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

BMC Genomics

Hanh Witte¹  Gabi Eberhardt¹  Marina Athanasouli¹  Christian Weiler¹  Ralf J. Sommer¹  Tobias Loschko¹  Christian Rödelsperger¹ 

[1] Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology;

关键词: Genome;    Evolution;    Caenorhabditis elegans;    Parasitic nematodes;    Orphan genes;   

DOI  :  10.1186/s12864-020-07100-0

来源: DOAJ

【 摘 要 】

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-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.

【 授权许可】

Unknown