Revisiting the Phylogenetic History of Helminths Through Genomics, the Case of the New Echinococcus oligarthrus Genome

MALDONADO, LUCAS L.; OLIVEIRA, GUILHERME CORRÊA DE; ARRABAL, JUAN PABLO; KAMENETZKY, LAURA; ROSENZVIT, MARA CECILIA

Frontiers in Genetics

NCBI

Año: 2019 vol. 10

1664-8021

The first parasitic helminth genome sequence was published in 2007; since then,only ~200 genomes have become available, most of them being draft assemblies.Nevertheless, despite the medical and economical global impact of helminthic infections,parasite genomes in public databases are underrepresented. Recently, through anintegrative approach involving morphological, genetic, and ecological aspects, wehave demonstrated that the complete life cycle of Echinococcus oligarthrus (Cestoda:Taeniidae) is present in South America. The neotropical E. oligarthrus parasite iscapable of developing in any felid species and producing human infections. Neotropicalechinococcosis is poorly understood yet and requires a complex medical examinationto provide the appropriate intervention. Only a few cases of echinococcosis have beenunequivocally identified and reported as a consequence of E. oligarthrus infections.Regarding phylogenetics, the analyses of mitogenomes and nuclear datasets haveresulted in discordant topologies, and there is no unequivocal taxonomic classificationof Echinococcus species so far. In this work, we sequenced and assembled the genomeof E. oligarthrus that was isolated from agoutis (Dasyprocta azarae) naturally infectedand performed the first comparative genomic study of a neotropical Echinococcusspecies. The E. oligarthrus genome assembly consisted of 86.22 Mb which showed~90% identity and 76.3% coverage with Echinococcus multilocularis and containedthe 85.0% of the total expected genes. Genetic variants analysis of whole genomerevealed a higher rate of intraspecific genetic variability (23,301 SNPs; 0.22 SNPs/kb)rather than for the genomes of E. multilocularis and Echinococcus canadensis G7 butlower with respect to Echinococcus granulosus G1. Comparative genomics against E.multilocularis, E. granulosus G1, and E. canadensis G7 revealed 38,762, 125,147, and170,049 homozygous polymorphic sites, respectively, indicating a higher genetic distancebetween E. oligarthrus and E. granulosus sensu lato species. The SNP distribution inchromosomes revealed a higher SNP density in the longest chromosomes. Phylogeneticanalysis using whole-genome SNPs demonstrated that E. oligarthrus is one of the basalspecies of the genus Echinococcus and is phylogenetically closer to E. multilocularis. This work sheds light on the Echinococcus phylogeny and settles the basis to study sylvaticEchinococcus species and their developmental evolutionary features.