Capacity: Biological Collections: Enhancement of the Caenorhabditis Natural Diversity Resource

Project: Research project

Project Details

Description

Project Summary Keywords: Natural variation, wild strains, Caenorhabditis, whole-genome sequences, GWAS Overview: Over the last forty years, the nematode Caenorhabditis elegans has been instrumental in numerous fundamental advances in genetics, developmental biology, and neurobiology. However, all of these discoveries come from studies of a single strain in the species. With this limitation in mind, a number of C. elegans research groups have turned to natural variation found in diverse wild strains. In order to perform these types of analyses, the average research group requires wild strains collected from nature, the whole-genome sequences and variants in those strains, and then statistical frameworks for genome-wide association (GWA) mappings. However, most groups do not have the combination of experimental, computational, and statistical training to make these studies possible. For this reason, we created the C. elegans Natural Diversity Resource (CeNDR) in April 2016. CeNDR has three major goals: (1) Collect, organize, and disseminate wild C. elegans strains; (2) Organize and disseminate whole-genome sequence and variant data for wild strains; and (3) Provide a GWA portal to facilitate these mappings and interpretations of results. Based on previous NSF Collections support, we expanded CeNDR into the Caenorhabditis Natural Diversity Resource (CaeNDR) by incorporating almost 2,500 additional strains from the two other selfing Caenorhabditis species, C. briggsae and C. tropicalis. We have cryopreserved all of these strains, collected whole-genome sequence data, called variants, and predicted their effects. Here, we propose to further increase the capacity of CaeNDR by expanding the set of strains and preparing them for easy dissemination to the community, adding new tools and extensibility to existing CaeNDR genomic resources, and releasing all of the data for the three Caenorhabditis species on an updated and redesigned website (CaeNDR.org) with critical improvements to security, infrastructure costs, and user interface and experience. The extensive CaeNDR user-base from C. elegans will be amplified by researchers using C. briggsae and C. tropicalis, allowing for novel comparative approaches across the Caenorhabditis genus. Intellectual Merit: CeNDR is a community-wide centerpiece of C. elegans studies. We provided valuable strains and data to facilitate over 100 publications, where studies of natural variation would not have been possible otherwise. These successes will be expanded to two related Caenorhabditis species C. briggsae and C. tropicalis, which each are used by a large number of researchers focused on questions of comparative evolutionary genetics and genomics. Our proposed expansion in capacity and capabilities to CaeNDR will create an unparalleled platform for discovery in animal systems. The described improvements are critical to the continued success of this resource and will enable future expansions as the user-base continues to grow. Importantly, CaeNDR’s improvements are completed in an open- science and open-access research environment making data, code, and reagents available to all. Broader Impacts: CaeNDR will bring the strains and tools to study natural variation to the broad nematode community. We will expand our FAQ and record video walk-throughs to explain the operation and power of the existing and newly created tools. Importantly, we will increase accessibility in a redesigned user interface and experience (UI/UX). Over the past six years, CeNDR has enabled genetics studies through an ope
StatusActive
Effective start/end date9/1/228/31/25

Funding

  • National Science Foundation (NOT SPECIFIED)

Fingerprint

Explore the research topics touched on by this project. These labels are generated based on the underlying awards/grants. Together they form a unique fingerprint.