CGC1, a new reference genome for Caenorhabditis elegans.

Area of Science:

• Genomics
• Molecular Biology
• Developmental Biology

Background:

• The Caenorhabditis elegans (C. elegans) N2 reference genome, established in 1998, has been foundational for research but was found to be incomplete.
• Genetic divergence in N2 strains used in research has impacted the reproducibility of C. elegans genetics and genomics.

Purpose of the Study:

• To generate a complete, gap-free, telomere-to-telomere genome assembly for C. elegans.
• To provide a high-quality, isogenic reference genome and strain (CGC1) to enhance reproducibility and enable new biological discoveries.

Main Methods:

• Utilized improved long-read sequencing technologies.
• Performed manual assembly of 43 challenging genomic regions, including tandem repeats and the 45S rRNA gene locus.
• Assembled a 106.4 Mb genome sequence from the isogenic CGC1 strain, a derivative of the N2 wild-type strain.

Main Results:

• Generated a 106.4 Mb gap-free, telomere-to-telomere genome assembly for C. elegans.
• The new assembly includes a 772 kb sequence for the 45S rRNA genes and resolves numerous repeat regions.
• Identified potential for 183 new protein-coding and 163 new non-coding RNA genes compared to previous assemblies, while 99.1% of protein-coding genes remain unchanged.

Conclusions:

• The CGC1 genome assembly provides a fully defined and accurate reference for C. elegans.
• This complete genome sequence and its corresponding isogenic strain offer enhanced opportunities for model and systems biology research.
• The improved reference genome will facilitate more reproducible and comprehensive genetic and genomic studies in C. elegans.