Advertisement

Journal of Molecular Evolution

, Volume 72, Issue 2, pp 169–181 | Cite as

Molecular Variability and Evolution of the Pectate Lyase (pel-2) Parasitism Gene in Cyst Nematodes Parasitizing Different Solanaceous Plants

  • Barbara Geric StareEmail author
  • Didier Fouville
  • Saša Širca
  • Aurore Gallot
  • Gregor Urek
  • Eric Grenier
Article

Abstract

While pectate lyases are major parasitism factors in plant-parasitic nematodes, there is little information on the variability of these genes within species and their utility as pathotype or host range molecular markers. We have analysed polymorphisms of pectate lyase 2 (pel-2) gene, which degrades the unesterified polygalacturonate (pectate) of the host cell-wall, in the genus Globodera. Molecular variability of the pel-2 gene and the predicted protein was evaluated in populations of G. rostochiensis, G. pallida, G.mexicana” and G. tabacum. Seventy eight pel-2 sequences were obtained and aligned. Point mutations were observed at 373 positions, 57% of these affect the coding part of the gene and produce 129 aa replacements. The observed polymorphism does not correlate either to the pathotypes proposed in potato cyst nematodes (PCN) or the subspecies described in tobacco cyst nematodes. The trees reveal a topology different from the admitted species topology as G. rostochiensis and G. pallida sequences are more similar to each other than to G. tabacum. Species-specific sites, potentially applicable for identification, and sites distinguishing PCN from tobacco cyst nematodes, were identified. As both G. rostochiensis and G. pallida display the same host range, but distinct from G. tabacum, which cannot parasitize potato plants, it is tempting to speculate that pel-2 genes polymorphism may be implicated in this adaptation, a view supported by the fact that no active pectate lyase 2 was found in G.mexicana”, a close relative of G. pallida that is unable to develop on cultivated potato varieties.

Keywords

Cell-wall degradation Globodera Parasitic factor Pectate lyase Plant-parasitic nematode Potato cyst nematode Convergent evolution Purifying selection 

Notes

Acknowledgments

This work was supported by the Slovenian Research Agency and the Ministry of Agriculture, Forestry and Food of the Republic of Slovenia (V4-0324 and BI-FR/07-08-INRA-003) and INRA and the Ministry of higher Education, Science and Technology (MESST). This work benefited from link funded via COST 872 action. We would like to thank Dr. Didier Mugniery, Dr. Björn Niere and Dr. Nicola Greco for providing the G. rostochiensis populations and Dr. Matej Butala for advice on 3D modelling.

Supplementary material

239_2010_9413_MOESM1_ESM.tif (1.5 mb)
Supplementary material, Figure S1: Entropy plots for determined DNA sequences of parasitism gene pel2 in G. pallida (A), G. tabacum (B) and G. rostochiensis (C) presents variability throughout the sequences. Alignment positions that do not exhibit any variability have the entropy of 0, whereas positions of high variability are represented by peaks in the entropy plots (Hall 1999). Organization of the determined gene sequences is presented below the entropy plots as a scheme; exons as black boxes, introns as white boxes, untranslated sequences (UTS) as grey, drawn schematically to indicate their relative position and sizes for the representing clone B1h. (TIFF 1550  kb)

