Editing Genome

{{Short description|All genetic material of an organism}}
{{Other uses}}
{{Use dmy dates|date=October 2021}}
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[[File:UCSC human chromosome colours.png|thumb|An image of the 46 chromosomes making up the diploid genome of a human male (the mitochondrial chromosomes are not shown).]]

A '''genome''' is all the genetic information of an organism.<ref name="Roth p. ">{{cite journal |last=Roth |first=Stephanie Clare |title=What is genomic medicine? |journal=Journal of the Medical Library Association |publisher=University Library System, University of Pittsburgh |volume=107 |issue=3 |date=2019-07-01 |pages=442–448 |issn=1558-9439 |pmid=31258451 |pmc=6579593 |doi=10.5195/jmla.2019.604 }}</ref> It consists of [[nucleotide]] sequences of [[DNA]] (or [[RNA]] in [[RNA virus]]es). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences (see [[non-coding DNA]]), and often a substantial fraction of [[junk DNA]] with no evident function.<ref name="Graur">{{Cite book |last1=Graur |first1=Dan |url=https://books.google.com/books?id=blOZjgEACAAJ |title=Molecular and Genome Evolution |last2=Sater |first2=Amy K. |last3=Cooper |first3=Tim F. |publisher=Sinauer Associates, Inc. |year=2016 |isbn=9781605354699 |oclc=951474209}}</ref><ref>{{cite journal |author=Brosius, J |title=The Fragmented Gene |url=https://nyaspubs.onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.2009.05004.x |journal=Annals of the New York Academy of Sciences |volume=1178 |issue=1 |pages=186–93 |year=2009 |bibcode=2009NYASA1178..186B |doi=10.1111/j.1749-6632.2009.05004.x |pmid=19845638 |s2cid=8279434|url-access=subscription }}</ref> Almost all [[eukaryote]]s have [[mitochondrial DNA|mitochondria]] and a small [[mitochondrial genome]].<ref name="Graur" /> Algae and plants also contain [[chloroplast DNA|chloroplasts]] with a chloroplast genome.

The study of the genome is called [[genomics]]. The genomes of many organisms have been [[Whole-genome sequencing|sequenced]] and various regions have been annotated. The first genome to be sequenced was that of the virus φX174 in 1977;<ref name=":0">{{cite journal | vauthors = Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M | display-authors = 6 | title = Nucleotide sequence of bacteriophage phi X174 DNA | journal = Nature | volume = 265 | issue = 5596 | pages = 687–95 | date = February 1977 | pmid = 870828 | doi = 10.1038/265687a0 | s2cid = 4206886 | bibcode = 1977Natur.265..687S }}</ref> the first genome sequence of a prokaryote (''Haemophilus influenzae'') was published in 1995;<ref name="Fleischmann">{{cite journal |display-authors=6 |vauthors=Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM |date=July 1995 |title=Whole-genome random sequencing and assembly of Haemophilus influenzae Rd |journal=Science |volume=269 |issue=5223 |pages=496–512 |bibcode=1995Sci...269..496F |doi=10.1126/science.7542800 |pmid=7542800 |s2cid=10423613}}</ref> the yeast (''Saccharomyces cerevisiae'') genome was the first eukaryotic genome to be sequenced in 1996.<ref name="Reference44">{{cite journal | vauthors = Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG | title = Life with 6000 genes | journal = Science | volume = 274 | issue = 5287 | pages = 546, 563–67 | year = 1996 | pmid = 8849441 | doi = 10.1126/science.274.5287.546 | bibcode = 1996Sci...274..546G | s2cid = 16763139 }}</ref> The [[Human Genome Project]] was started in October 1990, and the first draft sequences of the [[human genome]] were reported in February 2001.<ref>{{cite journal|vauthors=Olson MV | title=The Human Genome Project: A Player's Perspective|journal=Journal of Molecular Biology|volume=319|pages=931–942|year=2002| issue=4|doi=10.1016/S0022-2836(02)00333-9| pmid=12079320}}</ref>

== Origin of the term ==
The term ''genome'' was created in 1920 by [[Hans Winkler]],<ref>{{cite book |vauthors = Winkler HL |title = Verbreitung und Ursache der Parthenogenesis im Pflanzen- und Tierreiche|url = https://archive.org/details/verbreitungundur00wink |date=1920|publisher=Verlag Fischer|location=Jena}}</ref> professor of [[botany]] at the [[University of Hamburg]], Germany. The website [[Oxford Dictionaries (website)|Oxford Dictionaries]] and the [[Online Etymology Dictionary]] suggest the name is a blend of the words ''[[gene]]'' and ''[[chromosome]]''.<ref>{{cite web|title=definition of Genome in Oxford dictionary|url=http://www.oxforddictionaries.com/us/definition/american_english/genome|archive-url=https://web.archive.org/web/20140301022342/http://www.oxforddictionaries.com/us/definition/american_english/genome|url-status=dead|archive-date=1 March 2014|access-date=25 March 2014}}</ref><ref>{{Cite OED|genome}}</ref><ref>{{Cite dictionary |url=http://www.lexico.com/definition/genome |archive-url=https://web.archive.org/web/20220824013743/https://www.lexico.com/definition/genome |url-status=dead |archive-date=August 24, 2022 |title=genome |dictionary=[[Lexico]] UK English Dictionary |publisher=[[Oxford University Press]]}}</ref><ref>{{Cite OEtymD|genome}}</ref> However, see [[omics]] for a more thorough discussion. A few related ''-ome'' words already existed, such as ''[[biome]]'' and ''[[rhizome]]'', forming a vocabulary into which ''genome'' fits systematically.<ref>{{cite journal |last1=Lederberg |first1=Joshua |last2=McCray |first2=Alexa T. |name-list-style=vanc |date=2001 |title='Ome Sweet 'Omics – A Genealogical Treasury of Words |url=https://dla-mezczyzn.eu/d/pub2001047.pdf |url-status=dead |journal=The Scientist |volume=15 |issue=7}}</ref>

