Genomes and how they are mapped

A genome is all the genetic information of an organism. In prokaryotes, it is the DNA of the nucleoid plus any plasmids. In eukaryotes, it is the chromosomes in the nucleus plus the small DNA of the mitochondria and plastids.

Before a genome can be read, scientists map it: they find where things lie along the DNA. There are two kinds of map.

Genetic maps come from crossing over. The further apart two genes are on a chromosome, the more often crossing over separates them, so the recombination frequency between two places (loci) grows with their distance. One map unit = one centimorgan = 1% recombinant offspring. But only genes with visible effects can be placed this way, so genetic maps are sparse.

Physical maps place DNA features at known positions, measured in base pairs.

• Restriction mapping: the DNA is cut with enzymes such as EcoRI and BamHI, and the fragments sized on a gel. A single cut in a circular DNA gives one fragment; in a linear DNA, two. If one genome has gained or lost a restriction site compared with another, the fragment sizes differ: an RFLP.
• A large mammalian genome gives lakhs of fragments, too many to see on a gel. So Southern hybridisation with a probe is used to pick out just the relevant fragments. RFLPs that are inherited along with a disease in families can be mapped, as can differences between populations.
• Other landmarks: SSLPs, variations in the length of micro- and minisatellites; and STSs (sequence tagged sites), unique stretches of 200-500 bp at known places, found by PCR.

Combining these landmarks with restriction maps gives a finely detailed physical map.