Genome
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222046538
2008-06-27T08:49:50Z
George Gastin
7082572
{{otheruses}}
{{for|a non-technical introduction to the topic|Introduction to genetics}}
In [[biology]] the '''genome''' of an [[organism]] is its whole hereditary information and is encoded in the [[DNA]] (or, for some viruses, [[RNA]]). [[Image:Genome_gradient.jpg|300px|right|thumb|An image of multiple chromosomes, making up a [[genome]]]]This includes both the [[gene]]s and the [[Junk DNA|non-coding sequences]] of the DNA. The term was adapted in 1920 by [[Hans Winkler]], Professor of [[Botany]] at the [[University of Hamburg]], [[Germany]]. The Oxford English Dictionary suggests the name to be a [[portmanteau]] of the words '''''gen'''e'' and ''chromos'''ome''''', however, many related ''-ome'' words already existed, such as ''[[biome]]'' and ''[[rhizome]]'', forming a vocabulary into which ''genome'' fits systematically.<ref>{{cite journal |author = Joshua Lederberg and Alexa T. McCray | title='Ome Sweet 'Omics -- A Genealogical Treasury of Words | journal=The Scientist | volume=15 | issue=7 | year=2001 | url=http://lhncbc.nlm.nih.gov/lhc/docs/published/2001/pub2001047.pdf}}</ref>
More precisely, the genome of an organism is a complete [[genetic sequence]] on one set of [[chromosome]]s; 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 that stored on a complete set of ''[[cell nucleus|nuclear]] DNA'' (i.e., the "nuclear genome") but can also be applied to that stored within [[organelles]] that contain their own DNA, as with the [[mitochondrial genome]] or the [[chloroplast]] genome. When people say that the genome of a [[sexual reproduction|sexually reproducing]] [[species]] has been "[[sequencing|sequenced]]," typically they are referring to a determination of the sequences of one set of [[autosome]]s 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 read 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 [[gene]]s or groups of genes.
Both the number of [[base pair]]s and the number of genes vary widely from one species to another, and there is little connection between the two. At present, the highest known number of genes is around 60,000, for the [[protozoan]] causing [[trichomoniasis]] (see [[List of sequenced eukaryotic genomes]]), almost three times as many as in the [[human genome]].
An analogy to the human genome stored on DNA is that of instructions stored in a book:
* The book is over one billion words long;
* The book is bound 5000 volumes, each 300 pages long;
* The book fits into a cell nucleus the size of a pinpoint;
* A copy of the book (all 5000 volumes) is contained in almost every cell;
== Types ==
Most biological entities that are more complex than a [[virus (biology)|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 information stored on this auxiliary material, which is carried in [[plasmid]]s. In such circumstances then, "genome" describes all of the genes and information on non-coding DNA that have the potential to be present.
In [[eukaryote]]s such as plants, protozoa and animals, however, "genome" carries the typical connotation of only information on chromosomal DNA. So although these organisms contain [[mitochondria]] that have their own DNA, the genes in this ''mitochondrial DNA'' 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]]".
== Genomes and genetic variation ==
Note that a genome does not capture the genetic diversity or the genetic [[polymorphism (biology)|polymorphism]] of a species. For example, the human genome sequence in principle could be determined from just half the information on the DNA of one cell from one individual. To learn what variations in genetic information 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 the information in 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.
== Genome projects ==
{{details|Genome project}}
The [[Human Genome Project]] was organized to [[physical map|map]] and to [[sequencing|sequence]] the human genome. Other genome projects include [[mus musculus|mouse]], [[rice]], the plant ''[[Arabidopsis thaliana]]'', the [[puffer fish]], bacteria like [[E. coli]], etc. In 1976, [[Walter Fiers]] at the [[University of Ghent]] ([[Belgium]]) was the first to establish the complete nucleotide sequence of a viral RNA-genome ([[Bacteriophage|bacteriophage MS2]]). The first DNA-genome project to be completed was the [[Phi-X174 phage|Phage Φ-X174]], with only 5368 base pairs, which was sequenced by [[Fred Sanger]] in 1977 . The first bacterial genome to be completed was that of [[Haemophilus influenzae]], completed by a team at [[The Institute for Genomic Research]] in 1995.
