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Genome

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In biology the genome of an organism is its whole hereditary information and is encoded in the DNA (or, for some viruses, RNA). This includes both the genes and the non-coding sequences of the DNA. 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 chromosome.[1]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.Both the number of base pairs 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 is that of a book:

<ul>

<li>The book is over one billion words long. </li> <li>The book is bound in 5,000 300 page volumes. </li> <li>The book fits into a cell nucleus the size of a pinpoint. </li> <li>A copy of the book (all 5000 volumes) is contained in every cell (except red blood cells) as a strand of DNA over two miles in length. </li>

</ul>

~~<script type="text/javascript">//<![CDATA[~~ ~~if (window.showTocToggle) { var tocShowText = "show"; var tocHideText = "hide"; showTocToggle()~~  } ~~//]]></script><a id="Types" name="Types"></a>~~

<h2>Types</h2>

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 sheep and other various animals 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".

~~<a id="Genomes_and_genetic_variation" name="Genomes_and_genetic_variation"></a>~~

<h2>Genomes and genetic variation</h2>

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.

~~<a id="Genome_projects" name="Genome_projects"></a>~~

<h2>Genome projects</h2>

In May 2007, the New York Times announced that the full genome of DNA pioneer James D. Watson had been recorded.[1] 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.

~~<a id="Comparison_of_different_genome_sizes" name="Comparison_of_different_genome_sizes"></a>~~

<h2>Comparison of different genome sizes</h2>

<td>Virus, Bacteriophage MS2</td>

<td>First sequenced RNA-genome[2]</td>

</tr>

<tr>

<td>Virus, SV40</td>

</tr>

<tr>

<td>Virus, Phage Φ-X174;</td>

<td>First sequenced DNA-genome[4]</td>

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<tr>

<td>Plant, Arabidopsis thaliana</td>

<td>First plant genome sequenced, Dec 2000.[5]</td>

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<tr>

<td>Plant, Genlisea margaretae</td>

<td>Smallest recorded flowering plant genome, 2006.[5]</td>

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<td>Nematode, Caenorhabditis elegans</td>

<td>First multicellular animal genome, December 1998[6]</td>

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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.

~~<a id="Genome_evolution" name="Genome_evolution"></a>~~

<h2>Genome evolution</h2>

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).

<ul>

<li>gene </li> <li>gene family </li> <li>Genome Comparison </li> <li>Genome project </li> <li>Human genome </li> <li>List of omics topics in biology </li> <li>List of sequenced eukaryotic genomes </li> <li>List of sequenced prokaryotic genomes </li> <li>List of sequenced archeal genomes </li> <li>Minimal Genome Project </li> <li>Mitochondrial genome </li> <li>molecular systematics </li> <li>molecular evolution </li> <li>Honey Bee Genome Sequencing Consortium </li> <li>National Human Genome Research Institute </li>

