In biology, the genome of an organism is a complete DNA sequence of one set of chromosomes; for example, one of the two sets that a diploid individual carries in every somatic cell. When people say that the genome of a sexually reproducing species has been "sequenced," typically they are referring to a determination of the sequences of one set of autosomes and one of each type of sex chromosome, which together represent both of the possible sexes. Even in species that exist in only one sex, what is described as "a genome sequence" may be a composite from the chromosomes of various individuals.
Most biological entities more complex than a virus sometimes or always carry additional genetic material besides that which resides in their chromosomes. In some contexts, such as sequencing the genome of a pathogenic microbe, "genome" is meant to include this auxiliary material, which is carried in plasmids. In such circumstances then, "genome" describes all of the genes and non-coding DNA that have the potential to be present.
In vertebrates such as humans, however, "genome" carries the typical connotation of only chromosomal DNA. So although human mitochondria contain genes, these genes are not considered part of the genome. In fact, mitochondria are sometimes said to have their own genome, often referred to as the "mitochondrial genome".
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 explains the common usage of "genome" (which parallels a common usage of "gene") to refer not to any particular DNA sequence, but to a whole 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.
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2 Comparison of the sizes of different genomes
3 Genome evolution
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.
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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.