31-01-2013, 11:55 AM
Comparative Genomics
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What is Comparative Genomics?
Comparative genomics is the analysis and comparison of genomes from different species.
The purpose is to gain a better understanding of how species have evolved and to determine the function of genes and noncoding regions of the genome.
Researchers have learned a great deal about the function of human genes by examining their counterparts in simpler model organisms such as the mouse.
Genome researchers look at many different features when comparing genomes: sequence similarity, gene location, the length and number of coding regions (called exons) within genes, the amount of noncoding DNA in each genome, and highly conserved regions maintained in organisms as simple as bacteria and as complex as humans.
Comparative genomics involves the use of computer programs that can line up multiple genomes and look for regions of similarity among them.
What is compared?
Gene location
Gene structure
Exon number
Exon lengths
Intron lengths
Sequence similarity
Gene characteristics
Splice sites
Codon usage
Conserved synteny
What Is a Genome Made Of?
Although living creatures look and behave in a myriad of ways, all of their genomes consist of DNA, the chemical chain that harbors the genes that code for thousands of different kinds of proteins.
Within DNA are the instructions sufficient to make an organism and the means by which organisms pass information along to their offspring. Remarkably, this information is coded by only four nucleotides: adenosine (A), cytosine ©, guanine (G), and thymine(T).
Understanding the order of these nucleotides in linear DNA molecules has been an active pursuit since the discovery of DNA’s double-helical structure (Watson et al. 1953). As such, DNA sequencing has emerged as a fundamental approach to molecular biology research. The power of DNA sequencing as a research tool has spurred the dramatic advancement of DNA sequencing technology, which is allowing ever more genomes to be sequenced and making comparative genomics an accessible focal point for the study of any form of life.
What Genomes Have Been Sequenced?
In addition to sequencing the three billion letters in the human “genetic instruction book” (Lander et al. 2001), researchers involved in the InternationalHuman Genome Project (HGP) sequenced the genomes of a number of important model organisms. These include chimpanzee, mouse , rat , two puffer fish , fruit fly , two sea squirts , two roundworms , baker's yeast (Goffeau et al. 1996), and the bacterium Escherichia coli . Since the completion of the HGP, sequence drafts of the chicken , cow (Elsik et al.2009), dog (Lindblad-Toh et al. 2005), honey bee (Lindblad-Toh et al. 2006), sea urchin (Sodergren et al. 2006) and rhesus macaque monkey (Gibbs et al. 2007) (to name just a few) have also been established.
Together with over 1,000 prokaryote genomes, a total of over 1,300 species have been completely sequenced and published (ca. 2010; see here) and this number continues to grow at a prodigious rate, providing a rich source of genomic data for comparison.
Benefits of Comparative Genomics
Dramatic results have emerged from the rapidly developing field of comparative genomics. Comparison of the fruit fly genome with the human genome reveals that about sixty percent of genes are conserved (Adams et al. 2000). That is, the two organisms appear to share a core set of genes. Researchers have also found that two-thirds of human genes known to be involved in cancer have counterparts in the fruit fly.
In addition to its implications for human health, comparative genomics may benefit the broader animal world and ecological studies as well. As sequencing technology grows easier and less expensive, it will find wide applications in agriculture, biotechnology, and zoology as a tool to tease apart the often-subtle differences among animal and plant species. Such efforts might also lead to the rearrangement of our understanding of some branches of the evolutionary "tree of life," as well as point to new strategies for conserving rare and endangered species.