</ul>

</div>

<li id="_note-0">^ <cite style="~~FONT~~font-~~STYLE~~style: normal">Joshua Lederberg and Alexa T. McCray (2001). "'Ome Sweet 'Omics -- A Genealogical Treasury of Words". The Scientist 15 (7).</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=%27Ome+Sweet+%27Omics+--+A+Genealogical+Treasury+of+Words&rft.jtitle=The+Scientist&rft.date=2001&rft.volume=15&rft.issue=7&rft.au=Joshua+Lederberg+and+Alexa+T.+McCray&rft_id=http%3A%2F%2Flhncbc.nlm.nih.gov%2Flhc%2Fdocs%2Fpublished%2F2001%2Fpub2001047.pdf">  </li> <li id="_note-Fiers1976">^ <cite style="~~FONT~~font-~~STYLE~~style: normal">Fiers W, et al. (1976). "Complete nucleotide-sequence of bacteriophage MS2-RNA - primary and secondary structure of replicase gene". Nature 260: 500-507.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Complete+nucleotide-sequence+of+bacteriophage+MS2-RNA+-+primary+and+secondary+structure+of+replicase+gene&rft.jtitle=Nature&rft.date=1976&rft.volume=260&rft.au=Fiers+W%2C+%27%27et+al.%27%27&rft.pages=500-507">  </li> <li id="_note-Fiers1978">^ <cite style="~~FONT~~font-~~STYLE~~style: normal">Fiers W, Contreras R, Haegemann G, Rogiers R, Van de Voorde A, Van Heuverswyn H, Van Herreweghe J, Volckaert G, Ysebaert M (1978). "Complete nucleotide sequence of SV40 DNA". Nature 273 (5658): 113-120.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Complete+nucleotide+sequence+of+SV40+DNA&rft.jtitle=Nature&rft.date=1978&rft.volume=273&rft.issue=5658&rft.au=Fiers+W%2C+Contreras+R%2C+Haegemann+G%2C+Rogiers+R%2C+Van+de+Voorde+A%2C+Van+Heuverswyn+H%2C+Van+Herreweghe+J%2C+Volckaert+G%2C+Ysebaert+M&rft.pages=113-120">  </li> <li id="_note-Sanger1977">^ <cite style="~~FONT~~font-~~STYLE~~style: normal">Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M (1977). "Nucleotide sequence of bacteriophage phi X174 DNA". Nature 265 (5596): 687-695.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Nucleotide+sequence+of+bacteriophage+phi+X174+DNA&rft.jtitle=Nature&rft.date=1977&rft.volume=265&rft.issue=5596&rft.au=Sanger+F%2C+Air+GM%2C+Barrell+BG%2C+Brown+NL%2C+Coulson+AR%2C+Fiddes+CA%2C+Hutchison+CA%2C+Slocombe+PM%2C+Smith+M&rft.pages=687-695">  </li> <li id="_note-Greilhuber">^ a b Greilhuber, J., Borsch, T., Müller, K., Worberg, A., Porembski, S., and Barthlott, W. (2006). Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size. Plant Biology, 8: 770-777. </li> <li id="_note-1">^ <cite style="~~FONT~~font-~~STYLE~~style: normal">The C. elegans Sequencing Consortium (1998). Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282 (5396): 2012-2018. doi:10.1126/science.282.5396.2012. ISSN 0036-8075.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Genome+sequence+of+the+nematode+%27%27C.+elegans%27%27%3A+a+platform+for+investigating+biology&rft.jtitle=%5B%5BScience+%28journal%29%7CScience%5D%5D&rft.date=1998&rft.volume=282&rft.issue=5396&rft.au=The+%27%27C.+elegans%27%27+Sequencing+Consortium&rft.pages=2012-2018&rft.issn=0036-8075&rft_id=info:doi/10.1126%2Fscience.282.5396.2012&rft_id=http%3A%2F%2Fwww.sciencemag.org%2Fcgi%2Fcontent%2Fabstract%2F282%2F5396%2F2012%3Fmaxtoshow%3D%26HITS%3D10%26hits%3D10%26RESULTFORMAT%3D%26searchid%3D1%26FIRSTINDEX%3D0%26volume%3D282%26firstpage%3D2012%26resourcetype%3DHWCIT">  </li>

</ol>

<ul>

<li><cite ~~class~~style="~~book~~font-style: normal" id="Reference-Benfey-2004" ~~style~~class="~~FONT-STYLE: normal~~book">Benfey, P.; Protopapas, A.D. (2004). Essentials of Genomics. Prentice Hall.</cite>  </li> <li><cite ~~class~~style="~~book~~font-style: normal" id="Reference-Brown-2002" ~~style~~class="~~FONT-STYLE: normal~~book">Brown, Terence A. (2002). Genomes 2. Oxford: Bios Scientific Publishers. ISBN 978-1859960295.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=book&rft.btitle=Genomes+2&rft.aulast=Brown&rft.aufirst=Terence+A.&rft.pub=Bios+Scientific+Publishers&rft.place=Oxford&rft.isbn=978-1859960295">  </li> <li><cite ~~class~~style="~~book~~font-style: normal" id="Reference-Gibson-2004" ~~style~~class="~~FONT-STYLE: normal~~book">Gibson, Greg; Muse, Spencer V. (2004). A Primer of Genome Science, Second Edition, Sunderland, Mass: Sinauer Assoc. ISBN 0-87893-234-8.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=book&rft.btitle=A+Primer+of+Genome+Science&rft.aulast=Gibson&rft.aufirst=Greg&rft.edition=Second+Edition&rft.pub=Sinauer+Assoc&rft.place=Sunderland%2C+Mass&rft.isbn=0-87893-234-8">  </li> <li><cite ~~class~~style="~~book~~font-style: normal" id="Reference-Gregory-2005" ~~style~~class="~~FONT-STYLE: normal~~book">Gregory, T. Ryan (ed) (2005). The Evolution of the Genome. Elsevier. ISBN 0-12-301463-8.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=book&rft.btitle=%5B%5BThe+Evolution+of+the+Genome%5D%5D&rft.aulast=Gregory&rft.aufirst=T.+Ryan+%28ed%29&rft.pub=Elsevier&rft.isbn=0-12-301463-8">  </li> <li><cite ~~class~~style="~~book~~font-style: normal" id="Reference-Reece-2004" ~~style~~class="~~FONT-STYLE: normal~~book">Reece, Richard J. (2004). Analysis of Genes and Genomes. Chichester: John Wiley & Sons. ISBN 0-470-84379-9.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=book&rft.btitle=Analysis+of+Genes+and+Genomes&rft.aulast=Reece&rft.aufirst=Richard+J.&rft.pub=John+Wiley+%26+Sons&rft.place=Chichester&rft.isbn=0-470-84379-9">  </li> <li><cite ~~class~~style="~~book~~font-style: normal" id="Reference-Saccone-2003" ~~style~~class="~~FONT-STYLE: normal~~book">Saccone, Cecilia; Pesole, Graziano (2003). Handbook of Comparative Genomics. Chichester: John Wiley & Sons. ISBN 0-471-39128-X.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=book&rft.btitle=Handbook+of+Comparative+Genomics&rft.aulast=Saccone&rft.aufirst=Cecilia&rft.pub=John+Wiley+%26+Sons&rft.place=Chichester&rft.isbn=0-471-39128-X">  </li> <li><cite style="~~FONT~~font-~~STYLE~~style: normal">Werner, E. (2003). "In silico multicellular systems biology and minimal genomes". Drug Discov Today 8 (24): 1121-1127. PMID 14678738.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=In+silico+multicellular+systems+biology+and+minimal+genomes&rft.jtitle=Drug+Discov+Today&rft.date=2003&rft.volume=8&rft.issue=24&rft.aulast=Werner&rft.aufirst=E.&rft.pages=1121-1127&rft_id=info:pmid/14678738">  </li> <li><cite style="~~FONT~~font-~~STYLE~~style: normal">Witzany, G. (2006). "Natural Genome Editing Competences of Viruses". Acta Biotheoretica 54 (4): 235-253. PMID 17347785.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Natural+Genome+Editing+Competences+of+Viruses&rft.jtitle=Acta+Biotheoretica&rft.date=2006&rft.volume=54&rft.issue=4&rft.aulast=Witzany&rft.aufirst=G.&rft.pages=235-253&rft_id=info:pmid/17347785">  </li>

