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Research: Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes
- Neel Prabh and
- Christian Rödelsperger
Genome Res. July 2022 32: 1315-1327; Published in Advance May 26, 2022, doi:10.1101/gr.276431.121
...not be generalizable (Vakirlis et al. 2020). Finally, to characterize the evolutionary dynamics of different gene classes, deep taxonomic sampling is absolutely invaluable (Vakirlis et al. 2016; Prabh et al. 2018). We would therefore like to highlight the utility of the Pristionchus system with an extensive...
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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...profiles of P. pacificus nematodes in response to diverse microbiota and used them to test the hypothesis that the adaptation to novel microbiota might be facilitated by the evolution of novel genes (Athanasouli et al. 2023). This revealed evidence that novel genes might be preferentially integrated...
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Research: Single worm transcriptomics identifies a developmental core network of oscillating genes with deep conservation across nematodes
- Shuai Sun,
- Christian Rödelsperger,
- and Ralf J. Sommer
Genome Res. September 2021 31: 1590-1601; Published in Advance July 22, 2021, doi:10.1101/gr.275303.121
.... pacificus is one of around 50 species in the genus Pristionchus, all of which are available as living cultures for molecular investigations (Kanzaki et al. 2021). Building on this high phylogenetic resolution, recent transcriptomic studies and deep taxon sampling revealed high evolutionary dynamics of novel...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...time scale. Using several rice s, Zhang et al. (2019) managed to pinpoint precisely the mutations allowing emergence of de novo genes in closely related rice species. A recent state-of-the-art study used six nematode populations and confirmed the rapid turnover of de novo genes compared to duplicates...
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Resource: Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans
- Chuna Kim,
- Jun Kim,
- Sunghyun Kim,
- Daniel E. Cook,
- Kathryn S. Evans,
- Erik C. Andersen,
- and Junho Lee
Genome Res. June 2019 29: 1023-1035; Published in Advance May 23, 2019, doi:10.1101/gr.246082.118
...are enriched in chromosome arms, which also show a high recombination rate in many nematodes such as in the genera Pristionchus and Caenorhabditis (Rockman and Kruglyak 2009; Andersen et al. 2012; Rödelsperger et al. 2017; Yin et al. 2018). In particular, repeat sequences are enriched and essential genes...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...used functional inferences based on human gene expression profiles or in vitro screening, the comprehensive and deep phenotyping offered by HPO provides a more systematic perspective on the functional roles of human disease genes. We found a moderate but statistically significant inverse correlation...
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Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
- Nikolaos Vakirlis and
- Anne Kupczok
Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
...novelty can be discovered among them.One particularly well-sampled environment is the human gut, in which pans of the residing species have already been constructed (Almeida et al. 2021). Those pans contain the information of whether a gene family is found in one or multiple species, allowing direct SSOG...

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