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Rat Genome Assemblies, Annotation, and Variant Repository.

Monika Tutaj1, Jennifer R Smith2, Elizabeth R Bolton2

  • 1Department of Biomedical Engineering, Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA. motutaj@mcw.edu.

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|June 23, 2019
PubMed
Summary
This summary is machine-generated.

This study details the collaborative effort to refine the rat reference genome sequence, improving gene annotations and variant data. The Rat Genome Database now provides access to millions of genetic variations for researchers.

Keywords:
Gene model annotationsGenomic markersReference genomeSNPsVariants

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Area of Science:

  • Genomics
  • Bioinformatics
  • Comparative Genomics

Background:

  • The initial rat reference genome sequence (RGSC3.1) required significant community effort for refinement.
  • Previous genetic marker technologies (RAPD, AFLP, RFLP, SSLP) were crucial for early rat genetic studies.

Purpose of the Study:

  • To document the historical community-driven improvements to the rat reference genome sequence.
  • To highlight advancements in gene model annotation and genetic variation data accessibility.

Main Methods:

  • Iterative refinement of the genome assembly using diverse evidence resources, including RNA-Seq data.
  • Development of bioinformatics tools and software methodologies for gene annotation.
  • Collection and curation of genetic variation data from global researchers.

Main Results:

  • Significant improvements in genome assembly quality, gene models, and transcript annotations.
  • A substantial increase in the number of identified genes, protein-coding sequences, and transcripts.
  • The Rat Genome Database now houses details on approximately 605 million genetic variants.

Conclusions:

  • Community collaboration has been essential for creating a high-quality rat reference genome.
  • Enhanced genome data and variant information facilitate diverse research applications, including disease gene localization.
  • The Rat Genome Database serves as a vital resource for accessing and analyzing rat genetic variation.