Next Generation Sequencing and Genome Information of Parasite Biodiversity of medico-veterinary significance in North-East India
Here in, we present a straightforward approach for reconstructing novel mt genomes directly from NGS data generated from total genomic DNA extracts. We took advantage of the whole genome sequence data for F. buski (our unpublished results), generated by NGS and its comparison with the existing data for the F. hepatica mt genome sequence to design precise and specific primers for amplification of mt genome sequences of F. buski. We then carried out long-range PCR to create a NGS library enriched in mt DNA sequences. We utilized two different next generation sequencing platforms to completely sequence the mitochondrial genome, and applied innovative approaches to assemble the mitochondrial genome in silico and annotate it. When verifying one region of the assembly by Sanger sequencing it was found to match our assembly results. The purpose of the present study was to sequence the mt genome of F. buski for the first time with a novel strategy, compare its sequences and gene organization, identify any adaptive mutations in the 12 protein-coding genes of the intestinal parasite species, and to reconstruct the phylogenetic relationships of several species of Trematoda and Cestoda in the Phylum Platyhelminths, using mtDNA sequences available in GenBank.