Nematode Molecular Diagnostics: From bands to barcodes

Annual Review of Phytopathology

Volumn 42, Issue , 2004, Pages 367-383

  Powers, Tom ^a  

^a UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

18S ribosomal DNA; DNA barcode; Identification; Internally transcribed spacer; Plant parasitic nematodes

Indexed keywords

HELMINTH DNA; RNA 18S; RNA 28S;

ANIMAL; CLASSIFICATION; GENETICS; MOLECULAR GENETICS; NEMATODE; NUCLEOTIDE SEQUENCE; REVIEW;

ANIMALS; BASE SEQUENCE; DNA, HELMINTH; MOLECULAR SEQUENCE DATA; NEMATODA; RNA, RIBOSOMAL, 18S; RNA, RIBOSOMAL, 28S;

ANIMALIA; NEMATODA; VERMES;

EID: 4744354028     PISSN: 00664286     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.phyto.42.040803.140348     Document Type: Review

References (78)

1. Al-Banna L, Williamson V, Gardner SL. 1997. Phylogenetic analysis of nematodes of the genus Pratylenchus using nuclear 26S rDNA. Mol. Phylogenet. Evol. 7:94-102
2. Amiri S, Subbotin SA, Moens M. 2002. Identification of the beet cyst nematode Heterodera schachtii by PCR. Eur. J. Plant Pathol. 108:497-506
3. Armstrong M, Blok V, Phillips M. 2000. A multipartite mitochondrial genome in the potato cyst nematode Globodera pallida. Genetics 154:181-92
4. Besansky NJ, Severson DW, Ferdig MT. 2003. DNA barcoding of parasites and invertebrate disease vectors: what you don't know can hurt you. Trends in Parasitology 19:545-46
5. Bernard EC. 1992. Soil nematode biodiversity. Biol. Fertil. Soils 14:99-103
6. Blaxter M. 1998. Caenorhabditis elegans is a nematode. Science 282:2041-46
7. Blaxter M. 2003. Counting angels with DNA. Nature 421:122-24
8. Blaxter M, De Ley P, Garey JR, Lui LX, Scheldeman P, et al. 1998. A molecular evolutionary framework for the phylum Nematoda. Nature 392:71-75
9. Blok VC, Phillips MS, Fargette M. 1997. Comparison of sequences from the ribosomal DNA intergenic region of Meloidogyne mayaguensis and other major tropical root-knot nematodes. J. Nematol. 29:16-22
10. Blok VC, Wishart J, Fargette M, Berthier K, Phillips MS. 2002. Mitochondrial DNA differences distinguishing Meloidogyne mayaguensis from the major species of tropical root-knot nematodes. Nematology 4:773-81
11. Blouin MS. 2002. Molecular prospecting for cryptic species of nematodes: mitochondrial DNA versus internal transcribed spacer. Int. J. Parasitol. 32:527-31
12. Boag B, Yeates GW. 1998. Soil nematode biodiversity in terrestrial ecosystems. Biodivers. Conserv. 7:617-30
13. Brito J, Powers TO, Mullin PG, Inserra RN, Dickson DW. 2004. Morphological and molecular characterization of Meloidogyne mayaguensis isolates from Florida. J. Nematol. 36:In press
14. Brown WM. 1985. The mitochondrial genome of animals. In Molecular Evolutionary Genetics, ed. RH MacIntyre, pp. 95-130. New York: Plenum
15. Bulman SR, Marshall JW. 1997. Differentiation of Australasian potato cyst nematode (PCN) populations using the polymerase chain reaction (PCR). NZ J. Crop Hortic. Sci. 25:123-29
16. Carta LK, Skantar AM, Handoo ZA. 2001. Molecular, morphological and thermal characters of 19 Pratylenchus spp. and relatives using the D3 segment of the nuclear LSU rRNA gene. Nematropica 31:195-209
17. Chen P, Roberts PA, Metcalf AE, Hyman BC. 2003. Nucleotide substitution patterning within the Meloidogyne rDNA D3 region and its evolutionary implications. J. Nematol. 35:404-10