In May 2007, the ''New York Times'' announced that the full genome of DNA pioneer James D. Watson had been recorded.[http://www.nytimes.com/2007/05/31/science/31cnd-gene.html?em&ex=1180843200&en=19e1d55639350b73&ei=5087%0A] The article noted that some scientists believe this to be the gateway to upcoming personalized genomic medicine.
Many genomes have been sequenced by various genome projects. The cost of sequencing continues to drop.
== Comparison of different genome sizes ==
{{main|Genome size}}
{| class="wikitable"
!Organism
!Genome size ([[base pair]]s)
!Note
|-
|[[Virus]], [[Bacteriophage MS2]]
|3,569
| First sequenced RNA-genome<ref name=Fiers1976>{{cite journal |author=Fiers W, ''et al.'' |title=Complete nucleotide-sequence of bacteriophage MS2-RNA - primary and secondary structure of replicase gene |journal=Nature |volume=260 |pages=500–507 |year=1976| pmid=1264203|url=http://www.nature.com/nature/journal/v260/n5551/abs/260500a0.html|doi=10.1038/260500a0}}</ref>
|-
|[[Virus]], [[SV40]]
|5,224
|<ref name=Fiers1978>{{cite journal |author=Fiers W, Contreras R, Haegemann G, Rogiers R, Van de Voorde A, Van Heuverswyn H, Van Herreweghe J, Volckaert G, Ysebaert M |title=Complete nucleotide sequence of SV40 DNA |journal=Nature |volume=273 |issue=5658 |pages=113–120 |year=1978|doi=10.1038/273113a0| url=http://www.nature.com/nature/journal/v273/n5658/abs/273113a0.html | pmid=205802}}</ref>
|-
|[[Virus]], [[Phi-X174 phage|Phage Φ-X174;]]
|5,386
|First sequenced DNA-genome<ref name=Sanger1977>{{cite journal |author=Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M |title=Nucleotide sequence of bacteriophage phi X174 DNA |journal=Nature |volume=265 |issue=5596 |pages=687–695 |year=1977| pmid=870828| url=http://www.nature.com/nature/journal/v265/n5596/abs/265687a0.html | doi=10.1038/265687a0}}</ref>
|-
|[[Virus]], [[lambda phage|Phage λ]]
|50,000
|
|-
|[[Bacterium]], ''[[Haemophilus influenzae]]''
| 1,830,000
|First genome of living organism, July 1995<ref name=Fleichmann_1995>{{cite journal |author=Fleischmann R, Adams M, White O, Clayton R, Kirkness E, Kerlavage A, Bult C, Tomb J, Dougherty B, Merrick J |title=Whole-genome random sequencing and assembly of Haemophilus influenzae Rd |journal=Science |volume=269 |issue=5223 |pages=496–512 |year=1995 |pmid=7542800| doi=10.1126/science.7542800 |url=http://www.sciencemag.org/cgi/content/abstract/269/5223/496 }}</ref>
|-
|[[Bacterium]], ''[[Carsonella ruddii]]''
|160,000
|Smallest non-viral genome.<ref>{{cite journal |author=Nakabachi A, Yamashita A, Toh H, ''et al'' |title=The 160-kilobase genome of the bacterial endosymbiont Carsonella |journal=Science (journal) |volume=314 |issue=5797 |pages=267 |year=2006 |month=October |pmid=17038615 |doi=10.1126/science.1134196}}</ref>
|-
|[[Bacterium]], ''[[Buchnera aphidicola]]''
|600,000
|
|-
|[[Bacterium]], ''[[Wigglesworthia glossinidia]]''
|700,000
|
|-
|[[Bacterium]], ''[[Escherichia coli]]''
|4,000,000
| <ref>{{cite journal| journal=science| author=Frederick R. Blattner, Guy Plunkett III, et al. | volume=277| doi=10.1126/science.277.5331.1453 | title=The Complete Genome Sequence of Escherichia coli K-12 | url=http://www.sciencemag.org/cgi/content/abstract/277/5331/1453|pmid= 9278503| pages=1453–1462 | year=1997 }}</ref>
|-
|[[Amoeba]], ''[[Amoeba dubia]]''
|670,000,000,000
