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

• Published in: BMC genomics Vol. 21; no. 1; pp. 708 - 9
• Main Authors: Athanasouli, Marina, Witte, Hanh, Weiler, Christian, Loschko, Tobias, Eberhardt, Gabi, Sommer, Ralf J., Rödelsperger, Christian
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 12.10.2020; BioMed Central; BMC
• Subjects: Amino acids; Animals; Annotations; Automation; Caenorhabditis elegans; Caenorhabditis elegans - genetics; Candidates; Comparative analysis; Datasets; Evolution; Gene families; Gene loci; Genes; Genetic aspects; Genome; Genomes; Genomics; Genotypes; Identification and classification; Invertebrates; Microbial genetics; Molecular Sequence Annotation - methods; Molecular Sequence Annotation - standards; Nematodes; Orphan genes; Parasitic nematodes; Pristionchus pacificus; Proteins; Rhabditida - genetics; Roundworms; Species; Species comparisons; Species Specificity; Worms; Germany; Parasitic nematodes; Caenorhabditis elegans; Evolution; Orphan genes; Genome
• DOI: 10.1186/s12864-020-07100-0
• ISSN: 1471-2164

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. 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%. 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.