18. Clapp JP, Van Der Stoel CD, Van Der Putten WH. 2000. Rapid identification of cyst (Heterodera spp., Globodera spp.) and root-knot (Meloidogyne spp.) nematodes on the basis of ITS2 sequence variation detected by PCR-single-strand conformational polymorphism (PCR-SSCP) in cultures and field samples. Mol. Ecol. 9:1223-32
19. Dautova M, Overmars H, Bakker J, Smant G, Gommers F. 2002. Nuclear and mitochondrial DNA polymorphisms in three mitotic parthenogenetic Meloidogyne spp. Eur. J. Plant Pathol. 108:209-10
20. De Ley IT, De Ley P, Vierstraete A, Karssen G, Moens M, et al. 2002. Phylogenetic analyses of Meloidogyne small subunit rDNA. J. Nematol. 34(4):319-27
21. De Ley P, Blaxter M. 2002. Systematic position and phylogeny. In The Biology of Nematodes, ed. DL Lee, pp. 1-30. London: Taylor & Francis
22. De Ley P, Burt W. 2002. Video capture and editing as a tool for the storage, distribution, and illustration of morphological characters of nematodes. J. Nematol. 34:296-302
23. Duncan LW, Inserra RN, Thomas WK, Dunn D, Mustika I, et al. 1999. Molecular and morphological analysis of isolates of Pratylenchus coffeae and closely related species. Nematropica 29:61-80
24. Fargette M, Phillips M, Blok V, Waugh R, Trudgill D. 1996. An RFLP study of relationships between species population and resistance-breaking lines of tropical species of Meloidogyne. Fundam. Appl. Nematol. 2:193-200
25. Floyd R, Abebe E, Papert A, Blaxter M. 2002. The NoOH single-nematode DNA extraction method. http://nema.cap.ed.ac.uk/npg/naoh.html. April
26. Floyd R, Abebe E, Papert A, Blaxter M. 2002. Molecular barcodes for soil nematode identification. Mol. Ecol. 11:839-50
27. Guirao P, Moya A, Cenis JL. 1995. Optimal use of random amplified polymorphic DNA in estimating the genetic relationship of four major Meloidogyne spp. Phytopathology 85:547-51
28. Hebert PDN, Cywinska A, Ball SL, de Waard JR. 2003. Biological identifications through DNA barcodes. Proc. R. Soc. London Ser. B 270:313-22
29. Hebert PDN, Cywinska A, Ball SL, de Waard JR. 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. London Ser. B 270:S96-S99
30. Hubschen J, Kling L, Ipach U, Zinkernagel V, Bosselut N, et al. 2004. Validation of the specificity and sensitivity of species-specific primers that provide a reliable molecular diagnostic for Xiphinema diversicaudatum, X. index, and X. vuittenezi. Eur. J. Plant Pathol. In press
31. Hugall A, Moritz C, Stanton J, Wolstenholme DR. 1994. Low, but strongly structured mitochondrial DNA diversity in root-knot nematodes (Meloidogyne). Genetics 136:903-12
32. Hugall A, Stanton J, Moritz C. 1997. Evolution of the AT rich mitochondrial DNA of Meloidogyne hapla. Mol. Biol. Evol. 14:40-48
33. Hugall A, Stanton J, Moritz C. 1999. Reticulate evolution and the origins of ribosomal internal transcribed spacer diversity in apomictic Meloidogyne. Mol. Biol. Evol. 16(2):157-64
34. Hyman BC. 1988. Nematode mitochondrial DNA: anomalies and applications. J. Nematol. 20:523-31
35. Ibrahim SK, Baldwin JG, Roberts PA, Hyman BC. 1997. Genetic variation in Nacobbus aberrans: an approach toward taxonomic resolution. J. Nematol. 29:241-49
36. Janzen DH. 2004. Now is the time. Philos. Trans. R. Soc. In press
37. Jatala P. 1993. Nacobbus aberrans, one species or more? Nematropica 23:120
38. Jatala P, Golden M. 1977. Taxonomic status of Nacobbus species attacking potatoes in South America. Nematropica 7:9-10
39. Jones JT, Phillips MS, Armstrong MR. 1997. Molecular approaches in plant nematology. Fundam. Appl. Nematol. 20:1-14
