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Comparative genomics is the study of relationships between the genomes of different species or strains. Comparative genomics is an attempt to take advantage of the information provided by the signatures of selection to understand the function and evolutionary processes that act on genomes. While it is still a young field, it holds great promise to yield insights into many aspects of the evolution of modern species. The sheer amount of information contained in modern genomes (several gigabytes in the case of humans) necessitates that the methods of comparative genomics are mostly computational in nature. Gene finding is an important application of comparative genomics.

Comparative genomics exploits both similarities and differences in the proteins, RNA, and regulatory regions of different organisms to infer how selection has acted upon these elements. Those elements that are responsible for similarities between different species should be conserved through time (stabilizing selection, while those elements responsible for differences among species should be divergent (positive selection). Finally, those elements that are unimportant to the evolutionary success of the organism will be unconserved (selection is neutral).

Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is one of the important goals of the field. It is however often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. For this reason comparative genomics studies of small model organisms (for example yeast) are of great importance to advance our understanding of general mechanisms of evolution.

Having come a long way from its initial use of finding functional proteins, comparative genomics is now concentrating on finding regulatory regions and siRNA molecules. Recently, it has been discovered that distantly related species often share long conserved stretches of DNA that do not appear to code for any protein. It is unknown at this time what function such ultra-conserved regions serve.

See also


  • Kellis M, Patterson N, Endrizzi M, Birren B, Lander E (2003). Sequencing and Comparison of yeast species to identify genes and regulatory motifs. Nature, pp. 241-254 (15 May 2003).
  • Cliften P, Sudarsanam P, Desikan A (2003). Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science, pp. 71-76 (4 July 2003).
  • Bofffeli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM (2003). Phylogenetic shadowing of primate sequences to find functional regions of the human genome, Science, 299(5611):1391-1394.
  • Dujon B, et al. (2004). Genome evolution in yeasts. Nature, 430:35-44 (1 July 2004).
  • Filipski A, Kumar S (2005). Comparative genomics in eukaryotes. In The Evolution of the Genome (ed. T.R. Gregory), pp. 521-583. Elsevier, San Diego.
  • Gregory TR, DeSalle R (2005). Comparative genomics in prokaryotes. In The Evolution of the Genome (ed. T.R. Gregory), pp. 585-675. Elsevier, San Diego.
  • Hardison RC. Comparative genomics. PLoS biology, 1(2):e58.
  • Champ PC, Binnewies TT, Nielsen N, Zinman G, Kiil K, Wu H, Bohlin J, Ussery DW (2006). Genome update: purine strand bias in 280 bacterial chromosomes. Microbiology, 152(3):579-583. HubMed
  • Xie X, Lu J. Kulbokas EJ, Golub T, Mootha V, Lindblad-Toh K, Lander E, Kellis M (2005). Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature.

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