Searching journal content for articles similar to Chen and Stein 16 (5): 606.

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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
...its genetics and genomics fully reproducible by C. elegans laboratories over many years. CGC1 is available at the Caenorhabditis Genetics Center stock center (https://cgc.umn.edu/strain/CGC1).Genome sequencing and assemblyWe harvested genomic DNA (gDNA) from CGC1 and sequenced it in two sets apiece...
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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: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...; Lin et al. 2024), suggesting that there are substantial functional constraints to organization. Conservation of ALGs seems to be the norm at the phylum level, but several lineages at lower taxonomic levels have experienced genomic scrambling, including the breaking up or mixing of genes from different...
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Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
- Shelley Reich,
- Tobias Loschko,
- Julie Jung,
- Samantha Nestel,
- Ralf J. Sommer,
- and Michael S. Werner
Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
...and difficulties in laboratory rearing.The nematode Pristionchus pacificus was introduced as a model system for studying developmental plasticity in 2010 (Bento et al. 2010). Similar to Caenorhabditis elegans, P. pacificus has four larval stages (J1–J4), although the first stage remains enclosed in the egg...
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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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Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...et al. 1999). Differences in the scale and extent of synteny conservation have led to the concepts of micro- and macrosynteny. Microsynteny (also known as “collinearity” in genomics) refers to the conservation of gene content and order within sets of tightly linked orthologous genes. Generally...
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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-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity Natalia J. Martinez 1 , 2 , 3 , Maria C. Ow 2 , 3 , John S. Reece-Hoyes 1 , 2 , M. Inmaculada Barrasa 1 , 2 , Victor R. Ambros 2 , 4 , and Albertha J.M. Walhout 1 , 2 , 4 1 Program in Gene Function...
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Research: The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection
- Jialin Liu,
- Rebecca R. Viales,
- Pierre Khoueiry,
- James P. Reddington,
- Charles Girardot,
- Eileen E.M. Furlong,
- and Marc Robinson-Rechavi
Genome Res. September 2021 31: 1573-1581; Published in Advance July 15, 2021, doi:10.1101/gr.275212.121
...expression in the phylotypic period can be at least partly explained by conservation in gene regulation (Fig. 6). This provides a regulatory basis for the hourglass expression pattern. It was suggested that pleiotropic constraints might play important roles in the conservation of phylotypic stage (Duboule...
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Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
...genes in the model organism Caenorhabditis elegans. Extensive phylogenetic systems analysis using this comprehensive proteome annotation provides new insights into evolutionary processes of this metazoan group.Nematodes are one of the most diverse, abundant, and widespread metazoan phylum on earth...
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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
...11724, USA; 9Center for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada, M5S 3B2 The nematode Caenorhabditis briggsae is a model for comparative developmental evolution with C. elegans. Worldwide collections of C. briggsae have implicated an intriguing...

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