Molecular basis for identification of species/isolates of gastrointestinal nematode parasites

Gastrointestinal（GI） parasitism is the most serious constraint throughout the world in small ruminants which causes significant production loss in animals.GI parasites are major contributor to reduce productivity in terms of meat,milk and wool in animals.Control of GI parasite is done primarily by anthelmintic treatment where choice and schedule of treatment is done after identification and quantitation of individual parasite.Identification of GI parasites is done through microscopic method by identifying specific morphological characteristics of egg and larva（L3）.Since most of parasite eggs are having similar morphological characteristics, identification up to species level through microscopy is not possible in most of cases.To address this issue,molecular techniques are the viable alternative for identification of species as well as molecular level differences within a species（isolates） of parasites.Different DNA based molecular techniques viz.PCR,AFLP,RAPD,RFLP,PCR-SSCP,real time PCR,DNA microarray etc.have been used for identification and to assess the genetic diversity among parasite population.For identification of species,the characteristic sequence of genomic DNA of different species should differ to allow the delineation of species,but at the same time,no/minor variation within the species should exist.In contrast,for purpose of identifying population variants（strains/isolates）, a considerable degree of variation in the sequence should exist within a species.Various target regions,including nuclear ribosomal DNA（rDNA）,mitochondrial DNA（mtDNA） or repetitive DNA elements（microsatellite loci）,which show considerable variation in the number of repeats within individuals have been employed to achieve the identification of parasites species or strain.

Intra-species sequence variability in 28s rRNA gene of Oesophagostomum venulosum isolated from goats of West Bengal,India.

Objective:To identify genotypes of Oesophagostmum venulosum(O.venulosum) prevailing in West Bengal,India by comparing variation of nucleotide sequences among 28S rRNA.Methods: PCR amplification of partial segment of 28 S rRNA sequence and analysis of sequence amplified product by single strand conformation polymorphism(SSCP).Results:Two distinct conformers among male and female parasites were identified by PCR-SSCP analysis.Sequence analysis among conformers revealed the presence of five single nucleotide polymorphisms(SNP) in codon 64,66,86,125 and 146.Secondary RNA prediction structure showed that out of 5 SNPs,4 occurred at interior loop of RNA which confirmed evolutionary changes among isolates prevailing in this region.Conclusions:SNPs occured in different isolates of 0.venulosum might influence critical changes in rRNA folding pattern which influence evolutionary changes among isolates.