CGC1, a new reference genome for Caenorhabditis elegans

Ichikawa, K.; Shoura, M. J.; Artiles, K. L.; Jeong, D.-E.; Owa, C.; Kobayashi, H.; Suzuki, Y.; Kanamori, M.; Toyoshima, Y.; Iino, Y.; Rougvie, A. E.; Wahba, L.; Fire, A. Z.; Schwarz, E. M.; Morishita, S.

doi:10.1101/2024.12.04.626850

bioRxiv · 10.1101/2024.12.04.626850

CGC1, a new reference genome for Caenorhabditis elegans

Ichikawa, K.·Shoura, M. J.·Artiles, K. L.·Jeong, D.-E.·Owa, C.·Kobayashi, H.·Suzuki, Y.·Kanamori, M.·Toyoshima, Y.·Iino, Y.·Rougvie, A. E.·Wahba, L.·Fire, A. Z.·Schwarz, E. M.·Morishita, S.

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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 used 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. While many differences from earlier assemblies came from repeat regions, unique additions to the genome were 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.

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Ichikawa, K., Shoura, M. J., Artiles, K. L., Jeong, D.-E., Owa, C., Kobayashi, H., Suzuki, Y., Kanamori, M., Toyoshima, Y., Iino, Y., Rougvie, A. E., Wahba, L., Fire, A. Z., Schwarz, E. M., Morishita, S.. 2024-12-05. CGC1, a new reference genome for Caenorhabditis elegans. https://doi.org/10.1101/2024.12.04.626850

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