Resource

CGC1, a new reference genome for Caenorhabditis elegans

    • 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
    • 8 Present address: Phinomics, Incorporated, San Carlos, CA 94070, USA
Published July 15, 2025. https://doi.org/10.1101/gr.280274.124
Download PDF Cite Article Permissions Share
cover of Genome Research Vol 36 Issue 4
Current Issue:
April 2026, Vol. 36, No. 4
Focus view

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.

Back to top
Article contents

Announcement(s)