title: The mitochondrial genome of Paragonimus westermani (Kerbert, 1878), the Indian isolate of the lung fluke representative of the family Paragonimidae (Trematoda).
abstract: Among helminth parasites, Paragonimus (zoonotic lung fluke) gains considerable importance from veterinary and medical points of view because of its diversified effect on its host. Nearly fifty species of Paragonimus have been described across the globe. It is estimated that more than 20 million people are infected worldwide and the best known species is Paragonimus westermani, whose type locality is probably India and which infects millions of people in Asia causing disease symptoms that mimic tuberculosis. Human infections occur through eating raw crustaceans containing metacercarie or ingestion of uncooked meat of paratenic hosts such as pigs. Though the fluke is known to parasitize a wide range of mammalian hosts representing as many as eleven families, the status of its prevalence, host range, pathogenic manifestations and its possible survivors in nature from where the human beings contract the infection is not well documented in India. We took advantage of the whole genome sequence data for P. westermani, generated by Next Generation Sequencing, and its comparison with the existing data for the P. westermani for comparative mt DNA phylogenomic analyses. Specific primers were designed for the 12 protein coding genes with the aid of existing P. westermani mtDNA as the reference. The Ion torrent next generation sequencing platform was harnessed to completely sequence the mitochondrial genome, and applied innovative approaches to bioinformatically assemble and annotate it. A strategic PCR primer design utilizing the whole genome sequence data from P. westermani enabled us to design specific primers capable of amplifying all regions of the mitochondrial genome from P. westermani. Assembly of NGS data from libraries enriched in mtDNA sequence by PCR gave rise to a total of 11 contigs spanning the entire 14.7 kb mt DNA sequence of P. westermani available at NCBI. We conducted gap-filling by traditional Sanger sequencing to fill in the gaps. Annotation of non-protein coding genes successfully identified tRNA regions for the 24 tRNAs coded in mtDNA and 12 protein coding genes. Bayesian phylogenetic analyses of the concatenated protein coding genes placed P. westermani within the family Opisthorchida. The complete mtDNA sequence of P. westermani is 15,004 base pairs long; the lung fluke is the major etiological agent of paragonimiasis and the first Indian representative for the family Paragonimidae to be fully sequenced that provides important genetic markers for ecological, population and biogeographical studies and molecular diagnostic of digeneans that cause trematodiases.
authors.affiliation: Bioinformatics Centre, North-Eastern Hill University , Shillong, Meghalaya , India.
authors.forename: Devendra K
authors.initials: DK
authors.lastname: Biswal
authors.affiliation: Department of Biotechnology and Bioinformatics, North-Eastern Hill University , Shillong, Meghalaya , India.
authors.forename: Anupam
authors.initials: A
authors.lastname: Chatterjee
authors.affiliation: School of Life Sciences, Jawaharlal Nehru University , New Delhi , India.
authors.forename: Alok
authors.initials: A
authors.lastname: Bhattacharya
authors.affiliation: Bioinformatics Centre, North-Eastern Hill University , Shillong, Meghalaya , India ; Department of Zoology, North-Eastern Hill University , Shillong, Meghalaya , India.
authors.forename: Veena
authors.initials: V
authors.lastname: Tandon
keywords: Bayesian analysis; Mitochondria; Next generation sequencing; Paragonimus; Transfer RNA