A comparison of three molecular markers for the identification of populations of globodera pallida

Journal of Nematology

Volumn 44, Issue 1, 2012, Pages 7-17

  Hoolahan, Angelique H ^a   Blok, Vivian C ^b   Gibson, Tracey ^a   Dowton, Mark ^a  

^a UNIVERSITY OF WOLLONGONG   (Australia)

^b SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

Author keywords

Diagnostics; Effector; Genetic distance; Genetics; Globodera pallida; Internal transcribed spacer; Mitochondrial DNA; Phylogenetics; Potato cyst nematode; Rbp 1; Systematics

Indexed keywords

GLOBODERA; GLOBODERA PALLIDA; NEMATODA; SOLANUM TUBEROSUM;

EID: 84879157179     PISSN: 0022300X     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (45)

1. Armstrong, M. R., Blok, V. C., and Phillips, M. S. 2000. A multipartite mitochondrial genome in the potato cyst nematode Globodera pallida. Genetics 154:181-192.
2. Armstrong, M. R., Husmeier, D., Phillips, M. S., and Blok, V. C. 2007. Segregation and recombination of a multipartite mitochondrial DNA in populations of the potato cyst nematode Globodera pallida. Journal of Molecular Evolution 64:689-701.
3. Bates, J. A., Taylor, E. J. A., Gans, P. T., and Thomas, J. E. 2002. Determination of relative proportions of Globodera species in mixed populations of potato cyst nematodes using PCR product melting peak analysis. Molecular Plant Pathology 3:153-161.
4. Blanchard, A., Esquibet, M., Fouville, D., and Grenier, E. 2005. Ranbpm homologue genes characterised in the cyst nematodes Globodera pallida and Globodera 'mexicana'. Physiological and Molecular Plant Pathology 67:15-22.
5. Blok, V. C., Malloch, G., Harrower, B., Phillips, M. S., and Vrain, T. C. 1998. Intraspecific variation in ribosomal DNA in populations of the potato cyst nematode Globodera pallida. Journal of Nematology 30:262-74.
6. Canto Saenz, M., and De Scurrah, M. M. 1977. Races of the potato cyst nematode in the Andean region and a new system of classification. Nematologica 23:340-349.
7. Dwivedi, B., and Gadagkar, S. 2009. Phylogenetic inference under varying proportions of indel-induced alignment gaps. BMC Evolutionary Biology 9:211.
8. Evans, K., and Stone, A. R. 1977. A review of the distribution and biology of the potato cyst-nematodes Globodera rostochiensis and G. pallida. Tropical Pest Management 23:178-189.
9. Geric Stare, B., Fouville, D., Širca, S., Gallot, A., Urek, G., and Grenier, E. 2011. Molecular variability and evolution of the pectate lyase (pel-2) parasitism gene in cyst nematodes parasitizing different Solanaceous plants. Journal of Molecular Evolution 72:169- 181.
10. Gibson, T., Blok, V. C., Phillips, M. S., Hong, G., Kumarasinghe, D., Riley, I. T., and Dowton, M. 2007. The mitochondrial subgenomes of the nematode Globodera pallida are mosaics: Evidence of recombination in an animal mitochondrial genome. Journal of Molecular Evolution 64:463-71.
11. Golubchik, T., Wise, M. J., Easteal, S., and Jermiin, L. S. 2007. Mind the gaps: Evidence of bias in estimates of multiple sequence alignments. Molecular Biology and Evolution 24:2433-42.
12. Grenier, E., Bossis, M., Didier, F., Renault, L., and Didier, M. 2001. Molecular approaches to the taxonomic position of Peruvian potato cyst nematodes and gene pool similarities in indigenous and imported populations of Globodera. Heredity 86:277-290.
13. Hafez, S. L., and Sundararaj, P. 2007. First report of the pale cyst nematode, Globodera pallida, in the United States. Plant Disease 91:325-325.
14. Hall, T. A. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program forWindows 95/98/NT. Nucleic Acids Symposium Series 41:95-98.
15. Haydock, P. P. J., and Evans, K. 1998. Management of potato cyst nematodes in the UK: An integrated approach? Outlook on Agriculture 27:253-260.
16. Hebert, P.D. N., Cywinska, A., Ball, S. L., and J. R., d. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B-Biological Sciences 270:313-321.
17. Hijmans, R. J., and Spooner, D. M. 2001. Geographic distribution of wild potato species. American Journal of Botany 88:2101- 2112.
18. Hodda, M., and Cook, D. C. 2009. Economic impact from unrestricted spread of potato cyst nematodes in Australia. Phytopathology 99:1387-1393.
19. Hoolahan, A. H., Blok, V. C., Gibson, T., and Dowton, M. 2011. Paternal leakage of mitochondrial DNA in experimental crosses of populations of the potato cyst nematode Globodera pallida. Genetica 139:1509-1519.
20. Huelsenbeck, J. P., Ronquist, F., Nielsen, R., and Bollback, J. P. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
21. Kass, R. E., and Raftery, A. E. 1995. Bayes factors. Journal of American Statistics Association 90:773-795.
22. Katoh, K., Misawa, K., Kuma, K.-i., and Miyata, T. 2002. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30:3059-3066.
23. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16:111-120.
24. Kort, J., Ross, H., Rumpenhorst, H. J., and Stone, A. R. 1977. An international scheme for identifying and classifying pathotypes of potato cyst nematodes Globodera rostochiensis and G. pallida. Nematologica 23:333-339.
25. Madani, M., Subbotin, S. A., Ward, L. J., Li, X., and DeBoer, S. H. 2010. Molecular characterization of Canadian populations of potato cyst nematodes, Globodera rostochiensis and G. pallida using ribosomal nuclear RNA and cytochrome b genes. Canadian Journal of Plant Pathology 32:252-263.
26. Marshall, D. C. 2010. Cryptic failure of partitioned Bayesian phylogenetic analyses; Lost in the land of the long trees. Systems Biology 59:108-117.
27. Nelson, L. A., Wallman, J. F., and Dowton, M. 2007. Using COI barcodes to identify forensically and medically important blowflies. Medical and Veterinary Entomology 21:44-52.
28. Nylander, J. A. A. 2004. MrModeltest v2. In: Program distributed by the author, Evolutionary Biology Centre, Uppsala University, p.
29. Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in Biosciences 12:357-358.
30. Phillips, M. S., and Trudgill, D. L. 1998. Variation of virulence, in terms of quantitative reproduction of Globodera pallida populations, from Europe and South America, in relation to resistance from Solanum vernei and S. tuberosum ssp. Andigena Cpc 2802. Nematologica 44:409-423.
31. Picard, D., and Plantard, O. 2006. What constitutes a population for the plant parasitic nematode Globodera pallida in its native area (Peru)? International Journal for Parasitology 36:115-122.
32. Picard, D., Plantard, O., Scurrah, M., and Mugniéry, D. 2004. Inbreeding and population structure of the potato cyst nematode (Globodera pallida) in its native area (Peru). Molecular Ecology 13: 2899-2908.
33. Picard, D., Sempere, T., and Plantard, O. 2007. A northward colonisation of the Andes by the potato cyst nematode during geological times suggests multiple host-shifts from wild to cultivated potatoes. Molecular Phylogenetics and Evolution 42:308-316.
34. Plantard, O., Picard, D., Valette, S., Scurrah, M., Grenier, E., and Mugniéry, D. 2008. Origin and genetic diversity of Western European populations of the potato cyst nematode (Globodera pallida) inferred from mitochondrial sequences and microsatellite loci. Molecular Ecology 17:2208-2218.
35. Pylypenko, L. A., Phillips, M. S., and Blok, V. C. 2008. Characterisation of two Ukrainian populations of Globodera pallida in terms of their virulence and mtDNA, and the biological assessment of a new resistant cultivar Vales Everest. Nematology 10:585-590.
36. Pylypenko, L. A., Uehara, T., Phillips, M. S., Sigareva, D. D., and Blok, V. C. 2005. Identification of Globodera rostochiensis and G. pallida in the Ukraine by PCR. European Journal of Plant Pathology 111:39-46.
37. Qin, L., Overmars, H., Helder, J., Popeijus, H., van der Voort, J. R., Groenink,W., van Koert, P., Schots, A., Bakker, J., and Smant, G. 2000. An efficient cDNA-AFLP-based strategy for the identification of putative pathogenicity factors from the potato cyst nematode Globodera rostochiensis. Molecular Plant-Microbe Interactions 13:830-836.
38. Rehman, S., Postma, W., Tytgat, T., Prins, P., Qin, L., Overmars, H., Vossen, J., Spiridon, L., Petrescu, A., Goverse, A., Bakker, J., and Smant, G. 2009. A secreted SPRY domain-containing protein (SPRYSEC) from the plant-parasitic nematode Globodera rostochiensis interacts with a CC-NB-LRR protein from a susceptible tomato. Molecular Plant-Microbe Interactions 22:330-340.
39. Ronquist, F., and Huelsenbeck, J. P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
40. Ryan, N. A., Duffy, E. M., Cassells, A. C., and Jones, P. W. 2000. The effect of mycorrhizal fungi on the hatch of potato cyst nematodes. Applied Soil Ecology 15:233-240.
41. Sacco, M. A., Koropacka, K., Grenier, E., Jaubert,M. J., Blanchard, A., Goverse, A., Smant, G., and Moffett, P. 2009. The cyst nematode SPRYSEC protein RBP-1 elicits Gpa2- and RanGAP2-dependent plant cell death. PLoS Pathogens 5:e1000564.
42. Stone, A. R. 1985. Co-evolution of potato cyst nematodes and their hosts: Implications for pathotypes and resistance. EPPO Bulletin 15:131-137.
43. Subbotin, S. A., Halford, P. D., Warry, A., and Perry, R. N. 2000. Variations in ribosomal DNA sequences and phylogeny of Globodera parasitising solanaceous plants. Nematology 2:591-604.
44. Sunnucks, P., and Hales, D. F. 1996. Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae). Molecular Biology and Evolution 13:510-524.
45. Tamura, K., Dudley, J., Nei, M., and Kumar, S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24:1596-1599.