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

AbstractBackgroundNematode 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.ResultsHere, 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 and screens for atypical domain combinations and species-specific orphan genes resulted in 4,221 candidate genes that were subject to community-based curation. Corrections for 2,851 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%.ConclusionsOur 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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Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus

BMC Genomics ◽

10.1186/s12864-020-07100-0 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Marina Athanasouli ◽

Hanh Witte ◽

Christian Weiler ◽

Tobias Loschko ◽

Gabi Eberhardt ◽

...

Keyword(s):

Candidate Genes ◽

Model Organisms ◽

Parasitic Nematodes ◽

Comparative Genomic ◽

Orphan Genes ◽

Community Based ◽

Pristionchus Pacificus ◽

Gene Annotations ◽

Gene Models

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.

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Crowdsourcing and the feasibility of manual gene annotation: A pilot study in the nematode Pristionchus pacificus

Scientific Reports ◽

10.1038/s41598-019-55359-5 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 6

Author(s):

Christian Rödelsperger ◽

Marina Athanasouli ◽

Maša Lenuzzi ◽

Tobias Theska ◽

Shuai Sun ◽

...

Keyword(s):

Pilot Study ◽

Reverse Genetics ◽

Gene Annotation ◽

Small Scale ◽

Community Based ◽

Pristionchus Pacificus ◽

C Elegans ◽

Gene Annotations ◽

A Genome ◽

Gene Models

AbstractNematodes such as Caenorhabditis elegans are powerful systems to study basically all aspects of biology. Their species richness together with tremendous genetic knowledge from C. elegans facilitate the evolutionary study of biological functions using reverse genetics. However, the ability to identify orthologs of candidate genes in other species can be hampered by erroneous gene annotations. To improve gene annotation in the nematode model organism Pristionchus pacificus, we performed a genome-wide screen for C. elegans genes with potentially incorrectly annotated P. pacificus orthologs. We initiated a community-based project to manually inspect more than two thousand candidate loci and to propose new gene models based on recently generated Iso-seq and RNA-seq data. In most cases, misannotation of C. elegans orthologs was due to artificially fused gene predictions and completely missing gene models. The community-based curation raised the gene count from 25,517 to 28,036 and increased the single copy ortholog completeness level from 86% to 97%. This pilot study demonstrates how even small-scale crowdsourcing can drastically improve gene annotations. In future, similar approaches can be used for other species, gene sets, and even larger communities thus making manual annotation of large parts of the genome feasible.

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The community-curated Pristionchus pacificus genome facilitates automated gene annotation improvement in related nematodes

BMC Genomics ◽

10.1186/s12864-021-07529-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Christian Rödelsperger

Keyword(s):

Gene Annotation ◽

Rapid Evolution ◽

Model Organism ◽

Genomic Analysis ◽

Comparative Genomic ◽

Data Set ◽

Pristionchus Pacificus ◽

C Elegans ◽

Gene Annotations

Abstract Background The nematode Pristionchus pacificus is an established model organism for comparative studies with Caenorhabditis elegans. Over the past years, it developed into an independent animal model organism for elucidating the genetic basis of phenotypic plasticity. Community-based curations were employed recently to improve the quality of gene annotations of P. pacificus and to more easily facilitate reverse genetic studies using candidate genes from C. elegans. Results Here, I demonstrate that the reannotation of phylogenomic data from nine related nematode species using the community-curated P. pacificus gene set as homology data substantially improves the quality of gene annotations. Benchmarking of universal single copy orthologs (BUSCO) estimates a median completeness of 84% which corresponds to a 9% increase over previous annotations. Nevertheless, the ability to infer gene models based on homology already drops beyond the genus level reflecting the rapid evolution of nematode lineages. This also indicates that the highly curated C. elegans genome is not optimally suited for annotating non-Caenorhabditis genomes based on homology. Furthermore, comparative genomic analysis of apparently missing BUSCO genes indicates a failure of ortholog detection by the BUSCO pipeline due to the insufficient sample size and phylogenetic breadth of the underlying OrthoDB data set. As a consequence, the quality of multiple divergent nematode genomes might be underestimated. Conclusions This study highlights the need for optimizing gene annotation protocols and it demonstrates the benefit of a high quality genome for phylogenomic data of related species.

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Curated BLAST for Genomes

mSystems ◽

10.1128/msystems.00072-19 ◽

2019 ◽

Vol 4 (2) ◽

Cited By ~ 3

Author(s):

Morgan N. Price ◽

Adam P. Arkin

Keyword(s):

Enzymatic Activity ◽

Candidate Genes ◽

Genome Sequence ◽

Energy Sources ◽

Gene Annotations ◽

Link Type ◽

Automated Annotation ◽

A Genome ◽

Gene Models

ABSTRACT Curated BLAST for Genomes finds candidate genes for a process or an enzymatic activity within a genome of interest. In contrast to annotation tools, which usually predict a single activity for each protein, Curated BLAST asks if any of the proteins in the genome are similar to characterized proteins that are relevant. Given a query such as an enzyme’s name or an EC number, Curated BLAST searches the curated descriptions of over 100,000 characterized proteins, and it compares the relevant characterized proteins to the predicted proteins in the genome of interest. In case of errors in the gene models, Curated BLAST also searches the six-frame translation of the genome. Curated BLAST is available at http://papers.genomics.lbl.gov/curated. IMPORTANCE Given a microbe’s genome sequence, we often want to predict what capabilities the organism has, such as which nutrients it requires or which energy sources it can use. Or, we know the organism has a capability and we want to find the genes involved. Scientists often use automated gene annotations to find relevant genes, but automated annotations are often vague or incorrect. Curated BLAST finds candidate genes for a capability without relying on automated annotations. First, Curated BLAST finds proteins (usually from other organisms) whose functions have been studied experimentally and whose curated descriptions match a query. Then, it searches the genome of interest for similar proteins and returns a list of candidates. Curated BLAST is fast and often finds relevant genes that are missed by automated annotation.

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