Comparative genomics

Comparative analysis of other species genomes is a powerful tool, with multi-faceted applications relevant to the study of the human genome. The identification o f an orthologous counterpart to a human gene within another species generally circumvents any practical, ethical and social problems involved in experimental procedures to define the biological function of that gene. Important elements within a genome, not only the genes themselves but also regulatory sequences, can be conserved across many species. This not only facilitates the identification of these elements but can indicate whether these elements play an essential role in basic cellular processes. On a simplistic level, a gene identified in human that displays homology to genes identified in simple eukaryotic organisms, such as yeasts, or even prokaryotic bacteria, such as E.coli, would indicate a basic cellular function. If a human gene displayed homology to a vertebrate organism such as mouse but not an invertebrate, such as C.elegans, it could indicate that the gene in question had a distinct role in vertebrates. This is a basic example, but it also highlights another role of species comparison, that of addressing evolutionary relationships between organisms and their genomes. The vast majority of evolutionary theory has derived from species comparison.

In 1995 the first genome of a self-replicating organism. Haemophilias influenzae, was completely sequenced (Fleischmann et al, 1995). Since then, this number has increased dramatically (Karlin et al, 1998), with more complex and larger genomes now becoming available - the public release of the Drosophila genome is expected by the end of 1999 (Burtis and Hanley, 1999). It has been projected that human genome sequencing will be complete by the year 2003 (90-99.9% sequenced - SC and W UGSC, 1998; Venter et al,

1998; Goodman, 1998) and this is expected to be followed by mouse, the next best- mapped vertebrate (for review see Carver and Stubbs, 1997). The limiting factor in both human and mouse is the sheer size of the genome and the presence of repetitive elements and regions unstable in current cloning vectors (SC and WUGSC, 1998; Venter et al,

1998). Figures of 90-95% or 99.9% complete are being used, as until the final picture unfolds the degree of difficulty in finishing is yet unknown.

5.2.2.1 Other vertebrate models - Fugu rubripes and Gallus gallus

In 1993 Sydney Brenner and colleagues added another vertebrate to the select list of model organisms, the pufferfish Fugu rubripes (Brenner eta l, 1993). The rationale behind this project was that, remarkably, the Fugu genome displays an estimated 7.68 fold compression (genome size of 390 - 404Mb) with no evidence o f interspersed highly repetitive sequences that are characteristic of mouse and human DNA (review o f human repetitive elements in Smit, 1996). The reason for the compressed genome size has been postulated as; rather than being actively compressed over evolutionary time, the Fugu

genome could represent a vertebrate genome that hasn’t expanded by the acquisition of repetitive elements and therefore could be closer to an ancestral genome (Brenner et al,

1993). If synteny between the Fugu and human genomes could be demonstrated then a positional cloning project looking for a disease gene in 1Mb of human DNA could be reduced to 130kb in Fugu.

However, by studying the surfeit locus in Fugu it was shown that rather than

demonstrating clear regions of synteny, the genes of this family were interspersed across the Fugu genome as opposed to being closely linked in human (Gilley et al, 1997). Nevertheless, a growing number of human loci have been identified in Fugu and some syntenic regions compared (Trower et al, 1996; Tassone et al, 1999). It has become evident that Fugu genes are shorter, with the intron sizes responsible for the majority of compression (Brennen e ta l, 1993; Elgar, 1996).

The identification of economically important traits has been the major goal of

constructing genetic maps in livestock species (for review see Georges and Andersson, 1996). Of these livestock species, the domestic chicken {Gallus gallus) presents not only an economically important organism but also one that represents a class of species other than mammals (namely avian). Birds are thought to have diverged from a common ancestry with mammals approximately 300-350 million years ago (Kumar and Hedges,

1998) and are poorly studied in comparison to mammals. Study of an avian species will contribute to an understanding of vertebrate evolution, identifying elements that are

distinct amongst diverse vertebrates. One apparent element was the observation that avian karyotypes comprise two classes of chromosomes, micro and macro (Bloom, 1993). In

Gallus gallus one quarter of the genome is composed of microchromosomes,

cytologically indistinguishable due to their small size. Two thirds of the genome consists of macrochromosomes, designated so by their larger size, which are the only

chromosomes larger than the smallest human chromosome. The remainder o f the genome consists of intermediate sized chromosomes that have been designated larger

microchromosomes (Bloom, 1993). Chicken microchromosomes are hyperacetylated (associated with transcriptionally active DNA), early replicating (another indication of transcriptionally active DNA), and gene rich (McQueen et al, 1998). The chicken genome is also 60% smaller than the human genome (1,200Mb, Bloom, 1993) and it has been proposed that gene density on microchromosomes is comparable to that of Fugu due to compressed intron size (Hughes and Hughes, 1995; McQueen et al, 1998), as has been demonstrated with studies of the chicken MHC (Kaufman et al, 1995). Thus the benefits associated with the Fugu genome could be achieved with the chicken genome. An advantage over Fugu as a model system is the ease of genetic mapping in the chicken.

Fugu are large salt-water fish that are absent from European waters and cannot be bred in captivity (Little, 1993), whereas chickens are bred routinely as livestock throughout the world. Genetic maps of the chicken genome have been produced (examples being Bumstead and Palyga, 1992 and Groenen et al, 1998, comprehensive genetic maps available are found at http://www.ri.bbscr.ac.uk/genome mapping.html) and linkage groups between humans have been identified (reviewed by Burt et al, 1995).