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Keywords:

mitochondrial markers, gyrodactylosis, primer design, aquaculture, mitogenomics, salmo salor, ribosomal-rna genes, salmon salmo-salar, atlantic salmon, phylogenetic analysis, parasitic flatworms, rainbow-trout, dna variation, sequence, barcodes, amplification, Science & Technology, Life Sciences & Biomedicine, Genetics & Heredity, Salmo salor, ATLANTIC SALMON, PHYLOGENETIC ANALYSIS, SALARIS MALMBERG, DNA VARIATION, RNA GENES, AMPLIFICATION, ARRANGEMENT, POPULATIONS, CHARACTERS, EVOLUTION, Animals, Base Sequence, Chromosome Mapping, DNA Primers, Genetic Variation, Genome, Helminth, Genome, Mitochondrial, Molecular Sequence Data, Platyhelminths, Sequence Homology, Nucleic Acid, 0604 Genetics, 0606 Physiology, 1108 Medical Microbiology, Developmental Biology, 3101 Biochemistry and cell biology, 3102 Bioinformatics and computational biology, 3105 Genetics

Abstract:

Systematists and evolutionary biologists are constantly on the lookout for new sources of characters to discriminate amongst taxa and estimate interrelationships within and between taxa. Entire mitochondrial genomes provide a wealth of data, both at the nucleotide and amino acid level. Molecular markers are of particular utility when applied to small, morphologically conserved taxa, as is the case for many monogenean ectoparasites of fish. Gyrodactylus species display a considerable degree of anatomical conservatism, complicating diagnostics based solely on morphology, and some are significant pests of wild and cultured fish. Here we sequenced the complete mitochondrial genome of Gyrodactylus derjavinoides Malmberg, Collins, Cunningham & Behiar 2007, one of the most frequently found gyrodactylid species on salmonids in Scandinavia, and compared it with the recently published genomes of Gyrodactylus salaris Malmberg, 1957 and Gyrodactylus thymalli Zitnan 1960. Through comparative sliding window analysis we identified regions of high sequence variability and designed new primer sequences. In total, 6 new primer pairs have been developed, amplifying fragments of cox1, cox3, nad1, nad2, nad4, nad5 and atp6. Together, they amplify regions capturing almost half the nucleotide variability present in the complete mitochondrial genome. These degenerate primers should also work for other Gyrodactylus species parasitizing salmonids. In addition, we developed a multiplex assay that simultaneously amplifies four fragments in a single PCR reaction. Besides the diagnostic value, these fragments can be used for studying the transmission dynamics of Gyrodactylus, providing crucial information for an improved understanding of the spread and epidemiology of these important fish pathogens. (c) 2008 Elsevier B.V. All rights reserved.