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Table of Contents: 2023 JANUARY–FEBRUARY No. 450

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NIH Comparative Genomics Resource Project and the Potential Impact of Emerging Model Organisms on Human Health

NIH Comparative Genomics Resource Project and the Potential Impact of Emerging Model Organisms on Human Health. NLM Tech Bull. 2023 Jan-Feb;(450):e1.

2023 January 10 [posted]

Comparative genomics is a science that compares genomic data either within a species or across species to answer questions in biomedicine. Laboratory experiments can then investigate the functional impact of those genomics similarities and differences. The history of comparative genomics goes back to the mid-1990s, but comparative genomics is now accelerating. A flood of new data is emerging as DNA sequencing technology becomes cheaper and commoditized. While this growth poses many challenges to current tools and approaches, it also offers immense opportunity for scientific research and understanding. These insights continue to reveal novel model organisms that can further the impact of comparative genomics on human health.

Even before the emergence of comparative genomics as a scientific discipline, several organisms were identified as notable model organisms for specific aspects of human health. These animals are typically easy to maintain and breed in laboratory settings and have systems or other biological characteristics similar to human systems. Some of the most well-established model organisms include house mouse (Mus musculus), brown rat (Ratticus norveigcus), nematode (Caenorhabditis elegans), zebrafish (Danio rerio), western clawed frog (Xenopus tropicalis), and fruit fly (Drosophila melanogaster).

These established model organisms continue to be well-researched and frequently relied upon for studying a wide range of applications to human health. However, without as much reliance on laboratory maintenance and reproduction, and with the continually expanding library of available, high-quality genomes, comparative genomics is now being used to explore potentially more beneficial model organisms. These emerging models may not have been well-researched in the past, but their recently characterized genomes can be leveraged in comparative genomics studies to impact far-reaching aspects of human health.

The National Institutes of Health (NIH) is helping to harness the power of comparative genomics as a tool for scientific discovery through the NIH Comparative Genomics Resource (CGR) project. CGR is a multi-year project implemented by the National Library of Medicine (NLM) to maximize the impact of eukaryotic research organisms and their genomic data resources to biomedical research. The National Center for Biotechnology Information (NCBI), as part of NLM, is charged with engaging genomics communities on their comparative genomics needs and leading development of tools, knowledgebases, and repositories to meet those needs.

NCBI Developments for CGR

The CGR project aims to promote reliable comparative genomics analyses, accelerate new discoveries, and offer a seamless user experience. Newly accessible and improved NCBI tools will provide the genomics community with a core foundation of uncontaminated and consistently annotated eukaryotic genomes. For example, the NCBI Foreign Contamination Screen (FCS) tool puts contamination removal in the hands of the genomics community prior to submission to NCBI. Furthermore, the NCBI Eukaryotic Genome Annotation Pipeline (EGAP) will become publicly available to enable the genomics community to create and submit consistent, high-quality annotation across species.

In addition to the FCS and EGAP tools promoting high-quality genomic data, NCBI will improve existing tools and develop new ones to improve and simplify comparative analyses. NCBI Datasets offers web and programmatic interfaces to genome associated data. A new ClusteredNR database for BLAST provides reduced redundancy, faster searchers, and more informative results. Finally, a new Comparative Genome Viewer (CGV) allows quick comparison between different assemblies and makes it easier to visualize genomic structure changes.

By providing equal access to genomic data and tools for all eukaryotic research organisms—including those not represented by organism-specific resources—and improving the connectivity of their data, NCBI is increasing their potential contributions to research. NCBI is curating content, adding features to make it more usable for comparative analyses. CGR efforts will also enhance NCBI-held content with community supplied content and connect NCBI resources with community-provided resources to amplify the impact of such data and resources in support of greater scientific discovery.

The CGR project will maximize the impact of eukaryotic research organisms, as noted below, offering new opportunities for scientific advancement in the field of comparative genomics.

Emerging Model Organism Use Cases

To help investigators, students, medical librarians and others understand the importance of comparative genomics to scientific advances, NCBI staff identified use cases for emerging model organisms researched through comparative genomics. Specifically, they explored their potential impact to human health as an area where the CGR project may positively influence associated research activities.

  • Pig (Sus scrofa domesticus) – Xenotransplantation
  • Syrian Golden Hamster (Mesocricetus auratus) – COVID-19
  • Dog (Canis familiaris) – Oncology
  • Thirteen-lined ground squirrel (Ictidomys tridecemlineatus) – Hibernation studies
  • Killifish (Nothobranchius furzeri and other members of the order Cyprinodontiformes) – Aging studies
  • Bats (members of the order Chiroptera) – Infectious disease

From this short list, it is clear that research organisms can broadly inform our understanding of human biology and health. Comparative genomics plays a key role in delivering that knowledge. Details on these use cases and their impact to human health can be found on NCBI Insights.

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