</ul>

</div>

<li>[http://omics.org Omics.org]</li>

<li>[http://genomics.org Genomics.org]</li>

<li><a class="external text" title="http://www.dnai.org/" rel="nofollow" href="http://www.dnai.org/">DNA Interactive: The History of DNA Science</a> </li> <li><a class="external text" title="http://www.dnaftb.org/" rel="nofollow" href="http://www.dnaftb.org/">DNA From The Beginning</a> </li> <li><a class="external text" title="http://www.genome.gov/10001772" rel="nofollow" href="http://www.genome.gov/10001772">All About The Human Genome Project from Genome.gov</a> </li> <li><a class="external text" title="http://www.genomesize.com/" rel="nofollow" href="http://www.genomesize.com/">Animal genome size database</a> </li> <li><a class="external text" title="http://www.rbgkew.org.uk/cval/homepage.html" rel="nofollow" href="http://www.rbgkew.org.uk/cval/homepage.html">Plant genome size database</a> </li> <li><a class="external text" title="http://www.genomesonline.org/" rel="nofollow" href="http://www.genomesonline.org/">GOLD:Genomes OnLine Database</a> </li> <li><a class="external text" title="http://www.genomenewsnetwork.org/" rel="nofollow" href="http://www.genomenewsnetwork.org/">The Genome News Network</a> </li> <li><a class="external text" title="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj">NCBI Entrez Genome Project database</a> </li> <li><a class="external text" title="http://www.ncbi.nlm.nih.gov/About/primer/genetics_genome.html" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/About/primer/genetics_genome.html">NCBI Genome Primer</a> </li> <li><a class="external text" title="http://news.bbc.co.uk/1/hi/sci/tech/4994088.stm" rel="nofollow" href="http://news.bbc.co.uk/1/hi/sci/tech/4994088.stm">BBC News - Final genome 'chapter' published</a> </li> <li><a class="external text" title="http://www.skyjuicesoftware.com/3models/?wiki" rel="nofollow" href="http://www.skyjuicesoftware.com/3models/?wiki">Software that maps an Artificial Genome sequence to a Network and to a Lineage tree</a> </li> <li><a class="external text" title="http://img.jgi.doe.gov/" rel="nofollow" href="http://img.jgi.doe.gov/">IMG</a> The Integrated Microbial Genomes system, for genome analysis by the DOE-JGI. </li> <li><a class="external text" title="http://camera.calit2.net/index.php/" rel="nofollow" href="http://camera.calit2.net/index.php/">CAMERA</a> Cyberinfrastructure for Metagenomics, data repository and bioinformatics tools for metagenomic research </li>

</ul>

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