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Genome

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<p><font color="#000000"><font size="3">The&nbsp;<strong>genome</strong> is the entirety of a set of sequences in an organism that&nbsp;encodes information for survival and the&nbsp;continuation of the species it belongs to. </font></font></p><p><font color="#000000"><font size="3">The main function of genome is information storage and processing to form an entity that utilizes envergy to keep process processing signals to interact with other genomes in the whole eco-system.</font><br />
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<font size="3">The genome is universal in the universe and aliens living other planets also have genomes. </font></font></p><p><font color="#000000"><font size="3">The information is usually stored&nbsp;in DNA or RNA in the organisms found on Earth.<br />
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The information genome is usually storedoften classified&nbsp;in into the protein coding genes and the non-coding sequences of the DNA or RNA historically.<sup id="cite_ref-0" class="reference"><font size="2"><font size="3"><span>[</span>1</font><span><font size="3">]</font><br /></span></font></sup></font></font></p><p>&nbsp;</p><p><span style="FONT-SIZE: large"><font color="#000000">The essence of genome</font></span></p><p>&nbsp;</p><p><font color="#000000"><font size="3">The essence of genomes is that it is the foundation of spontaneous information processing network that can utilizes energy in the organisms found on Earthtime axis. The genome is a kind of linearly expressed language system.</font></font><font color="#000000"><font size="3"><br />
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The genome is often classified&nbsp;into the protein coding genes and the non-coding sequences of the DNA historically.</font><sup id="cite_ref-0" class="reference"></font size="2"><font size="3"/p><spanp>[&nbsp;</spanp>1</fontp><span><font sizestyle="3FONT-SIZE: large">]</font><br /></span></font></sup></font></p><h2><span id="Origin_of_Term" class="mw-headline"><font color="#000000">Origin of Term</font></span></h2span></p><p><span style="FONT-SIZE: small"><font color="#000000">The term was adapted in 1920 by [[Hans Winkler]], Professor of Botany at the University of Hamburg, Germany. In Greek, the word <em>genome</em> (&gamma;ί&nu;&omicron;&mu;&alpha;&iota;) means I become, I am born, to come into being. </font></span></p><p><span style="FONT-SIZE: small"><font color="#000000">The Oxford English Dictionary suggests the name to be a blend of the words <em><strong>gen</strong>e</em> and <em>chromos<strong>ome</strong></em>. A few related <em>-ome</em> words already existed, such as <em>biome</em> and <em>rhizome</em>, forming a vocabulary into which <em>genome</em> fits systematically.<sup id="cite_ref-1" class="reference"><font size="2"><span>[</span>2<span>]</spansup></font></supspan></fontp></p><h2span style="FONT-SIZE: large"><span id="Overview" class="mw-headline"><font color="#000000">Overview</font></span></h2span></p><p><span style="FONT-SIZE: small"><font color="#000000">Some organisms have multiple copies of chromosomes, diploid, triploid, tetraploid and so on. In classical genetics, in a sexually reproducing organism (typically eukarya) the gamete has half of the number of chromosome of the somatic cell and the genome is a full set of chromosomes in a gamete. In haploid organisms, including cells of bacteria, archaea, and in organelles including mitochondria and chloroplasts, or viruses, that similarly contain genes, the single or set of circular and/or linear chains of DNA (or RNA for some viruses), likewise constitute the <em>genome</em>. The term genome can be applied specifically to mean that stored on a complete set of <em>nuclear DNA</em> (i.e., the &quot;nuclear genome&quot;) but can also be applied to that stored within organelles that contain their own DNA, as with the &quot;mitochondrial genome&quot; or the &quot;chloroplast genome&quot;. Additionally, the genome can comprise nonchromosomal genetic elements such as viruses, plasmids, and transposable elements<sup id="cite_ref-Brock_2-0" class="reference"><font size="2"><span>[</span>3<span>]</span></font></sup>. When people say that the genome of a sexually reproducing species has been &quot;sequenced&quot;, 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 &quot;a genome sequence&quot; may be a composite read from the chromosomes of various individuals. In general use, the phrase &quot;genetic makeup&quot; 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.</font></span></p><p><span style="FONT-SIZE: small"><font color="#000000">Both the number of base pairs and the number of genes vary widely from one species to another, and there is only a rough correlation between the two (an observation known as the C-value paradox). 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.</font></span></p><p><span style="FONT-SIZE: small"><font color="#000000">An analogy to the human genome stored on DNA is that of instructions stored in a library:</font></span></p>