== Definition ==
{{Anchor|definition}}

The term "genome" usually refers to the DNA (or sometimes RNA) molecules that carry the genetic information in an organism, but sometimes it is uncertain which molecules to include; for example, bacteria usually have one or two large DNA molecules ([[chromosomes]]) that contain all of the essential genetic material but they also contain smaller extrachromosomal [[plasmid]] molecules that carry important genetic information. In the scientific literature, the term 'genome' usually refers to the large chromosomal DNA molecules in bacteria.<ref>{{cite journal |vauthors = Kirchberger PC, Schmidt ML, and Ochman H |date = 2020 |title = The ingenuity of bacterial genomes |journal = Annual Review of Microbiology |volume = 74 |pages = 815–834 |doi = 10.1146/annurev-micro-020518-115822|pmid = 32692614 |s2cid = 220699395 }}</ref>

===Nuclear genome===
Eukaryotic genomes are even more difficult to define because almost all eukaryotic species contain nuclear chromosomes plus extra DNA molecules in the [[Mitochondrion|mitochondria]]. In addition, algae and plants have [[chloroplast]] DNA. Most textbooks make a distinction between the nuclear genome and the organelle (mitochondria and chloroplast) genomes so when they speak of, say, the human genome, they are only referring to the genetic material in the nucleus.<ref name = Graur /><ref>{{ cite book |vauthors = Brown, TA |date = 2018 |title = Genomes 4 |publisher = Garland Science |place = New York, NY, USA |isbn = 9780815345084}}</ref> This is the most common use of 'genome' in the scientific literature.

===Ploidy===
Most eukaryotes are [[Ploidy|diploid]], meaning that there are two of each chromosome in the nucleus but the 'genome' refers to only one copy of each chromosome. Some eukaryotes have distinctive sex chromosomes, such as the X and Y chromosomes of mammals, so the technical definition of the genome must include both copies of the sex chromosomes. For example, the standard reference genome of humans consists of one copy of each of the 22 autosomes plus one X chromosome and one Y chromosome.<ref>{{cite web |url = https://useast.ensembl.org/Homo_sapiens/Info/Annotation |title = Ensembl Human Assembly and gene annotation (GRCh38) |publisher = Ensembl |access-date = May 30, 2022}}</ref>

== Sequencing and mapping ==
{{Further|Whole genome sequencing|Genome project}}
A '''genome sequence''' is the complete list of the [[nucleotide]]s (A, C, G, and T for DNA genomes) that make up all the [[chromosome]]s of an individual or a species. Within a species, the vast majority of nucleotides are identical between individuals, but sequencing multiple individuals is necessary to understand the genetic diversity. [[File:Part of DNA sequence prototypification of complete genome of virus 5418 nucleotides.gif|thumb|right|350 px|Part of DNA sequence – prototypification of complete genome of virus]]
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 next year, [[Fred Sanger]] completed the first DNA-genome sequence: [[Phi-X174 phage|Phage X174]], of 5386 base pairs.<ref>{{cite web|url=http://www.beowulf.org.uk/|title=All about genes|website=beowulf.org.uk}}</ref> The first bacterial genome to be sequenced was that of [[Haemophilus influenzae]], completed by a team at [[The Institute for Genomic Research]] in 1995. A few months later, the first eukaryotic genome was completed, with sequences of the 16 chromosomes of budding yeast ''[[Saccharomyces cerevisiae]]'' published as the result of a European-led effort begun in the mid-1980s. The first genome sequence for an [[Archaea|archaeon]], ''[[Methanococcus jannaschii]]'', was completed in 1996, again by The Institute for Genomic Research.<ref>{{cite web|url=https://www.jcvi.org/media-center/tigr-scientists-complete-first-genome-sequence-oral-pathogen-associated-severe-adult#:~:text=The%20Institute%20for%20Genomic%20Research%20(TIGR)%20is%20a%20not%2Dfor%2Dprofit&text=genome%20sequence%20of%20an%20archaea%20(Methanococcus%20jannaschii%2C%20in%201996) |title=TIGR Scientists Complete the First Genome Sequence of an Oral Pathogen Associated with Severe Adult Periodontal Disease |date=June 12, 2001}}</ref>

