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Rat Genome Assemblies, Annotation, and Variant Repository

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Rat Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2018))

Abstract

The first and only published version of the rat reference genome sequence was RGSC3.1, accomplished by the Rat Genome Sequencing Project Consortium. Here we present the history of the community effort in the correction of sequence errors and filling missing gaps in the process of refining and providing researchers with a high-quality rat reference sequence. The genome assembly improvements, addition of different evidence resources over time, such as RNA-Seq data, and software development methodologies had a positive impact on the gene model annotations. Over the years we observed a great increase in the numbers of genes, protein coding sequences, predicted transcripts and transcript features. Before the sequencing of the rat genome was possible, first biochemical and next genomic markers like RAPD, AFLP, RFLP, and SSLP were fundamental in research studies involving cross-breeding between different rat strains, in finding the level of polymorphism, linkage mapping, and phylogeny. Linkage maps provide information on recombination rates, give insight into intra- and interspecies gene rearrangements, and help to identify Mendelian loci and Quantitative Trait Loci (QTL). In the 1990s many reports were published on the construction of rat linkage maps that incorporated increasing numbers of markers and facilitated the localization of disease loci. Current genetic monitoring and linkage mapping relies on single nucleotide polymorphisms (SNPs). The Rat Genome Database collects information on genetic variation from the worldwide community of rat researchers and provides tools for searching and retrieving these data. As of today we show details about almost 605 million variants coming from many studies in our Variant Visualizer tool.

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Authors and Affiliations

  1. Department of Biomedical Engineering, Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA

    Monika Tutaj, Jennifer R. Smith & Elizabeth R. Bolton

Authors
  1. Monika Tutaj
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  2. Jennifer R. Smith
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  3. Elizabeth R. Bolton
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Correspondence to Monika Tutaj .

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Editors and Affiliations

  1. Department of Biomedical Engineering, Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA

    G. Thomas Hayman

  2. Department of Biomedical Engineering, Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA

    Jennifer R. Smith

  3. Department of Physiology, Rat Genome Database, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA

    Melinda R. Dwinell

  4. Department of Biomedical Engineering, Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA

    Mary Shimoyama

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Tutaj, M., Smith, J.R., Bolton, E.R. (2019). Rat Genome Assemblies, Annotation, and Variant Repository. In: Hayman, G., Smith, J., Dwinell, M., Shimoyama, M. (eds) Rat Genomics. Methods in Molecular Biology, vol 2018. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9581-3_2

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  • DOI: https://doi.org/10.1007/978-1-4939-9581-3_2

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9580-6

  • Online ISBN: 978-1-4939-9581-3

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