European Journal of Plant Pathology

, Volume 110, Issue 9, pp 949–957 | Cite as

Comparison of the sequences of the D3 expansion of the 26S ribosomal genes reveals different degrees of heterogeneity in different populations and species of Pratylenchus from the Mediterranean region

  • Francesca De luca
  • Elena Fanelli
  • Mauro Di vito
  • Aurelio Reyes
  • Carla De giorgi
Article

Abstract

Plant parasitic nematodes belonging to the genus Pratylenchus, also known as root lesion nematodes, cause serious economic damage to different crop plants. In order to explore genetic structures in different isolates, we investigated several P. thornei,P. neglectus and P. penetrans populations of different geographic origins. The analysis at the species level was also extended to P. penetrans, P. pinguicaudatus, P. vulnus and P. mediterraneus. Sequence analysis of a specific portion of DNA was carried out. In particular, the sequences of the D3 region of the 26S gene were obtained and compared with similar sequences available in databases. The results support the hypothesis that P. penetrans may represent a species complex, while in P. neglectus the intra-species heterogeneity observed is due to intra-individual variability. Furthermore, the specific conservation of some nucleotides in different P. thornei populations indicates their fixation in the rDNA repeats in this species. The presence of these nucleotides, the molecular signature of P. thornei, may assist in determining the nature of nematode infections.

D3 expansion segment sequences plant parasitic nematodes Pratylenchus species ribosomal DNA 
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References