The development of new technologies has made genome sequencing dramatically cheaper and easier, and the number of complete genome sequences is growing rapidly. The [[US National Institutes of Health]] maintains one of several comprehensive databases of genomic information.<ref>{{cite web|url=https://www.ncbi.nlm.nih.gov/sites/entrez?db=Genome&itool=toolbar |title=Genome Home |date=2010-12-08 |access-date=27 January 2011}}</ref> Among the thousands of completed genome sequencing projects include those for [[rice]], a [[mus musculus|mouse]], the plant ''[[Arabidopsis thaliana]]'', the [[puffer fish]], and the bacteria [[Escherichia coli|E. coli]]. In December 2013, scientists first sequenced the entire ''genome'' of a [[Neanderthal]], an extinct species of [[Archaic humans|humans]]. The genome was extracted from the [[toe bone]] of a 130,000-year-old Neanderthal found in a [[Denisova Cave|Siberian cave]].<ref name="NYT-20131218">{{cite news |last=Zimmer |first=Carl |name-list-style = vanc |author-link=Carl Zimmer |title=Toe Fossil Provides Complete Neanderthal Genome |url=https://www.nytimes.com/2013/12/19/science/toe-fossil-provides-complete-neanderthal-genome.html |archive-url=https://ghostarchive.org/archive/20220102/https://www.nytimes.com/2013/12/19/science/toe-fossil-provides-complete-neanderthal-genome.html |archive-date=2022-01-02 |url-access=limited |url-status=live |date=18 December 2013 |work=[[The New York Times]] |access-date=18 December 2013}}{{cbignore}}</ref><ref name="NAT-20131218">{{cite journal |vauthors = Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PL, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S |display-authors = 6 |title = The complete genome sequence of a Neanderthal from the Altai Mountains |journal = Nature |volume = 505 |issue = 7481 |pages = 43–49 |date = January 2014 |pmid = 24352235 |pmc = 4031459 |doi = 10.1038/nature12886 |bibcode = 2014Natur.505...43P }}</ref>

== Viral genomes ==
[[Virus#Genome|Viral genomes]] can be composed of either RNA or DNA. The genomes of [[RNA virus]]es can be either [[Single-stranded RNA virus|single-stranded RNA]] or [[Double-stranded RNA viruses|double-stranded RNA]], and may contain one or more separate RNA molecules (segments: monopartit or multipartit genome). DNA viruses can have either single-stranded or double-stranded genomes. Most DNA virus genomes are composed of a single, linear molecule of DNA, but some are made up of a circular DNA molecule.<ref>{{cite book|last1=Gelderblom|first1=Hans R.|title=Structure and Classification of Viruses |date=1996|publisher=The University of Texas Medical Branch at Galveston|location=Galveston, TX|pmid=21413309|isbn=9780963117212|edition=4th|url=https://www.ncbi.nlm.nih.gov/books/NBK8174/}}</ref>

== Prokaryotic genomes ==
Prokaryotes and eukaryotes have DNA genomes. Archaea and most bacteria have a single [[circular chromosome]],<ref>{{cite journal |vauthors = Samson RY, Bell SD |title = Archaeal chromosome biology |journal = Journal of Molecular Microbiology and Biotechnology |volume = 24 |issue = 5–6 |pages = 420–27 |date = 2014 |pmid = 25732343 |pmc = 5175462 |doi = 10.1159/000368854 }}</ref> however, some bacterial species have linear or multiple chromosomes.<ref>{{cite book|date=2005|pages=525–540|doi=10.1128/9781555817640.ch29|chapter-url=http://www.asmscience.org/content/book/10.1128/9781555817640.chap29 |last1 = Chaconas |first1 = George |last2 = Chen |first2 = Carton W. |title=The Bacterial Chromosome |chapter=Replication of Linear Bacterial Chromosomes: No Longer Going Around in Circles |name-list-style = vanc |isbn=9781555812324}}</ref><ref>{{cite web|url=http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/chroms-genes-prots/chromosomes.html|title=Bacterial Chromosomes|website=Microbial Genetics|year=2002}}</ref> If the DNA is replicated faster than the bacterial cells divide, multiple copies of the chromosome can be present in a single cell, and if the cells divide faster than the DNA can be replicated, multiple replication of the chromosome is initiated before the division occurs, allowing daughter cells to inherit complete genomes and already partially replicated chromosomes. Most prokaryotes have very little repetitive DNA in their genomes.<ref name="constraints and plasticity in genome and molecular">{{cite journal |vauthors = Koonin EV, Wolf YI |title = Constraints and plasticity in genome and molecular-phenome evolution |journal = Nature Reviews. Genetics |volume = 11 |issue = 7 |pages = 487–98 |date = July 2010 |pmid = 20548290 |pmc = 3273317 |doi = 10.1038/nrg2810 }}</ref> However, some [[symbiotic bacteria]] (e.g. ''[[Serratia symbiotica]]'') have reduced genomes and a high fraction of pseudogenes: only ~40% of their DNA encodes proteins.<ref>{{cite journal |vauthors = McCutcheon JP, Moran NA |title = Extreme genome reduction in symbiotic bacteria |journal = Nature Reviews. Microbiology |volume = 10 |issue = 1 |pages = 13–26 |date = November 2011 |pmid = 22064560 |doi = 10.1038/nrmicro2670 |s2cid = 7175976 }}</ref><ref>{{cite journal |vauthors = Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW |title = Insights from 20 years of bacterial genome sequencing |journal = Functional & Integrative Genomics |volume = 15 |issue = 2 |pages = 141–61 |date = March 2015 |pmid = 25722247 |pmc = 4361730 |doi = 10.1007/s10142-015-0433-4 }}</ref>

Some bacteria have auxiliary genetic material, also part of their genome, which is carried in [[plasmid]]s. For this, the word ''genome'' should not be used as a synonym of ''chromosome''.