<ul>
<li><span style="FONT-SIZE: small"><font color="#000000">The library would contain 46 books (chromosomes)</font> </span> </li> <li><span style="FONT-SIZE: small"><font color="#000000">The books range in size from 400 to 3340 pages (genes)</font> </span> </li> <li><span style="FONT-SIZE: small"><font color="#000000">which is 48 to 250 million letters (A,C,G,T) per book.</font> </span> </li> <li><span style="FONT-SIZE: small"><font color="#000000">Hence the library contains over six billion letters total;</font> </span> </li> <li><span style="FONT-SIZE: small"><font color="#000000">The library fits into a cell nucleus the size of a pinpoint;</font> </span> </li> <li><span style="FONT-SIZE: small"><font color="#000000">A copy of the library (all 46 books) is contained in almost every cell of our body.</font> </span> </li>
</ul>
<h2p><span style="FONT-SIZE: large"><span id="Types" class="mw-headline"><font color="#000000">Types</font></span></h2span></p><p><span style="FONT-SIZE: small"><font color="#000000">Most biological entities that are 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, &quot;genome&quot; is meant to include information stored on this auxiliary material, which is carried in plasmids. In such circumstances then, &quot;genome&quot; describes all of the genes and information on non-coding DNA that have the potential to be present.</font></span></p><p><span style="FONT-SIZE: small"><font color="#000000">In eukaryotes such as plants, protozoa and animals, however, &quot;genome&quot; carries the typical connotation of only information on chromosomal DNA. So although these organisms contain chloroplasts and/or mitochondria that have their own DNA, the genetic information contained by DNA within these organelles is not considered part of the genome. In fact, mitochondria are sometimes said to have their own genome often referred to as the &quot;mitochondrial genome&quot;. The DNA found within the chloroplast may be referred to as the &quot;plastome&quot;.</font></span></p><h2p><span style="FONT-SIZE: large"><span id="Genomes_and_genetic_variation" class="mw-headline"><font color="#000000">Genomes and genetic variation</font></span></h2span></p><p><span style="FONT-SIZE: small"><font color="#000000">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 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 &quot;genome&quot; (which parallels a common usage of &quot;gene&quot;) to refer not to the information in any particular DNA sequence, but to a whole family of sequences that share a biological context.</font></span></p><p><span style="FONT-SIZE: small"><font color="#000000">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 &quot;cheetah-ness&quot; from a single example of either.</font></span></p><h2p>&nbsp;</p><p><span style="FONT-SIZE: large"><span id="Sequencing_and_mapping" class="mw-headline"><font color="#000000">Sequencing and mapping</font></span></h2span></p><div class="rellink boilerplate seealso"><span style="FONT-SIZE: small"><font color="#000000">For more details on this topic, see Genome project.</font></span></div><p><span style="FONT-SIZE: small"><font color="#000000">The Human Genome Project was organized to map and to sequence the human genome. Other genome projects include mouse, rice, the plant <em>Arabidopsis thaliana</em>, 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 MS2). The first DNA-genome project to be completed was the Phage &Phi;-X174, with only 5386 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.</font></span></p><p><span style="FONT-SIZE: small"><font color="#000000">The development of new technologies has dramatically decreased the difficulty and cost of sequencing, and the number of complete genome sequences is rising rapidly. Among many genome database sites, the one maintained by the US National Institutes of Health is inclusive.<sup id="cite_ref-3" class="reference"><font size="2"><span>[</span>4<span>]</spansup></font></supspan></fontp></p><pspan style="FONT-SIZE: small"><font color="#000000">These new technologies open up the prospect of personal genome sequencing as an important diagnostic tool. A major step toward that goal was the May 2007 <em>New York Times</em> announcement that the full genome of DNA pioneer James D. Watson was deciphered.<sup id="cite_ref-4" class="reference"><font size="2"><span>[</span>5<span>]</spansup></font></supspan></fontp></p><pspan style="FONT-SIZE: small"><font color="#000000">Whereas a genome sequence lists the order of every DNA base in a genome, a genome map identifies the landmarks. A genome map is less detailed than a genome sequence and aids in navigating around the genome.<sup id="cite_ref-5" class="reference"><font size="2"><span>[</span>6<span>]</span></font></sup><sup id="cite_ref-6" class="reference"><font size="2"><span>[</span>7<span>]</spansup></font></sup></fontspan></p>
