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A single nucleotide polymorphism map of the mitochondrial genome of the parasitic nematode Cooperia oncophora

Published online by Cambridge University Press:  16 April 2004

M. VAN DER VEER  and
E. DE VRIES
M. VAN DER VEER
Affiliation:
Division of Parasitology and Tropical Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, PO Box 80.165, 3508 TD Utrecht, The Netherlands
E. DE VRIES
Affiliation:
Division of Parasitology and Tropical Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, PO Box 80.165, 3508 TD Utrecht, The Netherlands
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Abstract

The 13 636 bp mitochondrial (mt) genome sequence of the trichostrongylid nematode Cooperia oncophora was determined.Sequence data have been deposited in the EMBL/GenBank Data libraries under Accession number AY265417. The single nucleotide polymorphisms have been deposited in the dbSNP Database (http://www.ncbi.nlm.nih.gov/SNP) under ID numbers ss8485731-ss8486156. Like the mt genomes of other nematodes it is AT rich (76·75%) and cytidine is the least common nucleoside in the coding strand. There are 2 ribosomal RNA (rrn) genes, 22 transfer RNA (trn) genes and 12 protein coding genes. The relatively short AT-rich region (304 bp) and the lack of a non-coding region between two of the NADH dehydrogenase genes, nad3 and nad5, makes the mt genome of C. oncophora one of the smallest known to date, having only 525 bp of non-coding regions in total. The majority of the C. oncophora protein encoded genes are predicted to end in an abbreviated stop codon like T or TA. In total, 426 single nucleotide polymorphisms (SNP) were mapped on the mt genome of C. oncophora, which is an average of 1 polymorphism per 32 bp. The most common SNPs in the mt genome of C. oncophora were G/A (59·2%) and C/T (28·4%) transitions. Synonymous substitutions (86·4%) were favoured over non-synonymous substitutions. However, the degree of sequence conservation between individual protein genes of different parasitic nematode species did not always correspond to the relative number of non-synonymous SNPs. The mt genome sequence of C. oncophora presents the first mt genome of a member of the Trichostrongyloidea and will be of importance in refining phylogenetic relationships between nematodes. The, still limited, SNP map presented here provides a basis for obtaining insight into the genetic diversity present in the different protein coding genes, trn, rrn and non-coding regions. A more detailed study of the more variable regions will be of use in determining the population genetic structure of C. oncophora. Ultimately this knowledge will add to the understanding of the host–parasite relationship.

Keywords

Cooperia oncophoraparasitic nematodemitochondrial genomesingle nucleotide polymorphismintraspecific genetic variation
Type
Research Article
Information
Parasitology , Volume 128 , Issue 4 , April 2004 , pp. 421 - 431
Copyright
© 2004 Cambridge University Press

