In biology, the genome of a polyploid organism most often refers to the intact DNA sequence of one set of chromosomes--that is, to the genes and non-coding DNA arranged as they appear on the chromosomes of a typical individual.
In some contexts, such as sequencing the genome of a pathogenic microbe, "genome" is meant to include not only chromosomal DNA, but also the optional genetic material individual cells may carry as plasmids. In such circumstances then, "genome" describes all of the genes and non-coding DNA that have the potential to be present in a biological cell. Applied to humans, "genome" refers only to chromosomal DNA, however. So even though human mitochondria contain genes, for example, these genes are not considered part of the genome. (In fact, mitochondria are sometimes said to have their own genome, as in the term "mitochondrial genome"). Most organisms more complex than a virus carry some genes outside their chromosomes.
The Human Genome Project was organized to map and to sequence the human genome. Other genome projects include mouse, rice, the plant Arabidopsis, the puffer fish, bacteria like E. coli, etc. On the heels of this genome sequencing, many researchers are examining the protein products of the identified gene sequences. These gene products as a group are sometimes called a "proteome."
Note that a genome does not capture the genetic diversity or the genetic polymorphism of a species. For example, the human genome sequence in principle could be determined from just half the DNA of one cell from one individual. To learn what variations in DNA underlie particular traits or diseases requires comparisons across individuals. This point should also make clear that genome, like gene, refers to no particular DNA sequence, but to a family of sequences that share a biological context.
Although this concept may seem counter intuitive, it is the same concept that says there is no particular shape that is the shape of a cheetah. Cheetahs vary, and so do the sequences of their genomes. Yet both the individual animals and their sequences share commonalities, so one can may learn something about cheetahs and "cheetah-ness" from a single example of either.
Typical genome sizes
|Organism||Genome size (base pairs)|
Genomes are more than the sum of an organism's genes and have traits that may be measured and studied without reference to the details of any particular genes and their products. Researchers compare traits such as chromosome number, chromosome size, gene order, codon usage bias, and G-C content to determine what mechanisms could have produced the great variety of genomes that exist today.
Duplications play a major role in shaping the genome. Duplications may range from extension of short tandem repeats, to duplication of a cluster of genes, and all the way to duplications of entire chromosomes or even entire genomes. Such duplications are probably fundamental to the creation of genetic novelty.
Horizontal gene transfer is invoked to explain how there is often extreme similarity between small portions of the genomes of two organisms that are otherwise very distantly related. Horizontal gene transfer seems to be common among many microbes. Also, eukaryotic cells seem to have experienced a transfer of some genetic material from their chloroplast and mitochondrial genomes to their nuclear chromosomes.