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

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.

Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics

“…Manual inspection of gene models and underlying transcriptome data often reveals correctable mistakes such as the retention of noncoding sequences, incomplete coding sequences, missing or additional exons, and fused or split genes. Recent manual curation efforts in Pristionchus pacificus and H. contortus have led to substantial improvements in the quality of the reference annotation for these two species ( Doyle et al 2020 ; Rödelsperger 2021 ). Manual curation using multiple sources of experimental evidence will be necessary to further improve the quality of the QX1410 genome annotation.…”

Analysis of repeat elements in the Pristionchus pacificus genome reveals an ancient invasion by horizontally transferred transposons

“…The strand-specific transcriptome assembly of the P. pacificus reference strain PS312 (European Nucleotide Archive: HAKN01000000, [ 35 ]) was aligned to the P. pacificus genome assembly (version: El Paco [ 14 ]) with the help of the exonerate est2genome program (version 2.2.0, [ 58 ]). Subsequently, the PPCAC pipeline (version: 1.0) was adjusted to select one representative transcript per 100-bp window without any restriction on exon number or protein sequence length [ 59 ]. This resulted in a set of 48,605 non-redundant sequences with evidence of active transcription.…”

The improved genome of the nematode Parapristionchus giblindavisi provides insights into lineage-specific gene family evolution

“…Evidence-based gene annotations for the P. giblindavis i genome were generated based on protein homology and transcriptome data using the PPCAC software (version 1.0; Athanasouli et al 2020 ; Rödelsperger 2021 ). Specifically, the community-curated gene annotations of P. pacificus (El Paco gene annotations, version 3; Athanasouli et al 2020 ) and a mixed-stage transcriptome assembly of P. giblindavis i ( Rödelsperger et al 2018 ) were transferred to the new P. giblindavis i genome assembly by alignment with the software exonerate (version 2.2.0; Slater and Birney 2005 ).…”