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References

REFERENCES

ANDERSON, S., BANKIER, A. T., BARRELL, B. G., DE BRUIJN, M. H., COULSON, A. R., DROUIN, J., EPERON, I. C., NIERLICH, D. P., ROE, B. A., SANGER, F., SCHREIER, P. H., SMITH, A. J., STADEN, R. & YOUNG, I. G. (1981). Sequence and organization of the human mitochondrial genome. Nature, London 290, 457–465.CrossRefGoogle Scholar
ANDERSON, T. J., KOMUNIECKI, R., KOMUNIECKI, P. R. & JAENIKE, J. (1995). Are mitochondria inherited paternally in Ascaris? International Journal for Parasitology 25, 1001–1004.Google Scholar
BLAXTER, M. L., DE LEY, P., GAREY, J. R., LIU, L. X., SCHELDEMAN, P., VIERSTRAETE, A., VANFLETEREN, J. R., MACKEY, L. Y., DORRIS, M., FRISSE, L. M., VIDA, J. T. & THOMAS, W. K. (1998). A molecular evolutionary framework for the phylum Nematoda. Nature, London 392, 71–75.CrossRefGoogle Scholar
BLOUIN, M. S., DAME, J. B., TARRANT, C. A. & COURTNEY, C. H. (1992). Unusual population genetics of a parasitic nematode; mtDNA variation within and among populations. Evolution 46, 470–476.CrossRefGoogle Scholar
BLOUIN, M. S., YOWELL, C. A., COURTNEY, C. H. & DAME, J. B. (1995). Host movement and the genetic structure of populations of parasitic nematodes. Genetics 141, 1007–1014.Google Scholar
BOORE, J. L. (1999). Animal mitochondrial genomes. Nucleic Acids Research 27, 1767–1780.CrossRefGoogle Scholar
CLAYTON, D. A. (1982). Replication of animal mitochondrial DNA. Cell 28, 693–705.CrossRefGoogle Scholar
CLAYTON, D. A. (1991). Replication and transcription of vertebrate mitochondrial DNA. Annual Review of Cell Biology 7, 453–478.CrossRefGoogle Scholar
DAME, J. B., BLOUIN, M. S. & COURTNEY, C. H. (1993). Genetic structure of populations of Ostertagia ostertagi. Veterinary Parasitology 46, 55–62.CrossRefGoogle Scholar
DE VRIES, E. (1998). pUCPCR1. A vector for direct cloning of PCR products in a double Xcm1 restriction site offering compatible single 3′-overhanging T residues. Molecular Biotechnology 10, 273–274.CrossRefGoogle Scholar
DENVER, D. R., MORRIS, K., LYNCH, M., VASSILIEVA, L. L. & THOMAS, W. K. (2000). High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans. Science 289, 2342–2344.CrossRefGoogle Scholar
GYLLENSTEN, U., WHARTON, D. & WILSON, A. C. (1985). Maternal inheritance of mitochondrial DNA during backcrossing of two species of mice. Journal of Heredity 76, 321–324.CrossRefGoogle Scholar
HU, M., CHILTON, N. B. & GASSER, R. B. (2002). The mitochondrial genomes of the human hookworms, Ancylostoma duodenale and Necator americanus (Nematoda: Secernentea). International Journal for Parasitology 32, 145–158.CrossRefGoogle Scholar
JUKES, T. H. & OSAWA, S. (1993). Evolutionary changes in the genetic code. Comparative Biochemistry and Physiology, B 106, 489–494.CrossRefGoogle Scholar
KEDDIE, E. M., HIGAZI, T. & UNNASCH, T. R. (1998). The mitochondrial genome of Onchocerca volvulus: sequence, structure and phylogenetic analysis. Molecular and Biochemical Parasitology 95, 111–127.CrossRefGoogle Scholar
LAVROV, D. V. & BROWN, W. M. (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, 621–637.Google Scholar
MAFF (1986). Manual of Veterinary Parasitological Laboratory Techniques. ( Technical Bulletin No. 18, HMSO, London.)
OJALA, D., MONTOYA, J. & ATTARDI, G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature, London 290, 470–474.CrossRefGoogle Scholar
OKIMOTO, R., MACFARLANE, J. L., CLARY, D. O. & WOLSTENHOLME, D. R. (1992). The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics 130, 471–498.Google Scholar
PERRIERE, G. & GOUY, M. (1996). WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 78, 364–369.CrossRefGoogle Scholar
ROOS, M. H., BOERSEMA, J. H., BORGSTEEDE, F. H. M., CORNELISSEN, J., TAYLOR, M. & RUITENBERG, E. J. (1990). Molecular analysis of selection for benzimidazole resistance in the sheep parasite Haemonchus contortus. Molecular and Biochemical Parasitology 43, 77–88.CrossRefGoogle Scholar
TARRANT, C. A., BLOUIN, M. S., YOWELL, C. A. & DAME, J. B. (1992). Suitability of mitochondrial DNA for assaying interindividual genetic variation in small helminths. Journal of Parasitology 78, 374–378.CrossRefGoogle Scholar
THOMPSON, J. D., GIBSON, T. J., PLEWNIAK, F., JEANMOUGIN, F. & HIGGINS, D. G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25, 4876–4882.CrossRefGoogle Scholar
THOMPSON, J. D., HIGGINS, D. G. & GIBSON, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673–4680.CrossRefGoogle Scholar
WALLACE, D. C. (1999). Mitochondrial diseases in man and mouse. Science 283, 1482–1488.CrossRefGoogle Scholar
WOLSTENHOLME, D. R. (1992). Animal mitochondrial DNA: structure and evolution. International Review of Cytology 141, 173–216.CrossRefGoogle Scholar