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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
...with the array of tools available for C. elegans, using all three sequencing technologies (Illumina, PacBio, and Nanopore) would be optimal.ResultsGenome sequencing and C. elegans strainWe sought to generate a new C. elegans assembly that matches a modern and easily available reference strain, VC2010 (Flibotte...
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Resource: Genome sequencing of C. elegans balancer strains reveals previously unappreciated complex genomic rearrangements
- Tatiana Maroilley,
- Stephane Flibotte,
- Francesca Jean,
- Victoria Rodrigues Alves Barbosa,
- Andrew Galbraith,
- Afiya Razia Chida,
- Filip Cotra,
- Xiao Li,
- Larisa Oncea,
- Mark Edgley,
- Don Moerman,
- and Maja Tarailo-Graovac
Genome Res. January 2023 33: 154-167; Published in Advance December 5, 2022, doi:10.1101/gr.276988.122
.... Their structure has mostly been explored with low-resolution labor- and resource-intensive techniques such as genetic linkage mapping, fluorescence in situ hybridization, PCR analysis (Zhao et al. 2006), SNP mapping (Kadandale et al. 2005), and oligonucleotide array comparative genomic hybridization (Maydan et al...
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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
...,371 92.7% CNVs Variant class Method Called events Validated events % validated Duplications Array CGH 31 26 84% Deletions Array CGH 15 15 100% C. elegans mutation resource Genome Research 1751 www..org ild ild Thompson et al. 1752 Genome Research www..org the centers (Fig. 2B). This bias was not seen...
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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
...These authors contributed equally to this work. Corresponding author: elegans@snu.ac.krAbstractLong-read sequencing technologies have contributed greatly to comparative genomics among species and can also be applied to study genomics within a species. In this study, to determine how substantial genomic changes...
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Research: Genome-wide gene expression regulation as a function of genotype and age in C. elegans
- Ana Viñuela,
- L. Basten Snoek,
- Joost A.G. Riksen,
- and Jan E. Kammenga
Genome Res. July 2010 20: 929-937; Published in Advance May 20, 2010, doi:10.1101/gr.102160.109
...elegans pathogenesis model. Cell 96: 47–56. Maydan JS, Flibotte S, Edgley ML, Lau J, Selzer RR, Richmond TA, Pofahl NJ, Thomas JH, Moerman DG. 2007. Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative hybridization. Genome Res 17: 337–347. McCarroll SA, Murphy CT...
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ARTICLE: De novo discovery of a tissue-specific gene regulatory module in a chordate
- David S. Johnson,
- Qing Zhou,
- Kasumi Yagi,
- Nori Satoh,
- Wing Wong,
- and Arend Sidow
Genome Res. October 2005 15: 1315-1324; Published in Advance September 16, 2005, doi:10.1101/gr.4062605
..., J.L., and Ekker, M. 2003 . Regulatory roles of conserved intergenic domains in vertebrate Dlx bigene clusters. Genome Res. 13 : 533 -543. ↵ GuhaThakurta, D., Schriefer, L.A., Waterston, R.H., and Stormo, G.D. 2004 . Novel transcription regulatory elements in Caenorhabditis elegans muscle genes...
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Methods: Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
- Georg Zeller,
- Richard M. Clark,
- Korbinian Schneeberger,
- Anja Bohlen,
- Detlef Weigel,
- and Gunnar Rätsch
Genome Res. June 2008 18: 918-929; Published in Advance March 6, 2008, doi:10.1101/gr.070169.107
...oligonucleotide resequencing arrays have allowed the comprehensive discovery of single nucleotide polymorphisms (SNPs) in eukaryotic genomes of moderate to large size. With this technology, the detection rate for isolated SNPs is typically high. However, it is greatly reduced when other polymorphisms are located...
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
...of consensus TE sequences (Fig. 3A). Using a false-discovery threshold of q = 0.05, we searched for significant matches between our predicted ZNF binding motifs and TE consensus sequence and then compared them to equivalently sized libraries of nonrepetitive genomic sequence. For all four species, we observed...
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Methods: Genome-wide identification of spliced introns using a tiling microarray
- Zhihong Zhang,
- Jay R. Hesselberth,
- and Stanley Fields
Genome Res. April 2007 17: 503-509; Published in Advance March 9, 2007, doi:10.1101/gr.6049107
...introns via the detection of accumulated lariats, we isolated total RNA from diploid dbr1/dbr1 and DBR+/DBR+ yeast strains, labeled it as double-stranded cDNA, and hybridized the cDNA to S. cerevisiae tiling arrays. Signals enriched in the dbr1 strain were identified and mapped to genomic coordinates. We...
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ARTICLE: Gene copy number variation spanning 60 million years of human and primate evolution
- Laura Dumas,
- Young H. Kim,
- Anis Karimpour-Fard,
- Michael Cox,
- Janet Hopkins,
- Jonathan R. Pollack,
- and James M. Sikela
Genome Res. September 2007 17: 1266-1277; Published in Advance July 31, 2007, doi:10.1101/gr.6557307
...of Colorado at Denver and Health Sciences Center, Aurora, Colorado 80045, USA Abstract Given the evolutionary importance of gene duplication to the emergence of species-specific traits, we have extended the application of cDNA array-based comparative genomic hybridization (aCGH) to survey gene...

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