TY  - JOUR
A1  - Ichikawa, Kazuki
A1  - Shoura, Massa J.
A1  - Artiles, Karen L.
A1  - Jeong, Dae-Eun
A1  - Owa, Chie
A1  - Kobayashi, Haruka
A1  - Suzuki, Yoshihiko
A1  - Kanamori, Manami
A1  - Toyoshima, Yu
A1  - Iino, Yuichi
A1  - Rougvie, Ann E.
A1  - Wahba, Lamia
A1  - Fire, Andrew Z.
A1  - Schwarz, Erich M.
A1  - Morishita, Shinichi
T1  - CGC1, a new reference genome for Caenorhabditis elegans
Y1  - 2025/08/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1902 
EP  - 1918 
DO  - 10.1101/gr.280274.124 
VL  - 35 
IS  - 8 
UR  - http://genome.cshlp.org/content/35/8/1902.abstract 
N2  - 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. 
ER  -