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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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