<h2><span id="Comparison_of_different_genome_sizes" class="mw-headline"><font color="#000000">Comparison of different genome sizes</font></span></h2>
<div class="rellink relarticle mainarticle"><span style="FONT-SIZE: small"><font color="#000000">Main article: Genome size</font></span></div><p>
<table id="sortable_table_id_0" class="wikitable sortable">
<tbody>
<td><font color="#000000">SV40</font></td>
<td align="right"><font color="#000000">5,224</font></td>
<td><font color="#000000"></font>&nbsp;</td>
<td><sup id="cite_ref-Fiers1978_8-0" class="reference"><font size="2"><font color="#000000"><span>[</span>9<span>]</span></font></font></sup></td>
</tr>
<td><font color="#000000">Phage &Phi;-X174</font></td>
<td align="right"><font color="#000000">5,386</font></td>
<td><font color="#000000"></font>&nbsp;</td>
<td><font color="#000000">First sequenced DNA-genome<sup id="cite_ref-Sanger1977_9-0" class="reference"><font size="2"><span>[</span>10<span>]</span></font></sup></font></td>
</tr>
<td><font color="#000000">HIV</font></td>
<td align="right"><font color="#000000">9749<sup id="cite_ref-10" class="reference"><font size="2"><span>[</span>11<span>]</span></font></sup></font></td>
<td><font color="#000000" size="2"></font>&nbsp;</td> <td><font color="#000000" size="2"></font>&nbsp;</td>
</tr>
<tr>
<td><font color="#000000">Phage &lambda;</font></td>
<td align="right"><font color="#000000">48,502</font></td>
<td><font color="#000000"></font>&nbsp;</td>
</tr>
<tr>
<td><font color="#000000">Mimivirus</font></td>
<td align="right"><font color="#000000">1,181,404</font></td>
<td><font color="#000000"></font>&nbsp;</td>
<td><font color="#000000">Largest known viral genome</font></td>
</tr>
<td><em><font color="#000000">Haemophilus influenzae</font></em></td>
<td align="right"><font color="#000000">1,830,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
<td><font color="#000000">First genome of living organism, July 1995<sup id="cite_ref-Fleichmann_1995_11-0" class="reference"><font size="2"><span>[</span>12<span>]</span></font></sup></font></td>
</tr>
<td><em><font color="#000000">Carsonella ruddii</font></em></td>
<td align="right"><font color="#000000">159,662</font></td>
<td><font color="#000000"></font>&nbsp;</td>
<td><font color="#000000">Smallest non-viral genome.<sup id="cite_ref-12" class="reference"><font size="2"><span>[</span>13<span>]</span></font></sup></font></td>
</tr>
<td><em><font color="#000000">Buchnera aphidicola</font></em></td>
<td align="right"><font color="#000000">600,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
</tr>
<tr>
<td><em><font color="#000000">Wigglesworthia glossinidia</font></em></td>
<td align="right"><font color="#000000">700,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
</tr>
<tr>
<td><em><font color="#000000">Escherichia coli</font></em></td>
<td align="right"><font color="#000000">4,600,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
<td><sup id="cite_ref-13" class="reference"><font size="2"><font color="#000000"><span>[</span>14<span>]</span></font></font></sup></td>
</tr>
<td><font color="#000000"><em>Solibacter usitatus</em> (strain Ellin 6076)</font></td>
<td align="right"><font color="#000000">9,970,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
<td><font color="#000000">Largest known Bacterial genome</font></td>
</tr>
<td><em><font color="#000000">Arabidopsis thaliana</font></em></td>
<td align="right"><font color="#000000">157,000,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
<td><font color="#000000">First plant genome sequenced, December 2000.<sup id="cite_ref-Greilhuber_15-0" class="reference"><font size="2"><span>[</span>16<span>]</span></font></sup></font></td>
</tr>
<td><em><font color="#000000">Genlisea margaretae</font></em></td>
<td align="right"><font color="#000000">63,400,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
<td><font color="#000000">Smallest recorded flowering plant genome, 2006.<sup id="cite_ref-Greilhuber_15-1" class="reference"><font size="2"><span>[</span>16<span>]</span></font></sup></font></td>
</tr>
<td><em><font color="#000000">Fritillaria assyrica</font></em></td>
<td align="right"><font color="#000000">130,000,000,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
</tr>
<tr>
<td><em><font color="#000000">Populus trichocarpa</font></em></td>
<td align="right"><font color="#000000">480,000,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
