Genome
In
biology the
genome of an organism is the whole hereditary information of an organism that is encoded in the
DNA (or, for some viruses,
RNA). This includes both the
genes and the
non-coding sequences. The term was coined in
1920 by
Hans Winkler, Professor of
Botany at the
University of Hamburg,
Germany, as a
portmanteau of the words
gene and chromos
ome.
More precisely, 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. The term genome can be applied specifically to mean the complete set of
nuclear DNA (i.e., the "nuclear genome") but can also be applied to
organelles that contain their own DNA, as with the
mitochondrial genome or the
chloroplast genome. 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. In general use, the phrase "genetic makeup" is sometimes used conversationally to mean the genome of a particular individual or organism. The study of the global properties of genomes of related organisms is usually referred to as
genomics, which distinguishes it from
genetics which generally studies the properties of single
genes or groups of genes.
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 learn something about cheetahs and "cheetah-ness" from a single example of either.
Since genomes and their organisms are very complex, one research strategy is to reduce the number of genes in a genome to the bare minimum and still have the organism in question survive. There is experimental work being done on minimal genomes for single cell organisms as well as minimal genomes for multicellular organisms (see
Developmental biology). The work is both
in vivo and
in silico. By understanding the functioning of minimal organisms one hopes to add complexity incrementally leading to the understanding of multicellular diseases such as
Cancer.(see
#References)
Main article:
Genome projectThe
Human Genome Project was organized to
map and to
sequence the human genome. Other genome projects include
mouse,
rice, the plant
Arabidopsis thaliana, the
puffer fish, bacteria like
E. coli, etc. Many genomes have been sequenced by various genome projects. The cost of sequencing continues to drop, and it is possible that eventually an individual's genome could be
sequenced for around several thousand dollars (US).
Compare: proteomeFor an updated list of sequenced genomes and their sizes, visit the
Genomes OnLine Database (GOLD)| Organism | Genome size (base pairs) | | Virus, Phage Φ-X174; | 5386 - First sequenced genome |
| Virus, Phage λ | 5×104 |
| Archaeum, Nanoarchaeum equitans | 5×105 - Smallest non-viral genome Dec, 2005 |
| Bacterium, Buchnera aphidicola | 6×105 |
| Bacterium, Wigglesworthia glossinidia | 7×105 |
| Bacterium, Escherichia coli | 4×106 |
| Amoeba, Amoeba dubia | 6.7×1011 - Largest known genome Dec, 2005 |
| Plant, Fritillary assyrica | 1.3×1011 |
| Fungus,Saccharomyces cerevisiae | 2×107 |
| Nematode, Caenorhabditis elegans | 8×107 |
| Insect, Drosophila melanogaster | 2×108 |
| Mammal, Homo sapiens | 3×109 |
Note: The DNA from a single human cell has a length of ~1.8m.
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 (
karyotype),
genome size,
gene order,
codon usage bias, and
GC-content to determine what mechanisms could have produced the great variety of genomes that exist today (for recent overviews, see Brown
2002; Saccone and Pesole
2003; Benfey and Protopapas
2004; Gibson and Muse 2004; Reese 2004; Gregory
2005).
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.
*
Genome,
Proteome,
Expressome,
Metabolome,
Regulome,
Functome,
Phenome,
Textome,
Glycome*
Mitochondriomics,
Golgiome,
Ligandomics,
Eukaryome,
Bacteriome,
Archaeome*
Human genome,
Mitochondriome,
EukaryomeBenfey, P and Protopapas, AD (2004). Essentials of Genomics. Prentice Hall.
Brown, TA (2002). Genomes 2. Bios Scientific Publishers.
Gibson, G and Muse, SV (2004). A Primer of Genome Science (Second Edition). Sinauer Assoc.
Gregory, TR (ed) (2005).
The Evolution of the Genome. Elsevier.
Reece, RJ (2004). Analysis of Genes and Genomes. John Wiley & Sons.
Saccone, C and Pesole, G (2003). Handbook of Comparative Genomics. John Wiley & Sons.
Werner, E. In silico multicellular systems biology and minimal genomes, Drug Discov Today. 2003 Dec 15;8(24):1121-7.
*
Human genome*
Mitochondrial genome*
Genome size*
Genome project*
Genome degradation*
Genome reduction*
Genome annotation*
Genome screen*
Genome assembly*
Genome rearrangement*
HIV structure and genome*
Developmental biology*
evolution*
molecular systematics*
molecular evolution*
gene family*
gene*
Animal genome size database*
Plant genome size database*
Genomes OnLine Database*
The Genome News Network*
NCBI Entrez Genome Project database*
NCBI Genome Primer*
BBC News - Final genome 'chapter' published*
Software that maps an Artificial Genome sequence to a Network and to a Lineage tree