== Eukaryotic genomes ==
{{See also|Eukaryotic chromosome fine structure}}
[[File:Human karyotype with bands and sub-bands.png|thumb|In a typical human cell, the genome is contained in 22 pairs of [[autosome]]s, two [[sex chromosomes]] (the female and male variants shown at bottom right), as well as the [[human mitochondrial genetics|mitochondrial genome]] (shown to scale as "MT" at bottom left). {{further|Karyotype}}]]
Eukaryotic genomes are composed of one or more linear DNA chromosomes. The number of chromosomes varies widely from [[Jack jumper ant]]s and an [[Diploscapter pachys|asexual nemotode]],<ref>{{cite web|title=Scientists sequence asexual tiny worm whose lineage stretches back 18 million years|url=https://www.sciencedaily.com/releases/2017/09/170921141303.htm|website=ScienceDaily|access-date=7 November 2017}}</ref> which each have only one pair, to a [[Ophioglossum|fern species]] that has 720 pairs.<ref>{{cite journal|last1=Khandelwal|first1=Sharda |name-list-style = vanc |title=Chromosome evolution in the genus Ophioglossum L.|journal=Botanical Journal of the Linnean Society|date=March 1990|volume=102|issue=3|pages=205–17|doi=10.1111/j.1095-8339.1990.tb01876.x }}</ref> It is surprising the amount of DNA that eukaryotic genomes contain compared to other genomes. The amount is even more than what is necessary for DNA protein-coding and noncoding genes because eukaryotic genomes show as much as 64,000-fold variation in their sizes.<ref name=":0a" /> However, this special characteristic is caused by the presence of repetitive DNA, and transposable elements (TEs).

A typical human cell has two copies of each of 22 [[autosome]]s, one inherited from each parent, plus two [[sex chromosome]]s, making it diploid. [[Gamete]]s, such as ova, sperm, spores, and pollen, are haploid, meaning they carry only one copy of each chromosome. In addition to the chromosomes in the nucleus, organelles such as the [[chloroplasts]] and [[mitochondria]] have their own DNA. Mitochondria are sometimes said to have their own genome often referred to as the "[[mitochondrial genome]]". The DNA found within the chloroplast may be referred to as the "[[plastome]]". Like the bacteria they originated from, mitochondria and chloroplasts have a circular chromosome.

Unlike prokaryotes where exon-intron organization of protein coding genes exists but is rather exceptional, eukaryotes generally have these features in their genes and their genomes contain variable amounts of repetitive DNA. In mammals and plants, the majority of the genome is composed of repetitive DNA.<ref name="Lewin 2004">{{cite book |last = Lewin |first = Benjamin |name-list-style = vanc |title=Genes VIII|date=2004|publisher=Pearson/Prentice Hall|location=Upper Saddle River, NJ|isbn=978-0-13-143981-8|edition=8th}}</ref>

=== DNA sequencing ===
High-throughput technology makes sequencing to assemble new genomes accessible to everyone. Sequence polymorphisms are typically discovered by comparing resequenced isolates to a reference, whereas analyses of coverage depth and mapping topology can provide details regarding structural variations such as chromosomal translocations and segmental duplications.

=== Coding sequences ===
DNA sequences that carry the instructions to make proteins are referred to as coding sequences. The proportion of the genome occupied by coding sequences varies widely. A larger genome does not necessarily contain more genes, and the proportion of non-repetitive DNA decreases along with increasing genome size in complex eukaryotes.<ref name="Lewin 2004"/>

=== Noncoding sequences ===
{{Main|Non-coding DNA}}
{{See also|Intergenic region}}

Noncoding sequences include [[intron]]s, sequences for non-coding RNAs, regulatory regions, and repetitive DNA. Noncoding sequences make up 98% of the human genome. There are two categories of repetitive DNA in the genome: [[tandem repeats]] and interspersed repeats.<ref>{{cite book|editor-last=Stojanovic|editor-first=Nikola|name-list-style = vanc |title=Computational genomics : current methods|date=2007|publisher=Horizon Bioscience|location=Wymondham|isbn=978-1-904933-30-4}}</ref>

==== Tandem repeats ====
Short, non-coding sequences that are repeated head-to-tail are called [[tandem repeats]]. Microsatellites consisting of 2–5 basepair repeats, while minisatellite repeats are 30–35 bp. Tandem repeats make up about 4% of the human genome and 9% of the fruit fly genome.<ref name="Padeken">{{cite journal |vauthors = Padeken J, Zeller P, Gasser SM |title = Repeat DNA in genome organization and stability |journal = Current Opinion in Genetics & Development |volume = 31 |pages = 12–19 |date = April 2015 |pmid = 25917896 |doi = 10.1016/j.gde.2015.03.009 }}</ref> Tandem repeats can be functional. For example, [[telomere]]s are composed of the tandem repeat TTAGGG in mammals, and they play an important role in protecting the ends of the chromosome.

