Improving helminth genome resources in the post-genomic era

Genomic landscape of drug response reveals mediators of anthelmintic resistance

“…To determine the predicted functional consequence of individual variants, mpileup files were processed using bcftools (version 1.9; parameters: call -vm -Oz), after which annotation of the variant call format (VCF) file was performed using SNPeff ( Cingolani et al., 2012 ) (version 4.3r; parameters: -no-intergenic -no-downstream -no-upstream). The current annotation GFF used to build the annotation database is available at WormBase ParaSite (release 17; https://parasite.wormbase.org/index.html ) ( Doyle, 2022 ).…”

Helminthic host defense peptides: using the parasite to defend the host

“…Although these peptides were not individually tested, the authors were able to demonstrate the antimicrobial activity carried by EVs and ESP, validating the reliability of their approach [66]. Despite these encouraging outputs, the computer-assisted identification of novel HDP in helminths will remain a challenging task for the years to come, due to the variable quality of available helminth genome assemblies, the different technical approaches used for sequencing and assembly, the inherent complexity of these genomes and the risk of exogenous contamination [67]. Moreover, machine learning approaches require a list of known protein sequences as an input, which in the case of helminths often derives from incomplete gene annotations.…”

“…Undoubtedly, ongoing community efforts such as WormBase Parasite [56] will lead to further improvements in the quality of -omic resources available for helminths in the next few years, simplifying and amplifying the future identification of HDP in these organisms [67].…”

Genome structure and population genomics of the canine heartwormDirofilaria immitis

“…The copyright holder for this preprint (which this version posted April 26, 2023. ; https://doi.org/10.1101/2023.04.25.538225 doi: bioRxiv preprint resolve the genetics of resistance based on low sample numbers and limited drug susceptibility data among the available samples analysed here. However, these results demonstrate the value of a curated chromosomal genome assembly (Doyle, 2022), enabling a more precise differentiation between genetic variants associated with drug selection from unlinked background variation. Furthermore, it provides a scaffold for genetic mapping and genome-wide association experiments in D. immitis, which has been essential for understanding the genetics of anthelmintic resistance in other helminth species of humans (Doyle et al, 2017;Le Clec'h et al, 2021) and veterinary importance (Beesley et al, 2023;Doyle et al, 2022).…”