A standard workflow for community-driven manual curation of Strongyloides genome annotations

Advances in the functional genomics and bioinformatics toolkits for species have positioned these species as genetically tractable model systems for gastrointestinal parasitic nematodes. As community interest in mechanistic studies of species continues to grow, publicly accessible reference genomes...

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Vydané v:Philosophical transactions of the Royal Society of London. Series B. Biological sciences Ročník 379; číslo 1894; s. 20220443
Hlavní autori: Bryant, Astra S, Akimori, Damia, Stoltzfus, Jonathan D C, Hallem, Elissa A
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: England 15.01.2024
Predmet:
Animals
Databases, Genetic
Genome
Molecular Sequence Annotation
Phylogeny
Strongyloides - genetics
Workflow
Strongyloides
community curation
WormBase
genome annotation
comparative genomics
nematodes
ISSN:1471-2970, 1471-2970
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Popis
Shrnutí:Advances in the functional genomics and bioinformatics toolkits for species have positioned these species as genetically tractable model systems for gastrointestinal parasitic nematodes. As community interest in mechanistic studies of species continues to grow, publicly accessible reference genomes and associated genome annotations are critical resources for researchers. Genome annotations for multiple species 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 two species highlights the potential for errors in a large percentage of current gene models. Here, we present three examples of gene annotation updates within the rGC gene family; each example illustrates a type of error that may occur frequently within the annotation data for genomes. We also extend our analysis to 405 previously curated genes 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 ' : omics to worm-free populations'.
Bibliografia:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1471-2970
1471-2970
DOI:10.1098/rstb.2022.0443