References

  1. Abad P, Gouzy J, Aury J-M, Castagnone-Sereno P, Danchin EGJ, Deleury E et al (2008) Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol 26:909–915PubMedCrossRefGoogle Scholar
  2. Adam MAM, Phillips MS, Jones JT, Blok VC (2008) Characterisation of the cellulose-binding protein Mj-cbp-1 of the root knot nematode, Meloidogyne javanica. Physiol Mol Plant Pathol 72:21–28CrossRefGoogle Scholar
  3. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402PubMedCrossRefGoogle Scholar
  4. Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL Workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22:195–201PubMedCrossRefGoogle Scholar
  5. Baldwin JG, Mundo-Ocampo M (1991) Heteroderinae, cyst- and noncyst-forming nematodes. In: Nickle WR (ed) Manual of agricultural nematology. Marcel Dekker Inc., New york, Basel, Hong Kong, pp 275–362Google Scholar
  6. Bendezu F, Evans K (2001) Pathotype characterisation of populations of potato cyst nematodes Globodera pallida and G. rostochiensis by RAPD-PCR. Int J Nematol 11:200–208Google Scholar
  7. Blok VC, Malloch G, Harrower BE, Phillips MS, Vrain TC (1998) Intraspecific variation in ribosomal DNA in populations of the potato cyst nematode Globodera pallida. J Nematol 30:262–274PubMedGoogle Scholar
  8. Brown EB, Sykes GB (1983) Assessment of the losses caused to potatoes by the potato cyst nematodes, Globodera rostochiensis and G. pallida. Ann Appl Biol 103:271–276CrossRefGoogle Scholar
  9. Canto-Saenz M, de Scurrah MM (1977) Races of the potato cyst nematode in the Andean region and a new system of classification. Nematologica 23:340–349CrossRefGoogle Scholar
  10. da Cunha MJM, da Conceição ILPM, Abrantes IM de O, Santos MSN de A (2006) Assessment of the use of high-performance capillary gel electrophoresis to differentiate isolates of Globodera spp. Nematology 8:139–146Google Scholar
  11. Davis EL, Hussey RS, Baum TJ (2009) Parasitism genes: what they reveal about parasitism. In: Berg RH, Taylor CG (eds) Cell biology of plant nematode parasitism. Springer-Verlag, Berlin, Heidelbrg, pp 15–44CrossRefGoogle Scholar
  12. de Boer JM, McDermott JP, Davis EL, Hussey RS, Popeijus H, Smant G et al (2002) Cloning of a putative pectate lyase gene expressed in the subventral esophageal glands of Heterodera glycines. J Nematol 34:9–11PubMedGoogle Scholar
  13. Delport W, Poon AF, Frost SDW, Kosakovsky Pond SL (2010) Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26:2455–2457PubMedCrossRefGoogle Scholar
  14. Doyle EA, Lambert KN (2002) Cloning and characterization of an esophageal-gland-specific pectate lyase from the root-knot nematode Meloidogyne javanica. Mol Plant Microbe Interact 15:549–556PubMedCrossRefGoogle Scholar
  15. Folkertsma RT, van der Rouppe Voort JNAM, van Gent-Pelzer MPE, de Groot KE, van der Bos WJ, Schots A, Bakker J, Gommers FJ (1994) Inter- and intraspecific variation between populations of Globodera rostochiensis and G. pallida revealed by random amplified polymorphic DNA. Phytopathology 84:807–811CrossRefGoogle Scholar
  16. Folkertsma RT, van der Rouppe Voort JNAM, de Groot KE, van Zandvoort PM, Schots A, Gommers FJ, Helder J, Bakker J (1996) Gene pool similarities of potato cyst nematode populations assessed by AFLP analysis. Mol Plant Microbe Interact 9:47–54PubMedCrossRefGoogle Scholar
  17. Fox PC, Atkinson HJ (1984) Isoelectric focusing of general protein and specific enzymes from pathotypes of Globodera rostochiensis and G. pallida. Parasitology 88:131–139CrossRefGoogle Scholar
