The Rat Genome as a Rodent Model in Evolutionary Studies

Abstract

The genome sequence of the Brown Norway rat, Rattus norvegicus, revealed the precision with which genome analysis could trace the imprint of nucleotide changes associated with the radiation of mammalian species. Analysis of the protein‐coding repertoire and noncoding conserved elements (NCEs) including viable and decayed transposable elements, viruses and simple repeats provide landmarks for reconstructing past evolutionary events. From this analysis, it was possible to posit the configuration of genomes of long‐extinct mammalian ancestors. Application of evolutionary methods to subsets of the rat genome, the orthologues of human disease genes, permits the further validation of the laboratory rat as a model for studies of human pathogenesis.

Keywords: evolution; genome; disease; rodent; conservation; research

References

Bourque G, Pevzner PA and Tesler G (2004) Reconstructing the genomic architecture of ancestral mammals: lessons from the human mouse and rat genomes. Genome Research 14: 507–516.

Clemitson JR, Dixon RJ, Haines S et al. (2007) Genetic dissection of a blood pressure quantitative trait locus on rat chromosome 1 and gene expression analysis identifies SPON1 as a novel candidate hypertension gene. Circulation Research 100: 992–999.

Emes RD, Beatson SA, Ponting CP and Goodstadt L (2004) Evolution and comparative genomics of odorant‐ and pheromone‐associated genes in rodents. Genome Research 14: 591–602.

ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799–816.

Furney SJ, Alba MM and Lopez‐Bigas N (2006) Differences in the evolutionary history of disease genes affected by dominant or recessive mutations. BMC Genomics 7: 1471–2164.

Huang H, Winter EE, Wang HJ et al. (2004) Evolutionary conservation of human disease gene orthologs in the rat and mouse genomes. Genome Biology 5: R47.

Korstanje R and Paigen B (2002) From QTL to gene: the harvest begins. Nature Genetics 31: 235–236.

Ma J, Zhang L, Suh BB et al. (2006) Reconstructing contiguous regions of an ancestral genome. Genome Research 16: 1557–1565.

Mikkelsen TS, Wakefield MJ, Aken B et al. (2007) Genome of the marsupial Monodelphis domestica reveals innovation in non‐coding sequences. Nature 447: 167–178.

Rat Genome Sequencing Project Consortium, Gibbs RA, Weinstock GM, Metzker ML et al. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493–521.

Samuelson DJ, Hesselson SE, Aperavich BA et al. (2007) Rat Mcs5a is a compound quantitative trait locus with orthologous human loci that associate with breast cancer risk. Proceedings of the National Academy of Sciences of the USA 104: 6299–6304.

Shoja V and Zhang L (2006) A roadmap of tandemly arrayed genes in the genomes of human, mouse and rat. Molecular Biology and Evolution 23: 2134–2141.

Tu ZD, Wang L, Xu M et al. (2006) Further understanding human disease genes by comparing with housekeeping genes and other genes. BMC Genomics 7: 1–13.

Wang W, Zheng H, Yang S et al. (2005) Origin and evolution of new exons in rodents. Genome Research 15: 1258–1264.

Zosky GR and Sly PD (2007) Animal models of asthma. Clinical and Experimental Allergy 37: 973–988.

Further Reading

Alam SM, Ain R, Konno T, Ho‐Chen JK and Soares MJ (2006) The rat prolactin gene family locus: species‐specific gene family expansion. Mammalian Genome 17: 858–877.

Hurst LD (2002) The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends in Genetics 18: 486–487.

Malek RL, Wang HY, Kwitek AE et al. (2006) Physiogenomic resources for rat models of heart, lung and blood disorders. Nature Genetics 38: 234–239.

Mashimo T, Voigt B, Kuramoto T and Serikawa T (2005) Rat phenome project: the untapped potential of existing rat strains. Journal of Applied Physiology 98: 371–379.

Puente XS and Lopez‐Otin C (2004) A genomic analysis of rat proteases and protease inhibitors. Genome Research 14: 609–622.

Taylor MS, Ponting CP and Copley RR (2004) Occurrence and consequences of coding sequence insertions and deletions in mammalian genomes. Genome Research 14: 555–566.

Tuzun E, Bailey JA and Eichler EE (2004) Recent segmental duplication in the working draft assembly of the brown Norway rat. Genome Research 14: 493–506.

Yang S, Smit AF, Schwarts S et al. (2004) Patterns of insertions and their covariation with substitutions in the rat, mouse and human genomes. Genome Research 14: 517–527.

Yap VB and Pachter L (2004) Identification of evolutionary hotspots in the rodent genomes. Genome Research 14: 574–579.

Zhang Z, Burch PE, Cooney AJ et al. (2004) Genomic analysis of the nuclear receptor family: new insights into structure, and evolution from the rat genome. Genome Research 14: 580–590.

Zhao SY, Shetty J, Hou LH et al. (2004) Human, mouse, and rat genome large‐scale rearrangements: stability versus speciation. Genome Research 14: 1851–1860.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Fechtel, Kim(Mar 2008) The Rat Genome as a Rodent Model in Evolutionary Studies. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020755]