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  Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus

Athanasouli, M., Witte, H., Weiler, C., Loschko, T., Eberhardt, G., Sommer, R., et al. (2020). Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus. BMC Genomics, 21(1): 708. doi:10.1186/s12864-020-07100-0.

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Athanasouli, M1, Autor           
Witte, H1, Autor           
Weiler, C1, 2, Autor           
Loschko, T1, Autor           
Eberhardt, G1, Autor           
Sommer, RJ1, Autor           
Rödelsperger, C1, Autor           
Affiliations:
1Department Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Society, ou_3375786              
2Entomo-Nematology Group, Department Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Society, ou_3507713              

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 Zusammenfassung: 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-to-one 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.

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 Datum: 2020-10
 Publikationsstatus: Erschienen
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 Identifikatoren: DOI: 10.1186/s12864-020-07100-0
PMID: 33045985
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Titel: BMC Genomics
Genre der Quelle: Zeitschrift
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Ort, Verlag, Ausgabe: BioMed Central
Seiten: 9 Band / Heft: 21 (1) Artikelnummer: 708 Start- / Endseite: - Identifikator: ISSN: 1471-2164
CoNE: https://pure.mpg.de/cone/journals/resource/111000136905010