Phylogenetic analysis of geographically diverse Radopholus similis via rDNA sequence reveals a monomorphic motif

Journal of Nematology

Volumn 32, Issue 2, 2000, Pages 134-142

  Kaplan, D T ^a,b   Thomas, W K ^c   Frisse, L M ^c   Sarah, J L ^d   Stanton, J M ^e   Speijer, P R ^f   Marin, D H ^g   Opperman, C H ^h  

^a U S HORTICULTURAL RESEARCH LABORATORY   (United States)

^b University of Missouri ^*  (United States)

^c UNIVERSITY OF MISSOURI KANSAS CITY   (United States)

^d CIRAD   (France)

^e DEPARTMENT OF AGRICULTURE AND FISHERIES   (Australia)

^f INTERNATIONAL INSTITUTE OF TROPICAL AGRICULTURE   (Uganda)

^g University of Costa Rica   (Costa Rica)

^h NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

28S; Banana; Citrus; Evolution; Genetics; ITS1; Nematode; Pathotype; Phylogeny; Quarantine; Race; Radopholus similis; Rdna; Species concepts; Taxonomy

Indexed keywords

EID: 0034336736     PISSN: 0022300X     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (55)

1. Adams, B. J. 1998. Species concepts and evolutionary paradigm in modern nematology. Journal of Nematology 30:1-21.
2. Adams, B. J., A. M. Burnell, and T. O. Powers. 1998. A phylogenetic analysis of Heterorhabditis (Nemata: Rhabditidae) based on internal transcribed spacer 1 DNA sequence data. Journal of Nematology 30:22-39.
3. Baldwin, B. G., M. J. Sanderson, J. M. Porter, M. F. Wojciechowski, C. S. Campbell, and M. J. Donoghue. 1995. The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden 82:247-277.
4. Baldwin, J. G., L. M. Frisse, J. T. Vida, C. D. Eddleman, and W. K. Thomas. 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.
5. Bird, D. M., and D. L. Riddle. 1994. A genetic nomenclature for parasitic nematodes. Journal of Nematology 26:138-143.
6. Blaxter, M. L., P. DeLey, J. R. Garvey, L. 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.
7. Brown, D. D., P. C. Wensink, and E. Jordan. 1972. Journal of Molecular Biology 63:57-73.
8. Cabot, E. L., and Beckenbach, A. T. 1989. Simultaneous editing of multiple nucleic acid and protein sequences with ESEE. Comparative and Applied Biosciences 5:233-234.
9. Campbell, A. J. D., R. B. Gasser, and N. B. Chilton. 1995. Differences in rihosomal DNA sequence of Strongylus species allows identification of single eggs. International Journal for Parasitology 25:359-365.
10. Cherry, T., A. L. Szalanski, T. C. Todd, and T. O. Powers. 1997. The internal transcribed spacer region of Belonolaimus (Nemata: Belonolaimidae). Journal of Nematology 29:23-39.
11. Chilton, N. B., R. B. Gasser, and I. Beveridge. 1995. Differences in a ribosomal DNA sequence of morphologically indistinguishable species within the Hypodonlus macropi complex (Nematoda, Strongyloidea). International Journal of Parasitology 25:647-651.
12. Doyle, J. J. 1992. Gene trees and species trees: Molecular systematics as one-character taxonomy. Systematic Botany 17:144-163.
13. Doyle, J. J. 1995. The irrelevance of allele tree topologies for species delimitation, and a non-topological alternative. Systematic Botany 20:574-588.
14. DuCharme, E. P., and W. Birchfield. 1956. Physiological races of the burrowing nematode. Phytopathology 46:615-616.
15. Duncan, L. W., R. N. Inserra, W. K. Thomas, D. Dunn, I. Mustika, L. M. Frisse, M. L. Mendes, K. Morris, and D. T. Kaplan. 1999. Molecular and morphological analysis of isolates of Pratylenchus coffeae and closely related species. Nematropica 29:61-80.
16. Edwards, K., C. Johnstone, and C. Thompson. 1991. A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucleic Acids Research 19:1349.
