Phylogenetics of the laboratory rat Rattus norvegicus

  • The 2013 paper by Atanur et al describing the whole genome sequencing of 28 rat strains includes a phylogenetic analysis of those strains. The phylogenetic tree was based on the genetic distances between all possible pairs of strains, calculated as the ratio between the number of SNVs between each pair of strains and the length of the rat reference genome (assembly RGSC 3.4). Variants used in this analysis are available in RGD's Variant Visualizer tool for the 3.4 assembly and on the RGD FTP site.
    Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat.  Atanur SS et al. Cell. 2013 Aug 1;154(3):691-703. doi: 10.1016/j.cell.2013.06.040.   RGD ID: 7248424, PubMed Central.
  • In 2008, Nijman et al published a phylogenetic analysis based on a genome-wide panel of single nucleotide polymorphisms (SNPs) selected to be polymorphic between Brown Norway and SS or Wistar rat strains. This panel was used to genotype animals from 31 inbred strains and 2 outbred strains as well as 3 wild rats. Results are presented as both a neighbor-joining phylogenetic tree and a NeighborNet phylogenetic network.
    A genome-wide SNP panel for mapping and association studies in the rat.  Nijman IJ1, Kuipers S, Verheul M, Guryev V, Cuppen E. BMC Genomics. 2008; 9:95.  doi:10.1186/1471-2164-9-95.   RGD ID:10768827PubMed Central.

  • A phylogenic tree consisting of 132 strains is available at The National BioResource Project for the Rat in Japan (NBRP).  The original publication of this work appeared in BMC Genetics in 2006.
    A set of highly informative rat simple sequence length polymorphism (SSLP) markers and genetically defined rat strains.   Mashimo T, Voigt B, Tsurumi T, Naoi K, Nakanishi S, Yamasaki K, Kuramoto T, Serikawa T.  BMC Genet. 2006 Apr 4; 7:19.  doi:10.1186/1471-2156-7-19.  RGD ID:1581776PubMed Central.

  • With more than 200 rats strains being bred as models of human diseases, laboratory rats have played an important role in biomedical research for over 100 years. The ACP project at RGD genotyped 48 commonly used rat inbred strains by using over 4800 microsatellite markers with known genomic locations.  The microsatellite markers were integrated into the rat radiation hybrid (RH) map. In order to understand the relation between these markers, Canzian (RGD ID:4145419, listed below) had constructed a simple distance model based on percentages of genotype differences. The ACP project analysis (RGD ID:4145418) instead uses two commonly used models of microsatellite evolution to construct a phylogenetic tree. The resulting tree appears to more closely follow the derivation of some closely related strains which in the previous analysis appeared widely separated on the tree.

  • As the history of the generation and evolution of different rat strains is not well known, the generation of a phylogenetic tree by Canzian in 1997 was limited by the available information. This genealogic tree consists of 63 strains and 214 substrains with information on their genetic and biochemical markers. BN possesses a distinct genetic divergence from all the other strains being consistent with the reports showing its origin from wild rats. In this analysis, the BN strain is represented as the root of the phylogenetic tree.  RGD ID:4145419.

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