  18. Fullaondo A, Vicario A, Aguirre A, Barrena I, Salazar A (2001) Quantitative analysis of two-dimensional gel electrophoresis protein patterns: a method for studying genetic relationships among Globodera pallida populations. Heredity 87:266–272PubMedCrossRefGoogle Scholar
  19. Gao BL, Allen KD, Davis EL, Baum TJ, Hussey RS (2004) Developmental expression and biochemical properties of a beta-1,4-endoglucanase family in the soybean cyst nematode, Heterodera glycines. Mol Plant Pathol 5:93–104PubMedCrossRefGoogle Scholar
  20. Goetze E (2006) Elongation factor 1-[alpha] in marine copepods (Calanoida: Eucalanidae): phylogenetic utility and unique intron structure. Mol Phylogenetics Evol 40:880–886CrossRefGoogle Scholar
  21. Gonzalez JA, Phillips MS, Trudgill DL (1995) RFLP analysis in Canary Islands and North European populations of potato cyst nematodes (Globodera spp.) I. Analysis of high copy fragments. Nematologica 41:468–479CrossRefGoogle Scholar
  22. Greco N, Di Vito M, Brandonisio A, Giordano I, De Marinis G (1982) The effect of Globodera pallida and G. rostochiensis on potato yields. Nematologica 28:379–386CrossRefGoogle Scholar
  23. Grenier E, Fournet S, Petit E, Anthoine G (2010) A cyst nematode “species factory” called the Andes. Nematology 12:163–169CrossRefGoogle Scholar
  24. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  25. Huang G, Dong R, Allen R, Davis EL, Baum TJ, Hussey RS (2005) Developmental expression and molecular analysis of two Meloidogyne incognita pectate lyase genes. Int J Parasitol 35:685–692PubMedCrossRefGoogle Scholar
  26. Kikuchi T, Shibuya H, Aikawa T, Jones JT (2006) Cloning and characterization of pectate lyases expressed in the esophageal gland of the pine wood nematode Bursaphelenchus xylophilus. Mol Plant Microbe Interac 19:280–287CrossRefGoogle Scholar
  27. Kort J, Ross H, Rumpenhorst HJ, Stone AR (1977) An international scheme for the identification of pathotypes of potato cyst nematodes Globodera rostochiensis and G. pallida. Nematologica 23:333–339CrossRefGoogle Scholar
  28. Kosakovsky Pond SL, Frost SDW (2005) Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21:2531–2533CrossRefGoogle Scholar
  29. Kudla U, Milac A, Qin L, Overmars HA, Roze EHA, Holterman MHM et al (2007) Structural and functional characterization of a novel, host penetration-related pectate lyase from the potato cyst nematode Globodera rostochiensis. Mol Plant Pathol 8:293–305PubMedCrossRefGoogle Scholar
  30. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452PubMedCrossRefGoogle Scholar
  31. Marché L, Valette S, Grenier E, Mugniéry D (2001) Intra-species DNA polymorphism in the tobacco cyst–nematode complex (Globodera tabacum) using AFLP. Genome 44:941–946PubMedCrossRefGoogle Scholar
  32. Mugniéry D, Phillips MS, Rumpenhorst HJ, Stone AR, Treur A, Trudgill DL (1989) Assessment of partial resistance of potato to, and pathotype and virulence differences in, potato cyst nematodes. EPPO Bull 19:7–25CrossRefGoogle Scholar
  33. Mugniéry D, Plantard O, Fournet S, Grenier E, Caromel B, Kerlan MC, Picard D, Ellisseche D (2007) Evaluation de l’efficacité et de la durabilité des résistances à Globodera pallida PA2/3, provenant de Solanum vernei, S. spegazzinii et S. sparsipilum. Nematol Mediterr 35:143–153Google Scholar
  34. Nijboer H, Parlevliet JE (1990) Pathotype-specificity in potato cyst nematodes, a reconsideration. Euphytica 49:39–47CrossRefGoogle Scholar
  35. Pauly M, Scheller HV (2000) O-Acetylation of plant cell wall polysaccharides: identification and partial characterization of a rhamnogalacturonan O-acetyl-transferase from potato suspension-cultured cells. Planta 210:659–667PubMedCrossRefGoogle Scholar
