Genetic and genomic tools for C. briggsae research

Statement of work to be performed at Northwestern University (Andersen lab): Our efforts will be focused on Aim 1. We have collected short-read (Illumina) and long-read (PacBio HiFi and ONT) sequence data along with Hi-C contact data for the C. briggsae strain QX1410. These data will be used to create a second-generation assembly with minimal gaps. This second-generation assembly will be used for manual curation of the sequence data to make a telomere-to-telomere assembly. This “platinum-level” genome assembly will be used to predict gene models. These predictions will be manually curated using short-read (Illumina) and long-read (PacBio iso-seq) sequence data to make high-quality gene models for QX1410. All of these data will be released on the Caenorhabditis Natural Diversity Resource, NCBI, and SRA. We will aid PI Chamberlin on genome structure and any specific gene models to complete Aims 2 and 3. Explicit tasks will include but will not be limited to: • Second-generation genome assembly using our newest collected short- and long-read sequence data • “Platinum-level” genome assembly from telomere-to-telomere using manual curation of long-read data • Gene model ascertainment and manual curation using established pipelines and a trained team • Data release to the community