The genome is the totality of all of the DNA of an individual or a species. It is now taken to include all of the DNA, not just the genes. This definition is simple for the majority of genomes, but all of the minor DNA components must also be considered. For simple viruses, with a single nucleic acid molecule, the genome is obvious, although of course for RNA viruses it is RNA rather than DNA. For haploid prokaryotes, it is also straightforward, except for the plasmids, one copy of which is counted in the genome. Since prokaryotic strains and lineages differ by DNA sequence polymorphism and in the plasmids present, only genetic lineage genomes can be described with total accuracy. The genome of a species will be a compromise best representing all the known lineages, to make up a typical genome for the individuals of that species.
For eukaryotes, one haploid copy of the DNA of each of the diploid pairs of chromosomes (the autosomes) is included, plus one copy of the DNA of sex chromosomes. Thus the female and male genomes will differ if the sex chromosomes are different. One copy of the DNA from any organelles other than the nucleus, such as the mitochondria and chloroplasts, should be included; a complete list of such organelles is probably not yet available for any species, but many are normally unimportant. There is, of course, polymorphism of DNA sequences in a population of individuals, and the species’ genome is again a compromise to obtain a typical genome. The genome can be considered to include all of the information required to specify the species, but only for certain viruses has it actually been demonstrate that the lineage can be propagated from purified DNA. When the phrase "genome size" was first used to describe the total haploid DNA content, there were strong objections, based on the concept that there is additional information in the chromosomal proteins, and even in body structures, that is necessary to propagate the lineage. While that point of view is not common at present, the proof has not been made with eukaryotes that the DNA contains all of the information required for maintenance of the lineage or species.
The majority of the DNA of a genome is not in the genes themselves and their known associated regulatory sequence. While the phenomenon of gene regulation is beginning to be understood, little is known of the significance of the majority of the DNA, whether it has any functions other than acting as spacer between genes. In most species, a large fraction of the DNA is repeated sequences (see Repetitive DNA and Repeated DNA Sequence Interspersion) that cause genetic recombination and unequal crossing over, resulting in genomic rearrangements, but their overall significance is not understood.