  36. Phillips MS, Harrower BE, Trudgill DL, Catley MA, Waugh R (1992) Genetic variation in British populations of Globodera pallida as revealed by isozyme and DNA analyses. Nematologica 38:304–319CrossRefGoogle Scholar
  37. Plantard O, Picard D, Valette S, Scurrah M, Grenier E, Mugniery D (2008) Origin and genetic diversity of Western European populations of the potato cyst nematode (Globodera pallida) inferred from mitochondrial sequences and microsatellite loci. Mol Ecol 17:2208–2218PubMedCrossRefGoogle Scholar
  38. Popeijus H, Overmars H, Jones J, Blok V, Goverse A, Helder J et al (2000) Degradation of plant cell walls by a nematode. Nature 406:36–37PubMedCrossRefGoogle Scholar
  39. Posada D (2006) ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. Nucleic Acids Res 34:W700–W703PubMedCrossRefGoogle Scholar
  40. Qiu WG, Schisler N, Stoltzfus A (2004) The evolutionary gain of spliceosomal introns: sequence and phase preferences. Mol Biol Evol 21:1252–1263PubMedCrossRefGoogle Scholar
  41. Rokas A, Kathirithamby J, Holland PW (1999) Intron insertion as a phylogenetic character: the engrailed homeobox of Strepsiptera does not indicate affinity with Diptera. Insect Mol Biol 8:527–530PubMedCrossRefGoogle Scholar
  42. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar
  43. Scheffler K, Martin DP, Seoighe C (2006) Robust inference of positive selection from recombining coding sequences. Bioinformatics 22:2493–2499PubMedCrossRefGoogle Scholar
  44. Sippl MJ (2008) On distance and similarity in fold space. Bioinformatics 24:872–873PubMedCrossRefGoogle Scholar
  45. Sippl MJ, Wiederstein M (2008) A note on difficult structure alignment problems. Bioinformatics 24:426–427PubMedCrossRefGoogle Scholar
  46. Subbotin SA, Moens M (2006) Molecular taxonomy and phylogeny. In: Perry RN, Moens M (eds) Plant nematology. CABI publishing, London, pp 33–58CrossRefGoogle Scholar
  47. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599PubMedCrossRefGoogle Scholar
  48. Trudgill DL (1985) Potato cyst nematodes: a critical review of the current pathotyping scheme. EPPO Bulletin 15:273–279CrossRefGoogle Scholar
  49. Trudgill DL, Elliott MJ, Evans K, Phillips MS (2003) The white potato cyst nematode (Globodera pallida)—a critical analysis of the threat in Britain. Ann Appl Biol 143:73–80CrossRefGoogle Scholar
  50. Urek G, Širca S, Gerič Stare B, Dolničar P, Strajnar P (2008) The influence of potato cyst nematode G. rostochiensis infestation on different potato cultivars. J Cent Eur Agric 9:71–76Google Scholar
  51. Vanholme B, Van Thuyne W, Vanhouteghem K, De Meutter J, Cannoot B, Gheysen G (2007) Molecular characterization and functional importance of pectate lyase secreted by the cyst nematode Heterodera schachtii. Mol Plant Pathol 8:267–278PubMedCrossRefGoogle Scholar
  52. Wada H, Kobayashi M, Sato R, Satoh N, Miyasaka H, Shirayama Y (2002) Dynamic insertion-deletion of introns in deuterostome EF-1 alpha genes. J Mol Evol 54:118–128PubMedCrossRefGoogle Scholar
  53. Willats WGT, McCartney L, Mackie W, Knox JP (2001) Pectin: cell biology and prospects for functional analysis. Plant Mol Biol 47:9–27PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Barbara Geric Stare
    • 1
    Email author
  • Didier Fouville
    • 2
  • Saša Širca
    • 1
  • Aurore Gallot
    • 2
  • Gregor Urek
    • 1
  • Eric Grenier
    • 2
  1. 1.Plant Protection DepartmentAgricultural Institute of SloveniaLjubljanaSlovenia
  2. 2.INRAUMR1099 BiO3P (Biology of Organisms and Populations Applied to Plant Protection)Le RheuFrance

Personalised recommendations