In other cases, expansions in the number of tandem repeats in exons or introns can cause [[Trinucleotide repeat disorder|disease]].<ref name="Usdin">{{cite journal |vauthors = Usdin K |title = The biological effects of simple tandem repeats: lessons from the repeat expansion diseases |journal = Genome Research |volume = 18 |issue = 7 |pages = 1011–19 |date = July 2008 |pmid = 18593815 |pmc = 3960014 |doi = 10.1101/gr.070409.107 }}</ref> For example, the human gene huntingtin (Htt) typically contains 6–29 tandem repeats of the nucleotides CAG (encoding a polyglutamine tract). An expansion to over 36 repeats results in [[Huntington's disease]], a neurodegenerative disease. Twenty human disorders are known to result from similar tandem repeat expansions in various genes. The mechanism by which proteins with expanded polygulatamine tracts cause death of neurons is not fully understood. One possibility is that the proteins fail to fold properly and avoid degradation, instead accumulating in aggregates that also sequester important transcription factors, thereby altering gene expression.<ref name="Usdin"/>

Tandem repeats are usually caused by slippage during replication, unequal crossing-over and gene conversion.<ref>{{cite journal |vauthors = Li YC, Korol AB, Fahima T, Beiles A, Nevo E |title = Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review |journal = Molecular Ecology |volume = 11 |issue = 12 |pages = 2453–65 |date = December 2002 |pmid = 12453231 |doi = 10.1046/j.1365-294X.2002.01643.x |s2cid = 23606208 |doi-access = free |bibcode = 2002MolEc..11.2453L }}</ref>

==== Transposable elements ====
Transposable elements (TEs) are sequences of DNA with a defined structure that are able to change their location in the genome.<ref name="Padeken" /><ref name="constraints and plasticity in genome and molecular" /><ref name="Wessler 17600–17601">{{cite journal |vauthors = Wessler SR |title = Transposable elements and the evolution of eukaryotic genomes |journal = Proceedings of the National Academy of Sciences of the United States of America |volume = 103 |issue = 47 |pages = 17600–01 |date = November 2006 |pmid = 17101965 |doi = 10.1073/pnas.0607612103 |bibcode = 2006PNAS..10317600W |pmc = 1693792 |doi-access = free }}</ref> TEs are categorized as either as a mechanism that replicates by copy-and-paste or as a mechanism that can be excised from the genome and inserted at a new location. In the human genome, there are three important classes of TEs that make up more than 45% of the human DNA; these classes are The long interspersed nuclear elements (LINEs), The interspersed nuclear elements (SINEs), and endogenous retroviruses. These elements have a big potential to modify the genetic control in a host organism.<ref name=":0a">{{Cite journal|last1=Zhou|first1=Wanding|last2=Liang|first2=Gangning|last3=Molloy|first3=Peter L.|last4=Jones|first4=Peter A.|date=11 August 2020|title=DNA methylation enables transposable element-driven genome expansion|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=117|issue=32|pages=19359–19366|doi=10.1073/pnas.1921719117|issn=1091-6490|pmc=7431005|pmid=32719115|bibcode=2020PNAS..11719359Z |doi-access=free }}</ref>

The movement of TEs is a driving force of genome evolution in eukaryotes because their insertion can disrupt gene functions, homologous recombination between TEs can produce duplications, and TE can shuffle exons and regulatory sequences to new locations.<ref name="Kazazian 1626–1632">{{cite journal |vauthors = Kazazian HH |s2cid = 1956932 |title = Mobile elements: drivers of genome evolution |journal = Science |volume = 303 |issue = 5664 |pages = 1626–32 |date = March 2004 |pmid = 15016989 |doi = 10.1126/science.1089670 |bibcode = 2004Sci...303.1626K }}</ref>

===== Retrotransposons =====
[[Retrotransposon]]s<ref>{{Cite web|title=Transposon {{!}} genetics|url=https://www.britannica.com/science/transposon|access-date=2020-12-05|website=Encyclopedia Britannica}}</ref> are found mostly in eukaryotes but not found in prokaryotes. Retrotransposons form a large portion of the genomes of many eukaryotes. A retrotransposon is a transposable element that transposes through an [[RNA]] intermediate. Retrotransposons<ref>{{Cite book|last=Sanders|first=Mark Frederick|title=Genetic Analysis: an integrated approach third edition|publisher=Pearson, always learning, and mastering|year=2019|isbn=9780134605173|location=New York|pages=425}}</ref> are composed of [[DNA]], but are transcribed into RNA for transposition, then the RNA transcript is copied back to DNA formation with the help of a specific enzyme called reverse transcriptase. A retrotransposon that carries reverse transcriptase in its sequence can trigger its own transposition but retrotransposons that lack a reverse transcriptase must use reverse transcriptase synthesized by another retrotransposon. [[Retrotransposon]]s can be transcribed into RNA, which are then duplicated at another site into the genome.<ref>{{cite journal |vauthors = Deininger PL, Moran JV, Batzer MA, Kazazian HH |title = Mobile elements and mammalian genome evolution |journal = Current Opinion in Genetics & Development |volume = 13 |issue = 6 |pages = 651–58 |date = December 2003 |pmid = 14638329 |doi = 10.1016/j.gde.2003.10.013 }}</ref> Retrotransposons can be divided into [[long terminal repeat]]s (LTRs) and non-long terminal repeats (Non-LTRs).<ref name="Kazazian 1626–1632"/>

