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

Rödelsperger, Christian; Athanasouli, Marina; Lenuzzi, Maša; Theska, Tobias; Sun, Shuai; Dardiry, Mohannad; Wighard, Sara; Hu, Wen; Sharma, Devansh Raj; Han, Ziduan

doi:10.1038/s41598-019-55359-5

Cited by 24 publications

(36 citation statements)

References 63 publications

(93 reference statements)

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“…Therefore, we used the information about the predicted domains, RNA-seq data generated in this study, and Illumina and PacBio RNA-seq datasets generated earlier [26,95,96] to manually reannotate the NHR gene predictions in P. pacificus. We submitted the improved annotations to http://wormbase.org as part of a larger set of manually curated gene annotations [97]. For the tree of CAP domains in P. pacificus and P. fissidentatus, we predicted domains in the Pinocchio versions of gene predictions for both genomes [60] and selected genes that contained "PF00188" as a predicted PFAM domain.…”

Section: Phylogenetic Reconstructionsmentioning

confidence: 99%

Conserved nuclear hormone receptors controlling a novel plastic trait target fast-evolving genes expressed in a single cell

et al. 2020

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Environment shapes development through a phenomenon called developmental plasticity. Deciphering its genetic basis has potential to shed light on the origin of novel traits and adaptation to environmental change. However, molecular studies are scarce, and little is known about molecular mechanisms associated with plasticity. We investigated the gene regulatory network controlling predatory vs. non-predatory dimorphism in the nematode Pristionchus pacificus and found that it consists of genes of extremely different age classes. We isolated mutants in the conserved nuclear hormone receptor nhr-1 with previously unseen phenotypic effects. They disrupt mouth-form determination and result in animals combining features of both wild-type morphs. In contrast, mutants in another conserved nuclear hormone receptor nhr-40 display altered morph ratios, but no intermediate morphology. Despite divergent modes of control, NHR-1 and NHR-40 share transcriptional targets, which encode extracellular proteins that have no orthologs in Caenorhabditis elegans and result from lineage-specific expansions. An array of transcriptional reporters revealed co-expression of all tested targets in the same pharyngeal gland cell. Major morphological changes in this gland cell accompanied the evolution of teeth and predation, linking rapid gene turnover with morphological innovations. Thus, the origin of feeding plasticity involved novelty at the level of genes, cells and behavior. Author summaryRather than following a pre-determined genetic "blueprint", organisms can adjust their development when they perceive relevant environmental signals-a phenomenon called plasticity. This improves performance in changing environment and may also affect how species evolve. To learn how plasticity works on the mechanistic genetic level, we investigated the roundworm Pristionchus pacificus. It may develop either as a toothed predator or as a narrow-mouthed microbe-eater depending on food source and population density, an ability that evolved less than 100 million years ago. Previous studies identified switch PLOS GENETICS PLOS Genetics | https://doi.

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Section: Phylogenetic Reconstructionsmentioning

confidence: 99%

Conserved nuclear hormone receptors controlling a novel plastic trait target fast-evolving genes expressed in a single cell

et al. 2020

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“…In our previous study, we focused on the identification of missing one-to-one orthologous genes in the P. pacificus genome and the identification of artificial fusions between two adjacent P. pacificus genes both of which have one-to-one orthologous genes [23] . Here, we aim to further improve the quality of one-to-one orthologous genes by finding and curating P. pacificus genes that are either unusually large and or small with regard to their C. elegans counterpart.…”

Section: Protein Length Comparison Of Orthologs Identify Hundreds Of mentioning

confidence: 99%

“…We obtained 8,348 one-to-one orthologs between C. elegans and P. pacificus that were predicted based on best reciprocal BLASTP hits in a previous study [23] . We then calculated the protein length ratio between the P. pacificus and C. elegans one-to-one orthologs.…”

Section: Candidate Identification Based On Length Comparison Of Orthomentioning

confidence: 99%

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

Athanasouli

Witte

Weiler

et al. 2020

Preprint

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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 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%. 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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“…This would be valuable even when applied to only a single species, preferably one with a near-complete genome, which can then be used as a template to re-evaluate gene models of other oomycetes and train gene predictors. Especially community-based annotation would be a powerful resource (Rödelsperger et al, 2019 Reliable functional annotation of the predicted proteome is an additional prerequisite for identifying the fundamental components of genome-scale models. In Chapter 2, we performed an automated proteome annotation for 42 oomycete species, which revealed that the large majority of predicted proteins could not be assigned to a KEGG orthologous group (KO), which are protein ortholog clusters with validated functions (Mao et al, 2005).…”

Section: From Genome Sequence To Genome-scale Metabolic Modelmentioning

confidence: 99%

Uncovering oomycete metabolism using systems biology

Rodenburg

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Metabolism is essential for life. The metabolism of an organism defines its capabilities to take up nutrients from the environment and to convert these into its essential building blocks, such as nucleic acids and amino acids (Lazar and Birnbaum, 2012). Cellular metabolism can be described as a system of biochemical conversions (reactions), most of which are catalyzed by metabolic enzymes. Typically, a genome encodes a few thousand metabolic enzymes (Yilmaz and Walhout, 2017). Each enzyme acts on a selection of substrates and converts these into products, typically by adding or removing reactive groups. Reactions that share substrates or products can be considered functionally connected. Consequently, the collection of biochemical reactions within a cell forms a large interconnected network, representing the routes by which the organism converts simple nutrients into complex metabolites and vice-versa. This network is distributed over different subcellular compartments (organelles). Transporter proteins and channels facilitate the transport of metabolites across the lipid bilayers that surround the cell and the organelles (Sahoo et al., 2014). The overall system is subject to many parameters, such as variability in substrates, temperature, or the pH, not only between cells and the extracellular space but also within cells. Cells regulate this system to maintain homeostasis, i.e. the ability to perform important cellular functions despite variations (perturbations), and this provides robustness (Eberl, 2018; Nijhout et al., 2019). The ability to sense environmental variations and metabolic cues and to adapt metabolism accordingly, depends on a tightly interlinked regulatory system (Watson et al., 2015). This involves regulatory feedback loops embedded in interaction networks crossing metabolic, protein, transcript, and (epi)genetic levels (Figure 1). Pathogen G e n o m e T ra n s c ri p to m e P ro te o m e M e ta b o lo m e Host FIGURE 1 | The molecular layers of a cell are all interconnected, and form a complex and integrated system. In the symbiosis of a pathogen and a host, their systems are connected, and interactions occur between all molecular layers. As such, the phenotype of the cell is an emergent property of the system's complexity (Aderem, 2005). The rates of individual metabolic reactions are a direct consequence of the overall state General introduction

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

Cited by 24 publications

References 63 publications

Conserved nuclear hormone receptors controlling a novel plastic trait target fast-evolving genes expressed in a single cell

Conserved nuclear hormone receptors controlling a novel plastic trait target fast-evolving genes expressed in a single cell

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

Uncovering oomycete metabolism using systems biology

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