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

Christian Rödelsperger

doi:10.1186/s12864-021-07529-x

Abstract

BackgroundThe 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.ResultsHere, 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.ConclusionsThis 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.

Highlights

The nematode Pristionchus pacificus is an established model organism for comparative studies with Caenorhabditis elegans
High quality gene annotations are rare outside the Caenorhabditis clade In order to assess the current status of nematode genome quality, I analyzed gene annotations from 54 nematode species as obtained from WormBase ParaSite using the benchmarking universal single copy orthologs (BUSCO) approach, which tests for the presence of highly conserved single copy orthologs [2, 13]
As BUSCO genes are defined as genes that should be present as single copy in at least 90% of genomes, the low completeness values point towards substantial annotation problems in various genomes (Fig. 1)

Summary

Introduction

The nematode Pristionchus pacificus is an established model organism for comparative studies with Caenorhabditis elegans. Multiple representative genomes of the highly diverse and rapidly evolving nematode phylum are still poorly annotated To overcome this problem in the case of the nematode model organism Pristionchus pacificus, community-based curations have recently been initiated to improve the quality of gene annotations [3, 4]. Further strand-specific RNA-seq and Iso-seq data pointed towards the presence of numerous artificial gene fusions in gene dense regions of the genome [3] This motivated a screen for suspicious gene models based on comparative genomic approaches and to propose corrections after manual inspection by community annotators. Two rounds of community curations improved the BUSCO completeness level from 86 to 98% (nematode odb data set) [2,3,4]

Methods

Results

Discussion

Conclusion