What everybody should know about the rat genome and its online resources

Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA.
Nature Genetics (Impact Factor: 29.65). 06/2008; 40(5):523-7. DOI: 10.1038/ng0508-523
Source: PubMed

ABSTRACT It has been four years since the original publication of the draft sequence of the rat genome. Five groups are now working together to assemble, annotate and release an updated version of the rat genome. As the prevailing model for physiology, complex disease and pharmacological studies, there is an acute need for the rat's genomic resources to keep pace with the rat's prominence in the laboratory. In this commentary, we describe the current status of the rat genome sequence and the plans for its impending 'upgrade'. We then cover the key online resources providing access to the rat genome, including the new SNP views at Ensembl, the RefSeq and Genes databases at the US National Center for Biotechnology Information, Genome Browser at the University of California Santa Cruz and the disease portals for cardiovascular disease and obesity at the Rat Genome Database.

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Available from: Xose M Fernandez-Suarez, Aug 23, 2015
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    • "; Rat Genome Sequencing Project Consortium 2004; Chimpanzee Sequencing and Analysis Consortium 2005; Levy et al. 2007; Rhesus Macaque Genome Sequencing and Analysis Consortium 2007; Bentley et al. 2008; Twigger et al. 2008; Wang et al. 2008; Li et al. 2010; Gnerre et al. 2011; Kim et al. 2011; Lindblad-Toh et al. 2011; Locke et al. 2011; Xu et al. 2011; Yan et al. 2011; Perry et al. 2012; Prüfer et al. 2012; Scally et al. 2012 "
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    ABSTRACT: Genome studies of mammals in the superorder Euarchontoglires (a clade that comprises the orders Primates, Dermoptera, Scandentia, Rodentia, and Lagomorpha) are important for understanding the biological features of humans, particularly studies of medical model animals such as macaques and mice. Furthermore, the dynamic eco-evolutionary signatures of Euarchontoglires genomes may be discovered because many species in this clade are characterized by their successful adaptive radiation to various ecological niches. In the present study, we investigated the evolutionary trajectory of bitter taste receptor genes (TAS2Rs) in 28 Euarchontoglires species based on homology searches of 39 whole-genome assemblies. The Euarchontoglires species possessed variable numbers of intact TAS2Rs, which ranged from 16 to 40, and their last common ancestor had at least 26 intact TAS2Rs. The gene tree showed that there have been at least 7 lineage-specific events involving massive gene duplications. Gene duplications were particularly evident in the ancestral branches of anthropoids (the anthropoid cluster), which may have promoted the adaptive evolution of anthropoid characteristics, such as a trade-off between olfaction and other senses and the development of herbivorous characteristics. Subsequent whole-gene deletions of anthropoid cluster TAS2Rs in hominoid species suggest ongoing ectopic homologous recombination in the anthropoid cluster. These findings provide insights into the roles of adaptive sensory evolution in various ecological niches and important clues related to the molecular mechanisms that underlie taste diversity in Euarchontoglires mammalian species, including humans.
    Molecular Biology and Evolution 04/2014; 31(8). DOI:10.1093/molbev/msu144 · 14.31 Impact Factor
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    • "Rattini, the murid tribe that forms the focus of our investigation, comprises >167 species distributed among 34 genera (Wilson and Reeder 2005; see Table 2 in Lecompte et al. 2008). It harbours the biologically important model species, the Norway rat, R. norvegicus (Aplin et al. 2003), for which a vast amount of data, both genomic and immunogenetic, have been generated (see for example Aitman et al. 2008; Twigger et al. 2008). The other Rattini species have, however, attracted less attention. "
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    ABSTRACT: The Rattini (Muridae, Murinae) includes the biologically important model species Rattus norvegicus (RNO) and represents a group of rodents that are of clinical, agricultural and epidemiological importance. We present a comparative molecular cytogenetic investigation of ten Rattini species representative of the genera Maxomys, Leopoldamys, Niviventer, Berylmys, Bandicota and Rattus using chromosome banding, cross-species painting (Zoo-fluorescent in situ hybridization or FISH) and BAC-FISH mapping. Our results show that these taxa are characterised by slow to moderate rates of chromosome evolution that contrasts with the extensive chromosome restructuring identified in most other murid rodents, particularly the mouse lineage. This extends to genomic features such as NOR location (for example, NORs on RNO 3 are present on the corresponding chromosomes in all species except Bandicota savilei and Niviventer fulvescens, and the NORs on RNO 10 are conserved in all Rattini with the exception of Rattus). The satellite I DNA family detected and characterised herein appears to be taxon (Rattus) specific, and of recent origin (consistent with a feedback model of satellite evolution). BAC-mapping using clones that span regions responsible for the morphological variability exhibited by RNO 1, 12 and 13 (acrocentric/submetacentric) and their orthologues in Rattus species, demonstrated that the differences are most likely due to pericentric inversions as exemplified by data on Rattus tanezumi. Chromosomal characters detected using R. norvegicus and Maxomys surifer whole chromosome painting probes were mapped to a consensus sequence-based phylogenetic tree thus allowing an objective assessment of ancestral states for the reconstruction of the putative Rattini ancestral karyotype. This is thought to have comprised 46 chromosomes that, with the exception of a single pair of metacentric autosomes, were acrocentric in morphology.
    Chromosome Research 08/2011; 19(6):709-27. DOI:10.1007/s10577-011-9227-2 · 2.69 Impact Factor
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    • "The BN is one of several Brown Norway strains. It is a propitious strain for genetic studies because its genome has been sequenced (Gibbs et al. 2004; Twigger et al. 2008), and it has been extensively phenotyped in many domains, often being used as a control for other strains. The FHH strain, one of several Fawn Hooded strains, has been less well characterized. "
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    ABSTRACT: There has been extensive work to elucidate the behavioral and physiological mechanisms responsible for taste preferences of the rat but little attempt to delineate the underlying genetic architecture. Here, we exploit the FHH-Chr nBN/Mcwi consomic rat strain set to identify chromosomes carrying genes responsible for taste preferences. We screened the parental Fawn Hooded Hypertensive (FHH) and Brown Norway (BN) strains and 22 FHH-Chr nBN consomic strains, with 96-h 2-bottle tests, involving a choice between water and each of the following 16 solutions: 10 mM NaCl, 237 mM NaCl, 32 mM CaCl2, 1 mM saccharin, 100 mM NH4Cl, 32 mM sucrose, 100 mM KCl, 4% ethanol, 1 mM HCl, 10 mM monosodium glutamate, 1 mM citric acid, 32 μM quinine hydrochloride, 1% corn oil, 32 μM denatonium, 1% Polycose, and 1 μM capsaicin. Depending on the taste solution involved, between 1 and 16 chromosomes were implicated in the response. Few of these chromosomes carried genes believed to mediate taste transduction in the mouse, and many chromosomes with no candidate taste genes were revealed. The genetic architecture of taste preferences is considerably more complex than has heretofore been acknowledged. © The Author 2010. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: [email protected] /* */
    Chemical Senses 07/2010; 35(6):473-89. DOI:10.1093/chemse/bjq038 · 3.28 Impact Factor
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