root-knot nematodes from potato by electrophoresis of individual females. Electrophoresis 16:105-109.
29. Kishino, H., and M. Hasegawa. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order of the Hominoidea. Journal of Molecular Evolution 29:170-179.
30. Kluge, A. G., and J. S. Farris. 1969. Quantitative phylogenetics and the evolution of anurans. Systematic Zoology 18:1-32.
31. Lockhart, P. J., M. A. Steel, M. D. Hendy, and D. Penny. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Molecular Biology and Evolution 11:605-612.
32. Morrison, D. A., and J. T. Ellis. 1997. Effects of nucleotide sequence alignment on phylogeny estimation: A case study of 18S rDNAs of Apicomplexa. Molecular Biology and Evolution 14:428-441.
33. Nicholas, K. B., and H. B. Nicholas, Jr. 1997. GeneDoc v. 2.6.000. Multiple Sequence Alignment Editor and Shading Utility.
34. Nicholas, K. B., H. B. Nicholas, Jr., and D. W. Deerfield, II. 1997. GeneDoc: Analysis and Visualization of Genetic Variation. EMBNET.NEWS 4:14
35. Page, R. D. M. 1996. TREEVIEW: An application to view phylogenetic trees on personal computers. CABIOS 12:357-358.
36. Page, R. D. M., and E. C. Holmes. 1998. Molecular evolution: A phylogenetic approach. Oxford, UK: Blackwell Science Ltd.
37. Posada, D., and K. A. Crandall. 1998. MODELTEST: Testing the model of DNA substitution. Bioinformatics 14:817-818.
38. Powers, T. O., and L. J. Sandall. 1988. Estimation of genetic divergence in Meloidogyne mitochondrial DNA. Journal of Nematology 20:505-511.
39. Raes, J., and Y. Van De Peer. 1999. Forcon: A software tool for the conversion of sequence alignments. EMBnet. News 6:1; http://vulcan.rug.ac.be/~jerae/Forcon/index.html.
40. Saitou, N., and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.
41. Sokal, R. R., and F. J. Rohlf. 1981. Biometry, 2nd ed. San Francisco: W. H. Freeman.
42. Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies. Molecular Biology and Evolution 13:964-969.
43. Swofford, D. L. 2000. "PAUP*: Phylogenetic Analysis Using Parsimony (* and other methods)", Sunderland, MA: Sinauer Associates, Inc.
44. Szalanski, A. L., B. J. Adams, and T. O. Powers. 1997. Molecular systematics of Tylenchida using 18S ribosomal DNA. Journal of Nematology 29:607-608 (Abstr.).
45. Townshend, J. L., J. W. Potter, and T. R. Davidson. 1984. Some monocotyledonous and dicotyledonous hosts of Meloidogyne microtyla. Plant Disease 68:7-10.
46. Triantaphyllou, A. C. 1966. Polyploidy and reproductive patterns in the root-knot nematode Meloidogyne hapla. Journal of Morphology 118:403-414.
47. Triantaphyllou, A. C. 1985. Cytogenetics, cytotaxonomy, and phylogeny of root-knot nematodes. Pp. 113-126 in, J. N. Sasser and C. C. Carter, eds. An advanced treatise on Meloidogyne, vol. I. Biology and control. Raleigh, NC: North Carolina State University Graphics.
48. Van De Peer, Y., E. Robbrecht, S. de Hoog, A. Caers, P. De Rijk, and R. De Wachter. 1998. Database on the structure of small subunit ribosomal RNA. Nucleic Acid Research 271:179-183.
49. Van der Beek, J. G., R. Folkertsma, C. Zijlstra, P. H. G. Van Koert, L. Poleij, and J. Bakker. 1998. Genetic variation among parthenogenetic Meloidogyne species revealed by AFLPs and 2D-protein electrophoresis contrasted to morphology. Fundamental and Applied Nematology 21:401-411.
50. Waddell, P. J., and M. A. Steel. 1997. General time-reversible distances with unequal rates across sites: Mixing F and inverse Gaussian distributions with invariant sites. Molecular Phylogenetics and Evolution 8:398-414.
51. Wouts, W. M., and S. A. Sher. 1971. The genera of the subfamily Heteroderinae (Nematoda: Tylenchoidea) with a description of two new genera. Journal of Nematology 3:129-144.
52. Wuyts, J., Y. Van de Peer, and R. De Wachter. 2001. Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. Nucleic Acids Research 29:2017-5028.
53. Xue, B., D. Baillie, K. Beckenbach, and J. Webster. 1992. DNA hybridization probes for studying the affinities of three Meloidogyne populations. Fundamental and Applied Nematology 15:35-41.
54. Yang, Z., N. Goldman, and A. Friday. 1994. Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Molecular Biology and Evolution 11:316-324.