'''Long terminal repeats (LTRs)''' are derived from ancient retroviral infections, so they encode proteins related to retroviral proteins including gag (structural proteins of the virus), pol (reverse transcriptase and integrase), pro (protease), and in some cases env (envelope) genes.<ref name="Wessler 17600–17601"/> These genes are flanked by long repeats at both 5' and 3' ends. It has been reported that LTRs consist of the largest fraction in most plant genome and might account for the huge variation in genome size.<ref>{{cite journal |vauthors = Kidwell MG, Lisch DR |title = Transposable elements and host genome evolution |journal = Trends in Ecology & Evolution |volume = 15 |issue = 3 |pages = 95–99 |date = March 2000 |pmid = 10675923 |doi = 10.1016/S0169-5347(99)01817-0 |bibcode = 2000TEcoE..15...95K }}</ref>

'''Non-long terminal repeats (Non-LTRs)''' are classified as [[long interspersed nuclear element]]s (LINEs), [[short interspersed nuclear element]]s (SINEs), and Penelope-like elements (PLEs). In ''Dictyostelium discoideum'', there is another DIRS-like elements belong to Non-LTRs. Non-LTRs are widely spread in eukaryotic genomes.<ref>{{cite journal |vauthors = Richard GF, Kerrest A, Dujon B |title = Comparative genomics and molecular dynamics of DNA repeats in eukaryotes |journal = Microbiology and Molecular Biology Reviews |volume = 72 |issue = 4 |pages = 686–727 |date = December 2008 |pmid = 19052325 |pmc = 2593564 |doi = 10.1128/MMBR.00011-08 }}</ref>

Long interspersed elements (LINEs) encode genes for reverse transcriptase and endonuclease, making them autonomous transposable elements. The human genome has around 500,000 LINEs, taking around 17% of the genome.<ref>{{cite journal |vauthors = Cordaux R, Batzer MA |title = The impact of retrotransposons on human genome evolution |journal = Nature Reviews. Genetics |volume = 10 |issue = 10 |pages = 691–703 |date = October 2009 |pmid = 19763152 |pmc = 2884099 |doi = 10.1038/nrg2640 }}</ref>

Short interspersed elements (SINEs) are usually less than 500 base pairs and are non-autonomous, so they rely on the proteins encoded by LINEs for transposition.<ref>{{cite journal |vauthors = Han JS, Boeke JD |title = LINE-1 retrotransposons: modulators of quantity and quality of mammalian gene expression? |journal = BioEssays |volume = 27 |issue = 8 |pages = 775–84 |date = August 2005 |pmid = 16015595 |doi = 10.1002/bies.20257 |s2cid = 26424042 }}</ref> The [[Alu element]] is the most common SINE found in primates. It is about 350 base pairs and occupies about 11% of the human genome with around 1,500,000 copies.<ref name="Kazazian 1626–1632"/>

===== DNA transposons =====
[[DNA transposon]]s encode a transposase enzyme between inverted terminal repeats. When expressed, the transposase recognizes the terminal inverted repeats that flank the transposon and catalyzes its excision and reinsertion in a new site.<ref name="Padeken" /> This cut-and-paste mechanism typically reinserts transposons near their original location (within 100&nbsp;kb).<ref name="Kazazian 1626–1632"/> DNA transposons are found in bacteria and make up 3% of the human genome and 12% of the genome of the roundworm [[Caenorhabditis elegans|''C. elegans'']].<ref name="Kazazian 1626–1632"/>

== Genome size ==
[[File:Genome_size_vs_protein_count.svg|thumbnail|[[Log–log plot]] of the total number of annotated proteins in genomes submitted to [[GenBank]] as a function of genome size]]
[[Genome size]] is the total number of the DNA base pairs in one copy of a [[haploid]] genome. Genome size varies widely across species. Invertebrates have small genomes, this is also correlated to a small number of transposable elements. Fish and Amphibians have intermediate-size genomes, and birds have relatively small genomes but it has been suggested that birds lost a substantial portion of their genomes during the phase of transition to flight.&nbsp; Before this loss, DNA methylation allows the adequate expansion of the genome.<ref name=":0a" />

