title: The Echinococcus canadensis (G7) genome: a key knowledge of parasitic platyhelminth human diseases.
abstract: The parasite Echinococcus canadensis (G7) (phylum Platyhelminthes, class Cestoda) is one of the causative agents of echinococcosis. Echinococcosis is a worldwide chronic zoonosis affecting humans as well as domestic and wild mammals, which has been reported as a prioritized neglected disease by the World Health Organisation. No genomic data, comparative genomic analyses or efficient therapeutic and diagnostic tools are available for this severe disease. The information presented in this study will help to understand the peculiar biological characters and to design species-specific control tools.
  
  
  
  We sequenced, assembled and annotated the 115-Mb genome of E. canadensis (G7). Comparative genomic analyses using whole genome data of three Echinococcus species not only confirmed the status of E. canadensis (G7) as a separate species but also demonstrated a high nucleotide sequences divergence in relation to E. granulosus (G1). The E. canadensis (G7) genome contains 11,449 genes with a core set of 881 orthologs shared among five cestode species. Comparative genomics revealed that there are more single nucleotide polymorphisms (SNPs) between E. canadensis (G7) and E. granulosus (G1) than between E. canadensis (G7) and E. multilocularis. This result was unexpected since E. canadensis (G7) and E. granulosus (G1) were considered to belong to the species complex E. granulosus sensu lato. We described SNPs in known drug targets and metabolism genes in the E. canadensis (G7) genome. Regarding gene regulation, we analysed three particular features: CpG island distribution along the three Echinococcus genomes, DNA methylation system and small RNA pathway. The results suggest the occurrence of yet unknown gene regulation mechanisms in Echinococcus.
  
  
  
  This is the first work that addresses Echinococcus comparative genomics. The resources presented here will promote the study of mechanisms of parasite development as well as new tools for drug discovery. The availability of a high-quality genome assembly is critical for fully exploring the biology of a pathogenic organism. The E. canadensis (G7) genome presented in this study provides a unique opportunity to address the genetic diversity among the genus Echinococcus and its particular developmental features. At present, there is no unequivocal taxonomic classification of Echinococcus species; however, the genome-wide SNPs analysis performed here revealed the phylogenetic distance among these three Echinococcus species. Additional cestode genomes need to be sequenced to be able to resolve their phylogeny.
authors.affiliation: IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina. lucas.l.maldonado@gmail.com.
authors.forename: Lucas L
authors.initials: LL
authors.lastname: Maldonado
authors.affiliation: Genomics and Computational Biology Group, René Rachou Research Center, Oswaldo Cruz Foundation, Belo Horizonte, Brazil.
authors.forename: Juliana
authors.initials: J
authors.lastname: Assis
authors.affiliation: Genomics and Computational Biology Group, René Rachou Research Center, Oswaldo Cruz Foundation, Belo Horizonte, Brazil.
authors.forename: Flávio M Gomes
authors.initials: FM
authors.lastname: Araújo
authors.affiliation: Genomics and Computational Biology Group, René Rachou Research Center, Oswaldo Cruz Foundation, Belo Horizonte, Brazil.
authors.forename: Anna C M
authors.initials: AC
authors.lastname: Salim
authors.affiliation: IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
authors.forename: Natalia
authors.initials: N
authors.lastname: Macchiaroli
authors.affiliation: IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
authors.forename: Marcela
authors.initials: M
authors.lastname: Cucher
authors.affiliation: IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
authors.forename: Federico
authors.initials: F
authors.lastname: Camicia
authors.affiliation: IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
authors.forename: Adolfo
authors.initials: A
authors.lastname: Fox
authors.affiliation: IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
authors.forename: Mara
authors.initials: M
authors.lastname: Rosenzvit
authors.affiliation: Genomics and Computational Biology Group, René Rachou Research Center, Oswaldo Cruz Foundation, Belo Horizonte, Brazil.|Instituto Tecnológico Vale, Belém, Brazil.
authors.forename: Guilherme
authors.initials: G
authors.lastname: Oliveira
authors.affiliation: IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina. lkamenetzky@fmed.uba.ar.
authors.forename: Laura
authors.initials: L
authors.lastname: Kamenetzky
mesh_terms: D000818:Animals; D060565:Argonaute Proteins / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism; D055028:Comparative Genomic Hybridization; D020451:Contig Mapping; D018899:CpG Islands; D019175:DNA Methylation; D004443:Echinococcosis / Q000235:genetics* / Q000469:parasitology / Q000473:pathology; D004446:Echinococcus / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D018503:Genome, Protozoan; D006801:Humans; D020071:Interspersed Repetitive Sequences / Q000235:genetics; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D015800:Protozoan Proteins / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism
chemical_list: D060565:Argonaute Proteins; D015800:Protozoan Proteins
keywords: Comparative genomics; Drug targets; Echinococcus genome; Helminth parasites; SNPs