Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus
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RESEARCH ARTICLE
Open Access
Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus Marina Athanasouli, Hanh Witte, Christian Weiler, Tobias Loschko, Gabi Eberhardt, Ralf J. Sommer and Christian Rödelsperger*
Abstract Background: Nematode model organisms such as Caenorhabditis elegans and Pristionchus pacificus are powerful systems for studying the evolution of gene function at a mechanistic level. However, the identification of P. pacificus orthologs of candidate genes known from C. elegans is complicated by the discrepancy in the quality of gene annotations, a common problem in nematode and invertebrate genomics. Results: Here, we combine comparative genomic screens for suspicious gene models with community-based curation to further improve the quality of gene annotations in P. pacificus. We extend previous curations of one-toone orthologs to larger gene families and also orphan genes. Cross-species comparisons of protein lengths, screens for atypical domain combinations and species-specific orphan genes resulted in 4311 candidate genes that were subject to community-based curation. Corrections for 2946 gene models were implemented in a new version of the P. pacificus gene annotations. The new set of gene annotations contains 28,896 genes and has a single copy ortholog completeness level of 97.6%. Conclusions: Our work demonstrates the effectiveness of comparative genomic screens to identify suspicious gene models and the scalability of community-based approaches to improve the quality of thousands of gene models. Similar community-based approaches can help to improve the quality of gene annotations in other invertebrate species, including parasitic nematodes. Keywords: Genome, Evolution, Caenorhabditis elegans, Parasitic nematodes, Orphan genes
Background The nematode Pristionchus pacificus was initially introduced as a satellite model organism for comparing developmental processes to Caenorhabditis elegans [1, 2]. More recently, it has emerged as an independent model organism for studying the genetics of phenotypic plasticity [3–5] and behavior [6–8], interactions between host and microbes [9–11], and genome evolution [12–14]. Central to all these studies was the genome sequence of P. * Correspondence: [email protected] Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076 Tübingen, Germany
pacificus, which has undergone continuous improvements over time [15–17]. However, until recently, its gene annotations were almost exclusively based on automated pipelines that combined gene predictions and evidence-based annotations [18–20]. As a consequence, the gene annotations of P. pacificus did not match the quality of the highly curated C. elegans genome. This made it difficult for researchers from the C. elegans field to adapt P. pacificus for comparative studies, even though the availability of genetic toolkits including transgenic reporter lines and gene knock
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