40. Lavrov DV, Brown WM. 2001. Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAs and has a gene arrangement relatable to those of coelomate metazoans. Genetics 157:621-37
41. Luna R, Chitambar JJ. 2003. The California Department of Food and Agriculture. The Nematology Sample Processing Laboratory. http://www.cdfa.ca. gov/phpps/ppd/Nematology/NemaLabChanges/ProcLab/NemaSampleProcLab.htm. November
42. Lund HD, Whipple EL, Hyman CB. 1998. Mitochondrial DNA variable number tandem repeats (VNTRs): utility and problems in molecular ecology. Mol. Ecol. 7:1441-55
43. McKeand JB. 1998. Molecular diagnosis of parasitic nematodes. Parasitology 117:S87-S96
44. Mulholland V, Carde L, O'Donnell KJ, Fleming CC, Powers TO. 1996. Use of the polymerase chain reaction to discriminate potato cyst nematode at the species level. BCPC Symp. Proc. no. 65: Diagn. Crop Prod., pp. 247-52
45. Neher DA. 2001. Nematode communities as ecological indicators of agroecosystem health. In Agroecosystem Sustainability: Developing Practical Strategies, ed. SR Gliessman, pp. 105-20. Boca Raton, FL: CRC Press
46. Okimoto R, Chamberlin HM, Macfarlane JL, Wolstenholme DR. 1991. Repeated sequence sets in mitochondrial DNA molecules of root knot nematodes (Meloidogyne): nucleotide sequences, genome location and potential for host-race identification. Nucleic Acids Res. 19:1619-26
47. Orui Y. 1996. Discrimination of the main Pratylenchus species (Nematoda: Pratylenchidae) in Japan by PCR-RFLP analysis. Appl. Entomol. Zool. 31:505-14
48. Orui Y. 1998. Identification of Japanese species of the genus Meloidogyne (Nematoda: Meloidogynidae) by PCR-RFLP analysis. Appl. Entomol. Zool. 33:43-51
49. Pennisi E. 2003. Modernizing the tree of life. Science 300:1692-97
50. Perlman SJ, Spicer GS, Shoemaker DD, Jaenike JJ. 2003. Associations between mycophagous Drosophila and their Howardula nematode parasites: a worldwide phylogenetic shuffle. Mol. Ecol. 12:237-49
51. Petersen DJ, Vrain TC. 1996. Rapid identification of Meloidogyne chitwoodi, M. hapla and M. fallax using PCR primers to amplify their ribosomal intergenic spacer. Fundam. Appl. Nematol. 19:601-5
52. Powers TO, Harris TS. 1993. A polymerase chain reaction method for the identification of five major Meloidogyne species. J. Nematol. 25:1-6
53. Reid A, Podrucka K. 2004. Interspecific genetic diversity of 50 Steinernema species as determined by RFLP analysis of the ITS region. Nematology: In press
54. Siddiqi MR. 2000. Parasites of Plants and Insects. Wallingford, UK: CABI Publ. 2nd ed.
55. Stanton J, Hugall A, Moritz C. 1997. Nucleotide polymorphisms and an improved PCR-based mtDNA diagnostic for parthenogenetic root-knot nematodes (Meloidogyne spp.) Fundam. Appl. Nematol. 20:261-68
56. Stanton JM, McNicol CD, Steele V. 1998. Non-manual lysis of second-stage Meloidogyne juveniles for identification of pure and mixed samples based on the polymerase chain reaction. Aust. Plant Pathol. 27:112-15
57. Stratford R, Shields R. 1994. A transspliced leader RNA sequence in plant parasitic nematodes. Mol. Biochem. Parasitol. 67:147-55
58. Stein L, Boa Z, Blasiar D, Blumenthal T, Brent M, et al. 2003. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLOS Biol. 1:166-92
59. Stevens JR, Schofield CJ. 2003. Phylogenetics and sequence analysis - some problems for the unwary. Trends Parasitol. 19:582-88
60. Stoeckle M. 2003. Taxonomy, DNA and the barcode of life. BioScience 53:796-97
