Whole genome sequencing of neotropical species Echinococcus oligarthrus
Whole genome sequencing provides extraordinary information about any organism. The first genome sequence from a parasitic helminth was published in 2007, since then only ~200 genomes are available most of them being draft assemblies. Despite both, medical and economical global impact of helminthic infections, these parasite genomes are under-represented in the public genomic databases. Our work focuses on sequencing complete genomes of neglected parasitic helminthes. Recently, through an integrative approach that links morphological, genetic and ecological aspects we have demonstrated for the first time the presence of the complete life cycle of Echinococcus oligarthrus (Cestoda: Taeniidae). The neotropical E. oligarthrus species is capable of developing in any felid species and also producing human infections. Neotropical echinococcosis is a poorly understood disease and requires a complex medical examination to determine the appropriate type of intervention. Only few cases of echinococcosis have been unequivocally identified and reported as consecuence of E. oligarthrus infections and more genetic and genomic information is needed to perform accurate identifications. Moreover, phylogenetic analyses of the full mitogenome and nuclear data set have resulted in discordant topologies and there is no unequivocal taxonomic classification of Echinococccus species described so far. Hereby we sequenced and assembled the complete genome of E. oligarthrus isolated from natural infections of agoutis (Dasyprocta azarae), and performed the first comparative genomic study of a neotropical echinococcus species. Genetic variant analysis revealed a total of 23301 intra specific variant sites comprising a rate of 0.22 SNPs each 1000bp which is higher than the intraspecific genetic variability observed for genomes of Echinococcus multilocularis and Echinococcus canadensis G7 but lower than the intraspecific genetic variability observed in the genome of Echinococcus granulosus G1. Comparative genomics with Echinococcus multilocularis, Echinococcus granulosus (G1) and Echinococcus canadensis (G7) revealed 38762, 125127 and 170118 homozygous polymorphic sites respectively, indicating a higher genetic distance between domestic and wild Echinococcus species. Phylogenetic analysis using whole genome SNPs demonstrated that Echinococcus oligarthrus is the basal species and showed a very close phylogenetic relationship with E. multilocularis. This work allowed to resolve the Echinococcus phylogeny based on complete genome analysis of genetic variation.