CGC1, a new reference genome 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 Morishita1
- 1Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan;
- 2Department of Pathology, Stanford University, Stanford, California 94305, USA;
- 3Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan;
- 4Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55454, USA;
- 5Laboratory of Non-Canonical Modes of Inheritance, Rockefeller University, New York, New York 10065, USA;
- 6Department of Genetics, Stanford University, Stanford, California 94305, USA;
- 7Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
Abstract
The original 100.3 Mb reference genome for Caenorhabditis elegans, generated from the wild-type laboratory strain N2, has been crucial for analysis of C. elegans since 1998 and has been considered complete since 2005. Unexpectedly, this long-standing reference was shown to be incomplete in 2019 by a genome assembly from the N2-derived strain VC2010. Moreover, genetically divergent versions of N2 have arisen over decades of research and hindered reproducibility of C. elegans genetics and genomics. Here we provide a 106.4 Mb gap-free, telomere-to-telomere genome assembly of C. elegans, generated from CGC1, an isogenic derivative of the N2 strain. We use improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies and to assemble tandem repeat loci, including a 772 kb sequence for the 45S rRNA genes. Although many differences from earlier assemblies come from repeat regions, unique additions to the genome are also found. Of 19,972 protein-coding genes in the N2 assembly, 19,790 (99.1%) encode products that are unchanged in the CGC1 assembly. The CGC1 assembly also may encode 183 new protein-coding and 163 new ncRNA genes. CGC1 thus provides both a completely defined reference genome and corresponding isogenic wild-type strain for C. elegans, allowing unique opportunities for model and systems biology.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.280274.124.
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Freely available online through the Genome Research Open Access option.
- Received December 5, 2024.
- Accepted June 6, 2025.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