In humans, the nuclear genome comprises approximately 3.1 billion nucleotides of DNA, divided into 24 linear molecules, the shortest 45 000 000 nucleotides in length and the longest 248 000 000 nucleotides, each contained in a different chromosome.<ref name="human-T2T">{{cite journal |title=The complete sequence of a human genome |journal=Science |date=2022-03-31 |volume=376 |pages=44–53 |doi=10.1126/science.abj6987 |pmid=35357919|last1=Nurk |first1=Sergey |last2=Koren |first2=Sergey |last3=Rhie |first3=Arang |last4=Rautiainen |first4=Mikko |last5=Bzikadze |first5=Andrey V. |last6=Mikheenko |first6=Alla |last7=Vollger |first7=Mitchell R. |last8=Altemose |first8=Nicolas |last9=Uralsky |first9=Lev |last10=Gershman |first10=Ariel |last11=Aganezov |first11=Sergey |last12=Hoyt |first12=Savannah J. |last13=Diekhans |first13=Mark |last14=Logsdon |first14=Glennis A. |last15=Alonge |first15=Michael |last16=Antonarakis |first16=Stylianos E. |last17=Borchers |first17=Matthew |last18=Bouffard |first18=Gerard G. |last19=Brooks |first19=Shelise Y. |last20=Caldas |first20=Gina V. |last21=Chen |first21=Nae-Chyun |last22=Cheng |first22=Haoyu |last23=Chin |first23=Chen-Shan |last24=Chow |first24=William |last25=De Lima |first25=Leonardo G. |last26=Dishuck |first26=Philip C. |last27=Durbin |first27=Richard |last28=Dvorkina |first28=Tatiana |last29=Fiddes |first29=Ian T. |last30=Formenti |first30=Giulio |issue=6588 |pmc=9186530 |bibcode=2022Sci...376...44N |s2cid=235233625 |url=https://eprints.iisc.ac.in/71762/1/Sci_376-6588_44-531_2022%20.pdf |archive-url=https://web.archive.org/web/20220526104204/https://eprints.iisc.ac.in/71762/1/Sci_376-6588_44-531_2022%20.pdf |archive-date=2022-05-26 |url-status=live |display-authors=1 }}</ref> There is no clear and consistent correlation between morphological complexity and genome size in either [[bacterial genome size|prokaryotes]] or lower [[eukaryotes]].<ref name="Lewin 2004" /><ref>{{cite journal |vauthors = Gregory TR, Nicol JA, Tamm H, Kullman B, Kullman K, Leitch IJ, Murray BG, Kapraun DF, Greilhuber J, Bennett MD |title = Eukaryotic genome size databases |journal = Nucleic Acids Research |volume = 35 |issue = Database issue |pages = D332–38 |date = January 2007 |pmid = 17090588 |pmc = 1669731 |doi = 10.1093/nar/gkl828 }}</ref> Genome size is largely a function of the expansion and contraction of repetitive DNA elements.

Since genomes 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 multi-cellular organisms (see [[developmental biology]]). The work is both ''[[in vivo]]'' and ''[[in silico]]''.<ref>{{cite journal |vauthors = Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M, Hutchison CA, Smith HO, Venter JC |title = Essential genes of a minimal bacterium |journal = Proceedings of the National Academy of Sciences of the United States of America |volume = 103 |issue = 2 |pages = 425–30 |date = January 2006 |pmid = 16407165 |pmc = 1324956 |doi = 10.1073/pnas.0510013103 |bibcode = 2006PNAS..103..425G |doi-access = free }}
</ref><ref>{{cite journal |vauthors = Forster AC, Church GM |title = Towards synthesis of a minimal cell |journal = Molecular Systems Biology |volume = 2 |issue = 1 |pages = 45 |date = 2006 |pmid = 16924266 |pmc = 1681520 |doi = 10.1038/msb4100090 }}</ref>

=== Genome size differences due to transposable elements ===
[[File:Genome sizes.png|thumb|Comparison among genome sizes]]

There are many enormous differences in size in genomes, specially mentioned before in the multicellular eukaryotic genomes. Much of this is due to the differing abundances of transposable elements, which evolve by creating new copies of themselves in the chromosomes.<ref name=":0a"/> Eukaryote genomes often contain many thousands of copies of these elements, most of which have acquired mutations that make them defective.

== Genomic alterations ==
All the cells of an organism originate from a single cell, so they are expected to have identical genomes; however, in some cases, differences arise. Both the process of copying DNA during cell division and exposure to environmental mutagens can result in mutations in somatic cells. In some cases, such mutations lead to cancer because they cause cells to divide more quickly and invade surrounding tissues.<ref>{{cite journal |vauthors = Martincorena I, Campbell PJ |title = Somatic mutation in cancer and normal cells |journal = Science |volume = 349 |issue = 6255 |pages = 1483–89 |date = September 2015 |pmid = 26404825 |doi = 10.1126/science.aab4082 |bibcode = 2015Sci...349.1483M |s2cid = 13945473 }}</ref> In certain lymphocytes in the human immune system, [[V(D)J recombination]] generates different genomic sequences such that each cell produces a unique antibody or T cell receptors.

During [[meiosis]], diploid cells divide twice to produce haploid germ cells. During this process, recombination results in a reshuffling of the genetic material from homologous chromosomes so each gamete has a unique genome.

