A standard workflow for community-driven manual curation ofStrongyloidesgenome annotations

Abstract

Advances in the functional genomics and bioinformatics toolkits forStrongyloidesspecies have positioned these species as genetically tractable model systems for gastrointestinal parasitic nematodes. As community interest in mechanistic studies ofStrongyloidesspecies continues to grow, publicly accessible reference genomes and associated genome annotations are critical resources for researchers. Genome annotations for multipleStrongyloidesspecies are broadly available via the WormBase and WormBase ParaSite online repositories. However, a recent phylogenetic analysis of the receptor-type guanylate cyclase (rGC) gene family in twoStrongyloidesspecies highlights the potential for errors in a large percentage of currentStrongyloidesgene models. Here, we present three examples of gene annotation updates within theStrongyloidesrGC gene family; each example illustrates a type of error that may occur frequently within the annotation data forStrongyloidesgenomes. We also extend our analysis to 405 previously curatedStrongyloidesgenes to confirm that gene model errors are found at high rates across gene families. Finally, we introduce a standard manual curation workflow for assessing gene annotation quality and generating corrections, and we discuss how it may be used to facilitate community-driven curation of parasitic nematode biodata.This article is part of the Theo Murphy meeting issue ‘Strongyloides: omics to worm-free populations’.

Invade or die: behaviours and biochemical mechanisms that drive skin penetration in Strongyloides and other skin-penetrating nematodes

“…Generation of transgenic Strongyloides iL3s is accomplished by microinjection of transgene-encoding DNA into the gonads of free-living females or males using techniques adopted from C. elegans [108][109][110]112]. Some important considerations for the design of DNA constructs for expression in Strongyloides are as follows: (i) inclusion of a 3 0 untranslated region (3 0 UTR) from the Strongyloides genome, such as the Ss-era-1 3 0 UTR, improves the efficiency of transgenesis [117]; (ii) codon optimization improves transgene expression [118]; and (iii) gene annotations in WormBase ParaSite should be carefully examined for accuracy given that errors in automated gene annotations are common and require manual correction using publicly available RNA-sequencing (RNA-seq) data [29,119]. The injected DNA forms extrachromosomal arrays and the expression of transgenes from these arrays can be detected in the F 1 generation either by direct visualization or reverse transcription-polymerase chain reaction [108][109][110]117].…”

Strongyloides : omics to worm-free populations

“…Astra Bryant, Damia Akimori, Jonathan Stoltzfus and Elissa Hallem highlight gene annotation errors in the Strongyloides genomes and present a workflow for improving gene annotations and correcting errors (Bryant et al [38]).…”