61. Stoeckle M, Janzen D, Hallwachs W, Hanken J, Baker J. 2003. Taxonomy, DNA, and the Barcode of Life. Draft Conference Report. http://phe.rockefeller. edu/BarcodeConference/index.html
62. Stratford R, Shields R, Goldsbrough AP, Fleming C. 1992. Analysis of repetitive DNA sequences from potato cyst nematodes and their use as diagnostic probes. Phytopathology 82:881-86
63. Subbotin SA, Sturhan D, Rumpenhorst HJ, Moens M. 2003. Molecular and morphological characterisation of the Heterodera avenae species complex (Tylenchida:Heteroderidae). Nematology 5:515-38
64. Subbotin SA, Vierstraete A, DeLey P, Rowe J, Waeyenberge L, et al. 2001. Phylogenetic relationships within the cyst-forming nematodes (Nematoda, Heteroderidae) based on analysis of sequences from the ITS region of ribosomal DNA. Mol. Phylogenet. Evol. 21:1-16
65. Subbotin SA, Waeyenberge L, Moens M. 2000. Identification of cyst forming nematodes of the genus Heterodera (Nematoda: Heteroderidae) based on the ribosomal DNA-RFLP. Nematology 2:153-64
66. Subbotin SA, Waeyenberge L, Molokanova IA, Moens M. 1999. Idenification of Heterodera avenae group species by morphometrics and rDNA-RFLP. Nematology 1:195-207
67. Tanha Maafi Z, Subbotin SA, Moens M. 2003. Molecular identification of cyst-forming nematodes (Heteroderidae) from Iran and a phylogeny based on ITS-rDNA sequences. Nematology 5:99-111
68. Uehara T, Mizukubo T, Kushida A, Momota Y. 1998. Identification of Pratylenchus coffeae and P. loosi using specific primers for PCR amplification of ribosomal DNA. Nematologica 44:357-68
69. Vahidi H, Curran J, Nelson DW, Webster JM, McClure MA, et al. 1988. Unusual sequences, homologous to 5S RNA, in ribosomal DNA repeats of the nematode Meloidogyne arenaria. J. Mol. Biol. 27:222-27
70. Wang X, Bosselut N, Castagnone C, Voisin R, Abad P, et al. 2003. Multiplex polymerase chain reaction identification of single individuals of the Longidorid nematodes Xiphinema index, X diversicadatum, X. vuittenezi, and X. italilae using specific primers from ribosomal genes. Phytopathology 93:160-66
71. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-62
72. Waeyenberge L, Ryss A, Moens M, Pinochet J, Vrain TC. 2000. Molecular characteristics of 18 Pratylenchus species using rDNA restriction fragment length polymorphisms. Nematology 2:135-42
73. Whipple LE, Lunt DH, Hyman BC. 1998. Mitochondrial DNA length variation in Meloidogyne incognita isolates of established genetic relationships: utility for nematode population studies. Fundam. Appl. Nematol. 21:265-71
74. Williamson VM, Caswell-Chen EP, Wu FF, Hanson D. 1994. PCR for nematode identification. In Advances in Molecular Plant Nematology, ed. F Lamberti, C De Giorgi, DM Bird, pp. 119-27. New York: Plenum
75. Williamson VM, Caswell-Chen EP, Westerdahl BB, Wu FF, Caryl G. 1997. A PCR assay to identify and distinguish single juveniles of Meloidogyne hapla and M. chitwoodi. J. Nematol. 29:9-15
76. Xu J, Liu P, Meng Q, Long H. 2004. Characterisation of Meloidogyne species from China using isozyme phenotypes and amplified mitochondrial DNA restriction fragment length polymorphisms. Eur. J. Plant Pathol. In press
77. Zeng J, Subbotin SA, Waeyenberge L, Moens M. 2000. Molecular characterisation of Chinese Heterodera glycines and H. avenae populations based on RFLPs and sequences of rDNA-ITS regions. Russ. J. Nematol. 8:109-13
78. Zijlstra C, Lever AEM, Uenk BJ, Van Silfhout CH. 1995. Differences between ITS regions of isolates of root-knot nematodes Meloidogyne hapla and M. chitwoodi. Phytopathology 85:1231-37