|Largest known genome.<ref name=Parfrey2008>{{cite journal | author = Parfrey, L.W. | coauthors = Lahr, D.J.G.; Katz, L.A. | year = 2008 | title = The Dynamic Nature of Eukaryotic Genomes | journal = Molecular Biology and Evolution | volume = 25 | issue = 4 | pages = 787 | doi = 10.1093/molbev/msn032 | pmid = 18258610}}</ref>
|-
|[[Plant]], ''[[Arabidopsis thaliana]]''
|157,000,000
|First plant genome sequenced, Dec 2000.<ref name="Greilhuber">{{cite journal| author=Greilhuber, J., Borsch, T., Müller, K., Worberg, A., Porembski, S., and Barthlott, W. |date=2006| title= Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size |journal=Plant Biology| volume=8|pmid= 17203433| pages=770–777| doi= 10.1055/s-2006-924101}}</ref>
|-
|[[Plant]], ''[[Genlisea margaretae]]''
|63,400,000
|Smallest recorded [[flowering plant]] genome, 2006.<ref name="Greilhuber" />
|-
|[[Plant]], ''[[Fritillaria assyrica]]''
|130,000,000,000
|
|-
|[[Plant]], ''[[Poplar|Populus trichocarpa]]''
|480,000,000
|First tree genome, Sept 2006
|-
|[[Yeast]],''[[Saccharomyces cerevisiae]]''
|20,000,000
|<ref>{{cite journal| author= A. Goffeau et al. | journal=Science | title=Life with 6000 genes | doi = 10.1126/science.274.5287.546 | volume=274 | date=1996-10-25 | url=http://www.sciencemag.org/cgi/content/abstract/274/5287/546| pages=546–567 | pmid=8849441}}</ref>
|-
|[[Fungus]], ''[[Aspergillus nidulans]]''
|30,000,000
|
|-
|[[Nematoda|Nematode]], ''[[Caenorhabditis elegans]]''
|98,000,000
|First multicellular animal genome, December 1998<ref>{{cite journal | quotes=no |author=The ''C. elegans'' Sequencing Consortium |year=1998 |url=http://www.sciencemag.org/cgi/content/abstract/282/5396/2012
|title=Genome sequence of the nematode ''C. elegans'': a platform for investigating biology
|journal=[[Science (journal)|Science]] |issn=0036-8075
|volume=282 |issue=5396 |doi=10.1126/science.282.5396.2012 |pages=2012–2018| pmid=9851916}}</ref>
|-
|[[Insect]], ''[[Drosophila melanogaster]]'' aka Fruit Fly
|130,000,000
|<ref name=Adams_2000>{{cite journal | author = Adams MD, Celniker SE, Holt RA, ''et al'' | title = The genome sequence of ''Drosophila melanogaster'' | journal = Science | volume = 287 | issue = 5461 | pages = 2185–95 | year = 2000 | pmid = 10731132 | doi = 10.1126/science.287.5461.2185 | accessdate = 2007-05-25| url=http://www.sciencemag.org/cgi/content/abstract/287/5461/2185}}</ref>
|-
|[[Insect]], ''[[Bombyx mori]]'' aka Silk Moth
|530,000,000
|
|-
|[[Insect]], ''[[Apis mellifera]]'' aka Honey Bee
|1,770,000,000
|
|-
|[[Fish]], ''[[Tetraodon nigroviridis]]'', type of Puffer fish
|385,000,000
|Smallest vertebrate genome known
|-
|[[Mammal]], ''[[Homo sapiens]]''
|3,200,000,000
|
|-
|[[Fish]], ''[[Protopterus aethiopicus]]'' aka [[Marbled lungfish]]
|130,000,000,000
|Largest vertebrate genome known
|}
''Note:'' The DNA from a single human cell has a length of ~1.8 m (but at a width of ~2.4 nanometers).
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]]''.
== Genome evolution ==
Genomes are more than the sum of an organism's genes and have traits that may be [[Measurement|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).
[[gene duplication|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 [[polyploidy|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 [[microbe]]s. Also, [[Eukaryote|eukaryotic cells]] seem to have experienced a transfer of some genetic material from their [[chloroplast]] and [[mitochondria]]l genomes to their nuclear chromosomes.
