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 over time 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 an isogenic wild-type strain (CGC1) for improved reproducibility and advanced biological studies.

Main Methods:

• Utilized advanced long-read sequencing technologies.
• Performed manual assembly of challenging genomic regions, including tandem repeats.
• Assembled a 772-kb sequence for the 45S ribosomal RNA genes.

Main Results:

• Generated a 106.4 Mb gap-free genome assembly for C. elegans from the CGC1 strain.
• Identified and corrected deficiencies present in previous N2 and VC2010 assemblies.
• Found that 99.1% of protein-coding genes are conserved, with potential for 183 new protein-coding and 163 new ncRNA genes.

Conclusions:

• The CGC1 assembly provides a complete and accurate reference genome for C. elegans.
• The isogenic CGC1 strain and its genome assembly offer enhanced opportunities for model and systems biology research.
• This work addresses critical issues of reproducibility in C. elegans research.