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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
...CGC1, a new reference for Caenorhabditis elegans Kazuki Ichikawa1, Massa J. Shoura2,8, Karen L. Artiles2, Dae-Eun Jeong2, Chie Owa1, Haruka Kobayashi1, Yoshihiko Suzuki1, Manami Kanamori3, Yu Toyoshima3, Yuichi Iino3, Ann E. Rougvie4, Lamia Wahba5, Andrew Z. Fire2,6, Erich M. Schwarz7 and Shinichi...
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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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Resource: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
- Runsheng Li,
- Xiaoliang Ren,
- Qiutao Ding,
- Yu Bi,
- Dongying Xie,
- and Zhongying Zhao
Genome Res. February 2020 30: 287-298; Published in Advance February 5, 2020, doi:10.1101/gr.251512.119
...Technologies to study the transcriptome complexity in Caenorhabditis elegans. We generated approximately six million reads using native poly(A)-tailed mRNAs from three developmental stages, with average read lengths ranging from 900 to 1100 nt. Around half of the reads represent full-length transcripts...
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METHODS: High-Throughput Gene Mapping in Caenorhabditis elegans
- Kathryn A. Swan,
- Damian E. Curtis,
- Kathleen B. McKusick,
- Alexander V. Voinov,
- Felipa A. Mapa,
- and Michael R. Cancilla
Genome Res. July 1, 2002 12: 1100-1105; doi:10.1101/gr.208902
...High-Throughput Gene Mapping in Caenorhabditis elegans Kathryn A. Swan , Damian E. Curtis , Kathleen B. McKusick , Alexander V. Voinov , Felipa A. Mapa , and Michael R. Cancilla 1 Exelixis, Inc., South San Francisco...
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Method: High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection
- Sara J. Cooper,
- Gregory L. Finney,
- Shauna L. Brown,
- Sven K. Nelson,
- Jay Hesselberth,
- Michael J. MacCoss,
- and Stanley Fields
Genome Res. September 2010 20: 1288-1296; Published in Advance July 7, 2010, doi:10.1101/gr.105825.110
..., Heald JK, Rowland JJ, Oliver SG, Kell DB. 2003. High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat Biotechnol 21: 692–696. Blaise BJ, Giacomotto J, Elena B, DumasME, Toulhoat P, Segalat L, Emsley L. 2007. Metabotyping ofCaenorhabditis elegans...
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RESOURCE: Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity
- Natalia J. Martinez,
- Maria C. Ow,
- John S. Reece-Hoyes,
- M. Inmaculada Barrasa,
- Victor R. Ambros,
- and Albertha J.M. Walhout
Genome Res. December 2008 18: 2005-2015; Published in Advance November 3, 2008, doi:10.1101/gr.083055.108
.... Genome Res. 17 : 1478 – 1485 . ↵ Hunt-Newbury, R. , Viveiros, R. , Johnsen, R. , Mah, A. , Anastas, D. , Fang, L. , Halfnight, E. , Lee, D. , Lin, J. , Lorch, A. , et al. ( 2007 ) High-throughput in vivo analysis of gene expression in Caenorhabditis elegans . PLoS Biol. 5 : e237 , doi: 10.1371/journal...
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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
...selection biases the standing genetic variation.The nematode Caenorhabditis elegans is an important model organism in many areas of biology and was the first metazoan organism to have its mutational process characterized at the genomic level (Denver et al. 2000, 2004b). As genomic sequence data from C...
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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
...Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada We have created a library of 2007 mutagenized Caenorhabditis elegans strains, each sequenced to a target depth of 15-fold coverage, to provide the research community with mutant alleles for each of the worm...
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Methods: Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization
- Jason S. Maydan,
- Stephane Flibotte,
- Mark L. Edgley,
- Joanne Lau,
- Rebecca R. Selzer,
- Todd A. Richmond,
- Nathan J. Pofahl,
- James H. Thomas,
- and Donald G. Moerman
Genome Res. March 2007 17: 337-347; Published in Advance January 31, 2007, doi:10.1101/gr.5690307
...Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization Jason S. Maydan 1 , Stephane Flibotte 2 , Mark L. Edgley 3 , Joanne Lau 3 , Rebecca R. Selzer 5 , Todd A. Richmond 5...
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Resource: Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans
- Nicolas J. Tourasse,
- Jonathan R.M. Millet,
- and Denis Dupuy
Genome Res. December 2017 27: 2120-2128; Published in Advance October 31, 2017, doi:10.1101/gr.224626.117
...of the complete Caenorhabditis elegans using transcriptome sequencing (RNA-seq) (Hillier et al. 2009; Ramani et al. 2011; Gerstein et al. 2014; Kuroyanagi et al. 2014; Ragle et al. 2015). Most of these analyses reported previously unannotated splice junctions, indicating that saturation has not yet been reached...

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