==See also==
<div style="-moz-column-count:3; column-count:3;">
*[[gene]]
*[[gene family]]
*[[Genome Comparison]]
*[[Human genome]]
*[[Human microbiome project]]
*[[List of omics topics in biology]]
*[[List of sequenced eukaryotic genomes]]
*[[List of sequenced prokaryotic genomes]]
*[[List of sequenced archeal genomes]]
*[[Minimal Genome Project]]
*[[Mitochondrial genome]]
*[[molecular systematics]]
*[[molecular evolution]]
*[[Honey Bee Genome Sequencing Consortium]]
*[[National Human Genome Research Institute]]
</div>
==References==
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<div class="references-small">
<references />
* {{cite book|last=Benfey|first=P.|coauthors=Protopapas, A.D.|authorlink=|title=Essentials of Genomics|edition=|publisher=Prentice Hall|location=|year=2004|isbn=|series=}}
* {{cite book|last=Brown|first=Terence A.|coauthors=|authorlink=|title=Genomes 2|edition=|publisher=Bios Scientific Publishers|location=Oxford|year=2002|isbn=978-1859960295|series=}}
* {{cite book|last=Gibson|first=Greg|coauthors=Muse, Spencer V.|authorlink=|title=A Primer of Genome Science|edition=Second Edition|publisher=Sinauer Assoc|location=Sunderland, Mass|year=2004|isbn=0-87893-234-8|series=}}
* {{cite book|last=Gregory|first=T. Ryan (ed)|coauthors=|authorlink=|title=[[The Evolution of the Genome]]|edition=|publisher=Elsevier|location=|year=2005|isbn=0-12-301463-8|series=}}
* {{cite book|last=Reece|first=Richard J.|coauthors=|authorlink=|title=Analysis of Genes and Genomes|edition=|publisher=John Wiley & Sons|location=Chichester|year=2004|isbn=0-470-84379-9|series=}}
* {{cite book|last=Saccone|first=Cecilia|coauthors=Pesole, Graziano|authorlink=|title=Handbook of Comparative Genomics|edition=|publisher=John Wiley & Sons|location=Chichester|year=2003|isbn=0-471-39128-X|series=}}
* {{cite journal|last=Werner|first=E.|coauthors=|year=2003|title=In silico multicellular systems biology and minimal genomes|url=|journal=Drug Discov Today|issn=|volume=8|issue=24|pages=1121–1127|pmid=14678738|doi=10.1016/S1359-6446(03)02918-0}}
* {{cite journal|last=Witzany|first=G.|coauthors=|year=2006|title=Natural Genome Editing Competences of Viruses|url=|journal=Acta Biotheoretica|issn=|volume=54|issue=4|pages=235–253|pmid=17347785|doi=10.1007/s10441-006-9000-7}}
</div>
== External links ==
* [http://www.genomicsdirectory.com/ Genomics Directory: A genomics and biotechnology database for scientists and students]
* [http://www.dnai.org/ DNA Interactive: The History of DNA Science]
* [http://www.dnaftb.org/ DNA From The Beginning]
* [http://www.genome.gov/10001772 All About The Human Genome Project from Genome.gov]
* [http://www.genomesize.com/ Animal genome size database]
* [http://www.rbgkew.org.uk/cval/homepage.html Plant genome size database]
* [http://www.genomesonline.org/ GOLD:Genomes OnLine Database]
* [http://www.genomenewsnetwork.org/ The Genome News Network]
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj NCBI Entrez Genome Project database]
* [http://www.ncbi.nlm.nih.gov/About/primer/genetics_genome.html NCBI Genome Primer]
* [http://news.bbc.co.uk/1/hi/sci/tech/4994088.stm BBC News - Final genome 'chapter' published]
* [https://www.crops.org/genome/ The Plant Genome]
* [http://img.jgi.doe.gov/ IMG] The Integrated Microbial Genomes system, for genome analysis by the DOE-JGI.
* [http://camera.calit2.net/index.php/ CAMERA] Cyberinfrastructure for Metagenomics, data repository and bioinformatics tools for metagenomic research
* [http://www.genecards.org/ GeneCards] an integrated database of human genes.
[[Category:Genomics]]
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