The Echinococcus canadensis (G7) genome: a key knowledge of parasitic platyhelminth human diseases

Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3574-0) contains supplementary material, which is available to authorized users.

Unique pharmacological properties of serotoninergic G-protein coupled receptors from cestodes

“…Gene models coding for metabotropic 5-HT receptors were searched using the terms “5-hydroxytryptamine receptor”, “serotonin receptor”, “biogenic amine 5-HT receptor”, “G protein coupled 5 hydroxytryptamine receptor” in Echinococcus multilocularis [ 31 ], Echinococcus granulosus [ 32 ], Echinococcus canadensis [ 33 ] and Mesocestoides corti ( http://parasite.wormbase.org/Mesocestoides_corti_prjeb510/Info/Index/ , Helminth Genomes Consortium) databases. The retrieved gene models were also used as a query in the Blast tool from the NCBI for nucleotide (BLASTN 2.7.0+) and proteins (BLASTP 2.7.0+).…”

“…The availability of genome data from Echinococcus spp [ 31 , 32 , 33 ] and M . corti ( http://parasite.wormbase.org/ Mesocestoides_corti_prjeb510 / Info / Index /, Helminth Genomes Consortium) has now permitted us to search for 5HT-GPCR coding genes in these cestodes.…”

Echinococcus granulosus genotypes in Iran: a systematic review

“…;Pestechian et al, 2014;Sharafi et al, 2014;Vahedi et al, 2014;Fadakar et al, 2015;Farhadi et al, 2015;Rostami et al, 2015;Spotin et al, 2015;Oskouei et al, 2016;Maldonado et al, 2017 …”

Peer Review #2 of "Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies (v0.1)"

“…As a result, the number of genome sequences published has increased exponentially during the last decades (Park et al, 2006;Hahn et al, 2013;Tan et al, 2017;do Amaral et al, 2015;Vanhove et al, 2018). With the increase of studies using complete mitogenomes, several authors have recognized the virtues of a greater amount of nucleotide sequence data for inferring robust phylogenies in many taxonomic groups such as mammals (Arnason et al, 2002;Campbell and Lapointe, 2011), birds (Pacheco et al, 2011), insects (Cameron, 2014), and flatworms (Brabec et al, 2015(Brabec et al, , 2016Maldonado et al, 2017;Vanhove et al, 2018). In addition, we can also relate the power of resolution of the mitogenome to its genome-level characteristics such as gene arrangements and the positions of mobile genetic elements, which are good alternatives to resolve deeper phylogenetic questions (Waeschenbach et al, 2012;Guo, 2015;.…”

“…In spite of its undeniable informational content, whole mitogenomes are still relatively under explored in phylogenetic studies for a multitude of taxonomic groups, especially for those without commercial relevance, non-model organisms, and ancient DNA (Littlewood et al, 2008;Maldonado et al, 2017). The majority of these groups still have poorly understood phylogenetic histories.…”