17. Eernisse, D. J., and A. G. Kluge. 1993. Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Molecular Biology Evolution 10:1170-1195.
18. Elbardri, G. A. A., E. Geraert, and M. Moens. 1998. Morphological differences among Radopholus (Thorne, 1949) populations from ornamentals in Europe (Pratylenchidae: Nematoda). Mededlingen Faculteit Landbouwkundige en Toegepaste Biologische Watenschappen Gent.
19. Elbardri, G. A. A., E. Geraert, and M. Moens. 1999. Morphological differences among Radopholus populations (Nematode: Tylenchida) from banana in Africa. Journal of Nematode Morphology and Systematics 2:1-16.
20. Fallas, G. A., M. L. Hahn, M. Fargette, P. R. Burrows, and J. L. Sarah. 1996. Molecular and biochemical diversity among isolates of Radopholus spp. from different areas of the world. Journal of Nematology 28:422-431.
21. Federoff, N. V. 1979. On spacers. Cell 16:697-710.
22. Ferris, V. R., J. M. Ferris, and J. Faghihi. 1993. Variation in spacer ribosomal DNA in some cyst-forming species of plant-parasitic nematodes. Fundamental and Applied Nematology 16:177-184.
23. Ferris, V. R., J. M. Ferris, J. Faghihi, and A. Ireholm. 1994. Comparison of isolates of Heterodera avenae using 2-D PAGE protein patterns and ribosomal DNA. Journal of Nematology 26:144-151.
24. Ferris, V. R., L. I. Miller, J. Faghihi, and J. M. Ferris. 1995. Ribosomal DNA comparisons of Globodera from two continents. Journal of Nematology 27:273-283.
25. Files, J. G., and D. Hirsh. 1981. Ribosomal DNA of Caenorhabditis elegans. Journal of Molecular Biology 149: 223-240.
26. Fitch, D. H. 1997. Evolution of male tail development in rhaditid nematodes related to Caenorhabditis elegans. Systematic Biology 46:145-179.
27. Hahn, M. L., P. R. Burrows, N. C. Gnanapragasam, J. Bridge, N. Vines, and D. J. Wright. 1994. Molecular diversity amongst Radopholus similis populations from Sri Lanka detected by RAPD analysis. Fundamental and Applied Nematology 17:275-281.
28. Hasegawa, M., H. Kishino, and K. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22: 160-174.
29. Hillis, D. M., and M. T. Dixon. 1991. Ribosomal DNA: Molecular evolution and phylogenetic inference. Quarterly Review of Biology 66:411-453.
30. Hoste, H., N. B. Chilton, and I. Beveridge. 1995. Differences in the second internal transcribed spacer (ribosomal DNA) between five species of Trichostrongylus (Nematoda, Trichostrongylidae). International Journal for Parasitology 25:75-80.
31. Huettel, R. N., D. W. Dickson, and D. T. Kaplan. 1984. Radopholus citrophilus sp. n. (Nematoda), a sibling species of Radopholus similis. Proceedings of the Helminthological Society of Washington 51:32-35.
32. Huettel, R. N., and Yaegashi, T. Y. 1988. Morphological differences between Radopholus citrophilus and R. similis. Journal of Nematology 20:150-157.
33. Kaplan, D. T. 1994a. Measuring burrowing nematode virulence to select rootstocks for Florida citrus groves. Proceedings of the Florida State Horticultural Society 107:84-89.
34. Kaplan, D. T. 1994b. Molecular characterization of the burrowing nematode sibling species, Radopholus citrophilus and R. similis. Pp. 77-83 in F. Lamberti, C. De Georgi, and D. McK. Bird, eds. Advances in molecular plant nematology, New York: Plenum Press.
35. Kaplan, D. T., and E. L. Davis. 1990. Improved nematode extraction from carrot disk culture. Journal of Nematology 22:399-406.
36. Kaplan, D. T., and C. H. Opperman. 1997. Genome similarity implies that citrus-parasitic burrowing nematodes do not represent a unique species. Journal of Nematology 29:430-440.
37. Kaplan, D. T., and C. H. Opperman. 2000. Reproductive strategies and karyotype of the burrowing nematode, Radopholus similis. Journal of Nematology 23:126-133.