<td><font color="#000000">First tree genome, September 2006</font></td>
</tr>
<td><em><font color="#000000">Physcomitrella patens</font></em></td>
<td align="right"><font color="#000000">480,000,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
<td><font color="#000000">First genome of a bryophyte, January 2008 <sup id="cite_ref-16" class="reference"><font size="2"><span>[</span>17<span>]</span></font></sup></font></td>
</tr>
<td><em><font color="#000000">Saccharomyces cerevisiae</font></em></td>
<td align="right"><font color="#000000">12,100,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
<td><sup id="cite_ref-17" class="reference"><font size="2"><font color="#000000"><span>[</span>18<span>]</span></font></font></sup></td>
</tr>
<td><em><font color="#000000">Aspergillus nidulans</font></em></td>
<td align="right"><font color="#000000">30,000,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
</tr>
<tr>
<td><em><font color="#000000">Caenorhabditis elegans</font></em></td>
<td align="right"><font color="#000000">100,300,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
<td><font color="#000000">First multicellular animal genome, December 1998<sup id="cite_ref-18" class="reference"><font size="2"><span>[</span>19<span>]</span></font></sup></font></td>
</tr>
<td><em><font color="#000000">Pratylenchus coffeae</font></em></td>
<td align="right"><font color="#000000">20,000,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
<td><font color="#000000">Smallest animal genome known<sup id="cite_ref-19" class="reference"><font size="2"><span>[</span>20<span>]</span></font></sup></font></td>
</tr>
<td><font color="#000000"><em>Drosophila melanogaster</em> (fruit fly)</font></td>
<td align="right"><font color="#000000">130,000,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
<td><sup id="cite_ref-Adams_2000_20-0" class="reference"><font size="2"><font color="#000000"><span>[</span>21<span>]</span></font></font></sup></td>
</tr>
<td><font color="#000000"><em>Bombyx mori</em> (silk moth)</font></td>
<td align="right"><font color="#000000">530,000,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
</tr>
<tr>
<td><font color="#000000"><em>Apis mellifera</em> (honey bee)</font></td>
<td align="right"><font color="#000000">236,000,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
</tr>
<tr>
<td><font color="#000000"><em>Tetraodon nigroviridis</em> (type of puffer fish)</font></td>
<td align="right"><font color="#000000">385,000,000</font></td>
<td><font color="#000000"></font>&nbsp;</td>
<td><font color="#000000">Smallest vertebrate genome known</font></td>
</tr>
<td align="right"><font color="#000000">3,200,000,000</font></td>
<td align="right"><font color="#000000">3</font></td>
<td><font color="#000000"></font>&nbsp;</td>
</tr>
<tr>
</tbody>
</table>
</p><p><span style="FONT-SIZE: small"><font color="#000000"><em>Note:</em> The DNA from a single (diploid) human cell if the 46 chromosomes were connected end-to-end and straightened, would have a length of ~2 m and a width of ~2.4 nanometers.</font></span></p><p><span style="FONT-SIZE: small"><font color="#000000">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 <em>in vivo</em> and <em>in silico</em>.<sup id="cite_ref-21" class="reference"><font size="2"><span>[</span>22<span>]</span></font></sup><sup id="cite_ref-22" class="reference"><font size="2"><span>[</span>23<span>]</spansup></font></sup></fontspan></p>
<h2><span id="Genome_evolution" class="mw-headline"><font color="#000000">Genome evolution</font></span></h2>
<p><span style="FONT-SIZE: small"><font color="#000000">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 <em>chromosome number</em> (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).</font></span></p><p><span style="FONT-SIZE: small"><font color="#000000">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.</font></span></p><p><span style="FONT-SIZE: small"><font color="#000000">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.</font></span></p>
<h2><span id="References" class="mw-headline"><font color="#000000">References</font></span></h2>
<div style="column-count: 2; -moz-column-count: 2; -webkit-column-count: 2" class="references-small references-column-count references-column-count-2">
<h2><span id="External_links" class="mw-headline">External links</span></h2>
<ul>
<li><font color="#3366bb">[http://genomics.org Genomics.org]</font> </li>
<li>[http://omics.org Omics.org] </li>
<li><a class="external text" rel="nofollow" href="http://learn.genetics.utah.edu/content/begin/dna/builddna/"><font color="#3366bb">Build a DNA Molecule</font></a> </li>
<li><a class="external text" rel="nofollow" href="http://www.genomenewsnetwork.org/articles/02_01/Sizing_genomes.shtml"><font color="#3366bb">Some comparative genome sizes</font></a> </li>
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