  1. Al-Banna L, Williamson V and Gardner SL (1997) Phylogenetic analysis of nematodes of the genus Pratylenchus using nuclear 26S rDNA. Molecular Phylogenetic and Evolution 7: 94-102Google Scholar
  2. Blaxter ML, De Ley P, Garey JR, Liu LX, Scheldeman P, Vierstraete A, Van. eteren JR, Mackey LY, Dorris M, Frisse LM, Vida JT and Thomas WK (1998) A molecular evolutionary framework for the phylum Nematoda. Nature 392: 71-75Google Scholar
  3. Carta LK, Skantar AM and Handoo ZA (2001) Molecular, morphological, and thermal characters of 19 Pratylenchus spp. and relatives using the D3 segmant of the nuclear LSU rRNA gene. Nematropica 31: 193-207Google Scholar
  4. Carta LK, Handoo ZA, Skantar AM, Van Biljon J and Botha M (2002) Redescription of Pratylenchus teres Khan & Singh, 1974 (Nemata: Pratylenchidae), with the description of a new subspecies from South Africa and a phylogenetic analysis of related species. African Plant Protection 8: 13-24Google Scholar
  5. Clark CG, Tague BW, Ware VC and Gerbi SA (1984) Xenopus laevis 28S ribosomal RNA: A secondary structure model and its evolutionary and functional implications. Nucleic Acids Research 12: 6197-6220Google Scholar
  6. Corbett DCM and Clark CG (1983) Surface features in the taxonomy of Pratylenchus species. Revue de Nematologie 6: 85-98Google Scholar
  7. Courtright EM, Wall DH, Virginia RA, Frisse RA, Vida JT and Thomas WK (2000) Nuclear and mitochondrial DNA sequence diversity in the antarctic nematode Scottnema lindsayae. Journal of Nematology 32: 143-153Google Scholar
  8. De Giorgi C, De Luca F, Di Vito M and Lamberti F (1997) Modulation of expression at the level of splicing of cut-1 RNA in the infective second-stage juvenile of the plant parasitic nematode Meloidogyne artiellia. Molecular and General Genetics 253: 589-598Google Scholar
  9. De Giorgi C, Veronico P, De Luca F, Natilla A, Lanave C and Pesole G (2002) Structural and evolutionary analysis of the ribosomal genes of the parasitic nematode Meloidogyne artiellia suggests its ancient origin. Molecular and Biochemical Parasitology 124: 91-94Google Scholar
  10. Di Vito M, Catalano F and Zaccheo G (2002) Reproduction of six population of Pratylenchus spp. from the Mediterranean region on selected plant species. Nematologia Mediterranea 30: 103-105Google Scholar
  11. Duncan LW, Inserra RN, Thomas WK, Dunn D, Mustika I, Frisse LM, Mendes ML, Morris K and Kaplan DT (1999) Molecular and morphological analysis of isolates of Praty-lenchus co. eae and closely related species. Nematropica 29: 61-80Google Scholar
  12. Ellis RE, Sulston JE and Coulson AR (1986) The rDNA of C. elegans: Sequence and structure. Nucleic Acids Research 14: 2345-2364Google Scholar
  13. Floyd R, Abebe E, Papert A and Blaxter M (2002) Molecular barcodes for soil nematode identification. Molecular Ecology 11: 839-850Google Scholar
  14. Fitch DH, Bugaj-Gaweda B and Emmons SW (1995) 18S ribosomal RNA gene phylogeny for some Rhabditidae related to Caenorhabditis. Molecular Biology and Evolution 12: 346-358Google Scholar
  15. GCG (1994) GCG. Program manual for the GCG package, Madison WIGoogle Scholar
  16. Grant V (1957) The plant species in theory and practice. In: Mayr E (ed) The Species Problem (pp 67-77) American Association for the advancement of Science, Washington, DC, USAGoogle Scholar
  17. Hancock JM and Dover GA (1988) Molecular coevolution among cryptically simple expansion segments of eukaryotic 26S/28S rRNAs. Molecular Biology and Evolution 5: 377-391Google Scholar
  18. Handoo ZA, Carta LK and Skantar AM (2001) Morphological and molecular characterisation of Pratylenchus arlingtoni n. sp., P. convallariae and P. fallax (Nematoda: Pratylenchi-dae). Nematology 3: 607-618Google Scholar
  19. Heise M, Epe C and Schnieder T (1999) Differences in the second internal transcribed spacer (ITS-2) of eight species of gastrointestinal nematodes of ruminants. Journal of Parasitology 85: 431-435Google Scholar
  20. Hillis DM and Dixon MT (1991) Ribosomal DNA: Molecular evolution and phylogenetic inference. Quarterly Review of Biology 66: 411-453Google Scholar
  21. Hugall A, Stanton J and Moritz C (1999) Reticulate evolution and the origins of ribosomal internal transcribed spacer diversity in apomictic Meloidogyne. Molecular Biology and Evolution 16: 157-164Google Scholar
  22. Luc M (1987) A reappraisal of Tylenchida (nemata). 7. The family Pratylenchidae Thorne, 1949. Revue de Ne ´matologie 10: 203-218Google Scholar
  23. Marquez LM, Miller DJ, MacKenzie JB and Van Oppen MJ (2003) Pseudogenes contribute to the extreme diversity of nuclear ribosomal DNA in the hard coral Acropora. Molecular Biology and Evolution 20: 1077-1086Google Scholar
  24. Martins C, Wasko AP, Oliveira C, Porto-Foresti F, Parise-Maltempi PP, Wright JM and Foresti F (2002) Dynamics of 5S rDNA in the tilapia (Oreochromis niloticus ) genome: Repeat units, inverted sequences, pseudogenes and chromosome loci. Cytogenetic and Genome Research 98: 78-85Google Scholar
  25. Nadler SA, Hoberg EP, Hudspeth DS and Rickard LG (2000) Relationships of Nematodirus species and Nematodirus battus isolates (Nematoda: Trichostrongyloidea) based on nuclear ribosomal DNA sequences. Journal of Parasitology 86: 588-601Google Scholar
  26. Nygard O and Nilsson L (1987) The ribosomal binding site for eukaryotic elongation factor EF-2 contains 5 S ribosomal RNA. Biochimica and Biophysica Acta 908: 46-53Google Scholar
  27. Ouri Y and Mizikubo T (1999) Discrimination of seven Pratylenchus species (Nematoda: Pratylenchidae) in Japan, by PCR-RFLP analysis. Applied Entomology and Zoology 34: 205-211Google Scholar
  28. Petersen DJ, Zijlstra C, Wishart J, Blok V and Vrain TC (1997) Specific probes efficiently distinguish root-knot nematodes species using signature sequences in the ribosomal intergenic spacer. Fundamental and Applied Nematology 20: 619-626Google Scholar
  29. Powers TO, Todd TC, Burnell AM, Murray PCB, Fleming CC, Szalanski AL, Adams BA and Harris TS (1997) The rDNA internal transcribed region as a taxonomic marker for nematodes. Journal of Nematology 29: 441-450Google Scholar
  30. Saccone C, Lanave C, Pesole G and Preparata G (1990) Influence of base composition on quantitative estimate of gene evolution. Methods in Enzymology 183: 570-583Google Scholar
  31. Seperack P, Slatkin M and Arnheim N (1988) Linkage disequilibrium in human ribosomal genes: Implications for multigene family evolution. Genetics 119: 943-949Google Scholar
  32. Swofford DL (1998) PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods) Sinauer Associates, Sunderland, Massachusetts, USAGoogle Scholar
  33. Uehara T, Mizukubo T, Kushida A and Momota Y (1998) Identification of Pratylenchus co. eae and P. loosi using specific primers for PCR amplification of ribosomal DNA. Nematologica 44: 357-368Google Scholar
  34. Van Oppen MJ, McDonald BJ, Willis B and Miller DJ (2001) The evolutionary history of the coral genus Acropora (Scleractinia, Cnidaria) based on a mitochondrial and a nuclear marker: reticulation, incomplete lineage sorting, or morphological convergence? Molecular Biology and Evolution 18: 1315-1329Google Scholar
  35. Vahidi H, Purac A, LeBlanc JM and Honda BM (1991) Characterization of potentially functional 5S rRNA-encoding genes within ribosomal DNA repeats of the nematode Meloidogyne arenaria. Gene 108: 281-284Google Scholar
  36. Waeyenberge L, Ryss A, Moens M, Pinochet J and Vrain TC (2002) Molecular characterization of 18 Pratylenchus species using rDNA restriction fragment length polymorphism. Nematology 2: 135-142Google Scholar
  37. Young TW (1954) An incubation method for collecting migratory endoparasitic nematodes. Plant Diseases Reporter 38: 794-795Google Scholar
  38. Zijlstra C, Lever AEM, Uenk BJ and Van Silfhout CH (1995) Differences between ITS regions of isolates of root-knot nematodes Meloidogyne hapla and M. chitwoodi. Phytopathology 85: 1231-1237Google Scholar

Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • Francesca De luca
    • 1
  • Elena Fanelli
    • 2
  • Mauro Di vito
    • 1
  • Aurelio Reyes
    • 3
  • Carla De giorgi
    • 2
  1. 1.Istituto per la Protezione delle PianteSezione di BariItaly
  2. 2.Dipartimento di Biochimica e Biologia MolecolareUniversity of BariVia OrabonaItaly
  3. 3.Sezione di Bioinformatica e GenomicaIstituto di Tecnologie Biome-dicheItaly

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