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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
..., a Moerman Gene Knockout Laboratory subculture of N2 obtained from the Caenorhabditis Genetics Center (https://cgc.umn.edu) in 2002 and first described by Flibotte et al. (2010).C. elegans and gene annotation versionsIn analyzing gDNA from the N2 assembly, we have used the most recent stable version from...
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Resource: Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
- Timothy J. Durham,
- Riza M. Daza,
- Louis Gevirtzman,
- Darren A. Cusanovich,
- Olubusayo Bolonduro,
- William Stafford Noble,
- Jay Shendure,
- and Robert H. Waterston
Genome Res. October 2021 31: 1952-1969; Published in Advance April 22, 2021, doi:10.1101/gr.271791.120
...in other single-cell genomics technologies can now also characterize the regulatory context of the that gives rise to these gene expression levels at a single-cell resolution. To explore the regulatory DNA of individual cell types in C. elegans, we collected single-cell chromatin accessibility data using...
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Resource: Recompleting the Caenorhabditis elegans genome
- Jun Yoshimura,
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Idan Gabdank,
- Lamia Wahba,
- Cheryl L. Smith,
- Mark L. Edgley,
- Ann E. Rougvie,
- Andrew Z. Fire,
- Shinichi Morishita,
- and Erich M. Schwarz
Genome Res. June 2019 29: 1009-1022; Published in Advance May 23, 2019, doi:10.1101/gr.244830.118
..., such highly tandem regions may be important for identifying rapidly evolving virulence factors (Raffaele and Kamoun 2012); for free-living nematodes such as C. elegans, such regions may be crucial for understanding fast-evolving gene families relevant to nematode ecology (Frezal and Felix 2015).For the novel...
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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
...genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus. BMC Genomics 21: 708. doi:10.1186/s12864-020-07100-0 ↵Athanasouli M, Akduman N, Röseler W, Theam P, Rödelsperger C. 2023. Thousands of Pristionchus pacificus orphan genes were integrated...
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Research: Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay
- Marcus J. Viscardi,
- Enisha Sehgal,
- and Joshua A. Arribere
Genome Res. June 2025 35: 1337-1348; Published in Advance May 9, 2025, doi:10.1101/gr.280046.124
...analysis identified genes with mRNAs significantly upregulated in each mutant: 389 genes (smg-2), 363 genes (smg-5), 160 genes (smg-6), and 16 genes (smg-7; Methods) (Fig. 1B).View larger version: In this window In a new window Figure 1. C. elegans UPF1, SMG-5, and SMG-6 repress a common set of endogenous...
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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
..., such as Caenorhabditis elegans.C. elegans is a small nematode with an ∼100 Mb and ∼20,000 genes (Heger et al. 2009). Median gene length is ∼2 kb, and intergenic distances between genes (excluding operons encompassing ∼15% of genes) range from ∼2 to 10 kb (Nelson et al. 2004; Girard et al. 2007; Allen et al. 2011). Like...
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Research: Systematic transcriptome analysis associated with physiological and chronological aging in Caenorhabditis elegans
- Seokjin Ham,
- Sieun S. Kim,
- Sangsoon Park,
- Eun Ji E. Kim,
- Sujeong Kwon,
- Hae-Eun H. Park,
- Yoonji Jung,
- and Seung-Jae V. Lee
Genome Res. November/December 2022 32: 2003-2014; Published in Advance November 9, 2022, doi:10.1101/gr.276515.121
...correlation coefficient r and its significance P are marked. (B) Gene expression contribution to variance in isoform level. See Supplemental Figure S2A for the schematic overview. (C–E) Enrichment of different RNA-processing events in isoform fractions that were up-regulated during Caenorhabditis elegans...
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Review: k-mer approaches for biodiversity genomics
- Katharine M. Jenike,
- Lucía Campos-Domínguez,
- Marilou Boddé,
- José Cerca,
- Christina N. Hodson,
- Michael C. Schatz,
- and Kamil S. Jaron
Genome Res. February 2025 35: 219-230; Published in Advance January 31, 2025, doi:10.1101/gr.279452.124
...-free techniques for species assignment as well as detection of horizontal gene transfer candidates (for review, see Ren et al. 2018).For most applications we need to select a k long enough so that most k-mers in the will be found only once. The proportion of k-mers corresponding to a unique position...
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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...specific genomic sequences while interacting with regulatory proteins, RNA polymerase II, and the chromatin environment to direct gene expression programs. The set of expressed TFs and their activity in a cell determines which genes are expressed and to what level, thereby dictating cellular fate...
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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
..., and the evolution of oscillating genes in nematodes. Nematodes are the largest phylum of multicellular animals with an expected number of 1–10 million species (Lambshead and Boucher 2003). Besides the well-studied model organism C. elegans, the nematodes contain many important parasites of plants, livestock, other...

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