38. Kaplan, D. T., M. C. Vanderspool, C. Garrett, S. Chang, and C. H. Opperman. 1996. Molecular polymorphisms associated with host range in the highly conserved genomes of burrowing nematodes, Radopholus spp. Molecular Plant-Microbe Interactions 9:32-38.
39. Kaplan, D. T., M. C. Vanderspool, and C. H. Opperman. 1997. Sequence tag site and host range assays demonstrate that Radopholus similis and R. citrophilus are not reproductively isolated. Journal of Nematology 29: 421-429.
40. Marin, D. H., D. T. Kaplan, and C. H. Opperman. 1999. Randomly amplified polymorphic DNA differs with burrowing nematode collection site, but not with host range. Journal of Nematology 31:232-239.
41. Nadler, S. A. 1992. Phylogeny of some ascaridoid nematodes, inferred from comparison of 18S and 28S rRNA sequences. Molecular Biology Evolution 9:932-944.
42. Powers, T. O., T. C. Todd, A. M. Burnell, P. C. B. Murray, C. C. Flemming, A. L. Szalanski, B. J. Adams, and T. S. Harris. 1997. The rDNA internal transcribed spacer region as a taxonomic marker for nematodes. Journal of Nematology 29:441-450.
43. Siddiqi, M. R. 1985. Tylenchida: Parasites of plants and insects. St. Albans, UK: CAB International.
44. Strimmer, K., and A. von Haesler, 1996. Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Molecular Biology and Evolution 13:964-969.
45. Strimmer, K., and A. von Haeseler. 1997. PUZZLE ver 4.0.2. http://members.tripod.de/korbi/puzzle/ (28 April 1999).
46. Szalanski, A. L., D. D. Sui, T. S. Harris, and T. O. Powers. 1997. Identification of cyst nematodes of agronomic and regulatory concern with PCR-RFLP of ITS1. Journal of Nematology 29:255-267.
47. Thiery, M., and D. Mugniery. 1996. Interspecific rDNA restriction fragment length polymorphism in Globodera species, parasites of solanaceous plants. Fundamental and Applied Nematology 19:471-480.
48. Thomas, W. K., J. T. Vida, L. M. Frisse, M. Mundo, and J. G. Baldwin. 1997. DNA sequences from formalin-fixed nematodes: Integrating molecular and morphological approaches to taxonomy. Journal of Nematology 29:250-254.
49. Thompson, J. D., D. G. Higgins, and T. J. Gibson, 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties, and weight matrix choice. Nucleic Acids Research, 22:4673-4680.
50. Uehara, T., T. Mizukubo, A. Kushida, and Y. Momota. 1998. Identification of Pratylenchus coffeae and P. loosi using specific primers for PCR amplification of ribosomal DNA. Nematologica 44:357-368.
51. Valette, C., D. Mounport, M. Nicole, J. L. Sarah, and P. Baujard. 1998. Scanning electron microscope studies of two African populations of Radopholus similis (Nematoda: Pratylenchidae) and proposal of R. citrophilus as a junior synonym of R. similis. Fundamental and Applied Nematology 21:139-146.
52. Vrain, T. C., D. A. Wakarchuk, A. C. Levesque, and R. I. Hamilton. 1992. Intraspecific rDNA restriction fragment length polymorphism in the Xiphinema americanum group. Fundamental and Applied Nematology 15:563-573.
53. Xie, H., O. Bain, and S. A. Williams. 1994. Molecular phylogenetic studies on filarial parasites based on 5S ribosomal spacer sequences. Parasite 1:141-151.
54. Zijlstra, C., A. E. M. Lever, B. J. Uenk, and C. H. Van Silfhout. 1995. Differences between ITS regions of isolates of root-knot nematodes Meloidogyne hapla and M. chitwoodi. Phytopathology 85:1231-1237.
55. Zijlstra, C., B. J. Uenk, and C. H. Van Silfhout. 1997. A reliable, precise method to differentiate species of root-knot nematodes in mixtures on the basis of ITS-RFLPs. Fundamental and Applied Nematology 20:59-63.