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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
...organization, and the functions of highly repetitive genomic loci. Genetic polymorphism in wild isolates of C. elegans should be more reliably assigned to SNVs and genomic islands of elevated diversity in the CGC1 assembly than in N2 (Crombie et al. 2019; Lee et al. 2021). Even for putatively identical wild...
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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
...of the highest possible quality. For Caenorhabditis elegans, such an assembly for the wild-type strain N2 has existed for 20 yr (The C. elegans Sequencing Consortium 1998). However, this assembly was generated with sequence data from N2 and CB1392 [nuc-1(e1392)] populations of uncertain lineage grown in at least...
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Research: A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans
- Thiago L. Knittel,
- Brooke E. Montgomery,
- Alex J. Tate,
- Ennis W. Deihl,
- Anastasia S. Nawrocki,
- Frederic J. Hoerndli,
- and Taiowa A. Montgomery
Genome Res. December 2024 34: 2203-2216; Published in Advance December 2, 2024, doi:10.1101/gr.279083.124
...and Ruvkun 2020).Endogenous siRNAs may constitute a distinct class of small RNAs largely overlooked in C. elegans. Presumably, such siRNAs are rare in wild-type C. elegans since they have not emerged from high-throughput small RNA sequencing (sRNA-seq) studies characterizing small RNAs (Ruby et al. 2006...
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Research: Natural variation in C. elegans short tandem repeats
- Gaotian Zhang,
- Ye Wang,
- and Erik C. Andersen
Genome Res. October 2022 32: 1852-1861; Published in Advance October 4, 2022, doi:10.1101/gr.277067.122
...been identified among wild Caenorhabditis elegans strains, the natural diversity in STRs remains unknown. Here, we characterized the distribution of 31,991 STRs with motif lengths of 1–6 bp in the reference of C. elegans. Of these STRs, 27,667 harbored polymorphisms across 540 wild strains and only...
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Research: Mutability of mononucleotide repeats, not oxidative stress, explains the discrepancy between laboratory-accumulated mutations and the natural allele-frequency spectrum in C. elegans
- Moein Rajaei,
- Ayush Shekhar Saxena,
- Lindsay M. Johnson,
- Michael C. Snyder,
- Timothy A. Crombie,
- Robyn E. Tanny,
- Erik C. Andersen,
- Joanna Joyner-Matos,
- and Charles F. Baer
Genome Res. September 2021 31: 1602-1613; Published in Advance August 17, 2021, doi:10.1101/gr.275372.121
.... elegans MA lines and wild isolates have accumulated, it has become apparent that the base-substitution spectrum in laboratory-accumulated mutations differs from that of wild isolates in a consistent way: There are more transversions in the laboratory than there are in nature. The ratio of transitions...
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Resource: The million mutation project: A new approach to genetics in Caenorhabditis elegans
- Owen Thompson,
- Mark Edgley,
- Pnina Strasbourger,
- Stephane Flibotte,
- Brent Ewing,
- Ryan Adair,
- Vinci Au,
- Iasha Chaudhry,
- Lisa Fernando,
- Harald Hutter,
- Armelle Kieffer,
- Joanne Lau,
- Norris Lee,
- Angela Miller,
- Greta Raymant,
- Bin Shen,
- Jay Shendure,
- Jon Taylor,
- Emily H. Turner,
- LaDeana W. Hillier,
- Donald G. Moerman,
- and Robert H. Waterston
Genome Res. October 2013 23: 1749-1762; Published in Advance June 25, 2013, doi:10.1101/gr.157651.113
..., in which we obtained the sequences for 2007 mutagenized strains. These contain more than 800,000 single nucleotide variants (SNV), 14,800 insertions and deletions (indels), and 1400 larger chromosomal rearrangements. In addition, we sequenced 40 different wild isolates, with a distinct mutational spectrum...
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Research: Natural genetic variation in C. elegans identified genomic loci controlling metabolite levels
- Arwen W. Gao,
- Mark G. Sterken,
- Jelmi uit de Bos,
- Jelle van Creij,
- Rashmi Kamble,
- Basten L. Snoek,
- Jan E. Kammenga,
- and Riekelt H. Houtkooper
Genome Res. September 2018 28: 1296-1308; Published in Advance August 14, 2018, doi:10.1101/gr.232322.117
...inbred lines (RILs) in the nematode Caenorhabditis elegans. We focused on the genomic regions that control metabolite levels by measuring fatty acid (FA) and amino acid (AA) composition in the RILs using targeted metabolomics. The genetically diverse RILs showed a large variation in their FA and AA...
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Research: Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae
- Asher D. Cutter and
- Jae Young Choi
Genome Res. August 2010 20: 1103-1111; Published in Advance May 27, 2010, doi:10.1101/gr.104331.109
...Caenorhabditis briggsae. We find that nearly half of -wide variation in nucleotide polymorphism is explained by differences in local recombination rates. By quantifying divergence between several reproductively isolated lineages, we demonstrate that ancestral polymorphism generates a spurious signal of RAM...
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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
...a highly contiguous of the CB4856 strain by de novo assembly using long-read sequencing. Because of chromosome-scale selective sweeps in C. elegans wild strains, some strains, including CB4856, exhibit distinct polymorphism patterns from most other wild strains (Andersen et al. 2012). For this reason, our...
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Research: Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis
- Cristel G. Thomas,
- Wei Wang,
- Richard Jovelin,
- Rajarshi Ghosh,
- Tatiana Lomasko,
- Quang Trinh,
- Leonid Kruglyak,
- Lincoln D. Stein,
- and Asher D. Cutter
Genome Res. May 2015 25: 667-678; Published in Advance March 17, 2015, doi:10.1101/gr.187237.114
...and demographic histories to their genomic signatures in a global sample of C. briggsae. Results Low recombination regions show drastic skews in polymorphism We sequenced 37 wild isolate s of C. briggsae to high coverage (median 32×) (Supplemental Table 1) and identified a total of 2.70 million single nucleotide...

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