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

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Athanasouli,  M
Department Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

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Witte,  H
Department Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

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Weiler,  C
Department Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Society;
Entomo-Nematology Group, Department Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

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Loschko,  T
Department Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

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Eberhardt,  G
Department Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

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Sommer,  RJ
Department Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

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Rödelsperger,  C
Department Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

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引用

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


引用: https://hdl.handle.net/21.11116/0000-000A-547F-A
要旨
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.