=== Genome-wide reprogramming ===
Genome-wide reprogramming in mouse [[germ cell|primordial germ cells]] involves [[epigenetics|epigenetic]] imprint erasure leading to [[cell potency|totipotency]]. Reprogramming is facilitated by active [[DNA demethylation]], a process that entails the DNA [[base excision repair]] pathway.<ref name="pmid20595612">{{cite journal |vauthors=Hajkova P, Jeffries SJ, Lee C, Miller N, Jackson SP, Surani MA |title=Genome-wide reprogramming in the mouse germ line entails the base excision repair pathway |journal=Science |volume=329 |issue=5987 |pages=78–82 |date=July 2010 |pmid=20595612 |pmc=3863715 |doi=10.1126/science.1187945 |bibcode=2010Sci...329...78H }}</ref> This pathway is employed in the erasure of [[DNA methylation|CpG methylation]] (5mC) in primordial germ cells. The erasure of 5mC occurs via its conversion to [[5-hydroxymethylcytosine]] (5hmC) driven by high levels of the ten-eleven dioxygenase enzymes [[Tet methylcytosine dioxygenase 1|TET1]] and [[Tet methylcytosine dioxygenase 2|TET2]].<ref name="pmid23223451">{{cite journal |vauthors=Hackett JA, Sengupta R, Zylicz JJ, Murakami K, Lee C, Down TA, Surani MA |title=Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine |journal=Science |volume=339 |issue=6118 |pages=448–52 |date=January 2013 |pmid=23223451 |pmc=3847602 |doi=10.1126/science.1229277 |bibcode=2013Sci...339..448H }}</ref>

== Genome evolution ==
Genomes are more than the sum of an organism's [[gene]]s 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 [[karyotype]] (chromosome number), [[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. Duplication may range from extension of [[short tandem repeats]], to duplication of a cluster of genes, and all the way to duplication 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 an 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. Recent empirical data suggest an important role of viruses and sub-viral RNA-networks to represent a main driving role to generate genetic novelty and natural genome editing.

== In fiction ==
Works of science fiction illustrate concerns about the availability of genome sequences.

Michael Crichton's 1990 novel [[Jurassic Park (novel)|''Jurassic Park'']] and the subsequent [[Jurassic Park (film)|film]] tell the story of a billionaire who creates a theme park of cloned dinosaurs on a remote island, with disastrous outcomes. A geneticist extracts dinosaur DNA from the blood of ancient mosquitoes and fills in the gaps with DNA from modern species to create several species of dinosaurs. A chaos theorist is asked to give his expert opinion on the safety of engineering an ecosystem with the dinosaurs, and he repeatedly warns that the outcomes of the project will be unpredictable and ultimately uncontrollable. These warnings about the perils of using genomic information are a major theme of the book.

The 1997 film ''[[Gattaca]]'' is set in a futurist society where genomes of children are engineered to contain the most ideal combination of their parents' traits, and metrics such as risk of heart disease and predicted life expectancy are documented for each person based on their genome. People conceived outside of the eugenics program, known as "In-Valids" suffer discrimination and are relegated to menial occupations. The protagonist of the film is an In-Valid who works to defy the supposed genetic odds and achieve his dream of working as a space navigator. The film warns against a future where genomic information fuels prejudice and extreme class differences between those who can and cannot afford genetically engineered children.<ref>{{cite web |title = Gattaca (movie) |url = https://www.rottentomatoes.com/m/gattaca/ |work = Rotten Tomatoes |date = 24 October 1997 }}</ref>

== See also ==
{{col div|colwidth=20em}}
* [[Bacterial genome size]]
* [[Cryoconservation of animal genetic resources]]
* [[DNA methylation]]
* [[UCSC Genome Browser|Genome Browser]]
* [[Genome Compiler]]
* [[Circuit topology|Genome topology]]
* [[Genome-wide association study]]
* [[List of sequenced animal genomes]]
* [[List of sequenced archaeal genomes]]
* [[List of sequenced bacterial genomes]]
* [[List of sequenced eukaryotic genomes]]
* [[List of sequenced fungi genomes]]
* [[List of sequenced plant genomes]]
* [[List of sequenced plastomes]]
* [[List of sequenced protist genomes]]
* [[Metagenomics]]
* [[Microbiome]]
* [[Molecular epidemiology]]
* [[Molecular pathological epidemiology]]
* [[Molecular pathology]]
* [[Nucleic acid sequence]]
* [[Pan-genome]]
* [[Precision medicine]]
* [[Regulator gene]]
* [[Whole genome sequencing]]
{{_colend}}

== References ==
{{reflist}}

== Further reading ==
* {{cite book |vauthors = Benfey P, Protopapas AD|title=Essentials of Genomics|publisher=Prentice Hall|date=2004}}
* {{cite book |last1=Brown|first1=Terence A. |name-list-style = vanc |title=Genomes 2|publisher=Bios Scientific Publishers|location=Oxford|date=2002|isbn=978-1-85996-029-5 }}
* {{cite book|last1=Gibson|first1=Greg|last2=Muse|first2=Spencer V.|name-list-style=vanc|title=A Primer of Genome Science|edition=Second|publisher=Sinauer Assoc|location=Sunderland, Mass|date=2004|isbn=978-0-87893-234-4|url-access=registration|url=https://archive.org/details/primerofgenomesc00greg}}
* {{cite book|last=Gregory|first=T. Ryan |name-list-style = vanc |title=The Evolution of the Genome|publisher=Elsevier|date=2005|isbn=978-0-12-301463-4|title-link=The Evolution of the Genome }}
* {{cite book|last=Reece|first=Richard J.|name-list-style = vanc |title=Analysis of Genes and Genomes|publisher=John Wiley & Sons|location=Chichester|date=2004|isbn=978-0-470-84379-6}}
* {{cite book|last1=Saccone|first1=Cecilia|last2=Pesole |first2 = Graziano |name-list-style = vanc |title=Handbook of Comparative Genomics|publisher=John Wiley & Sons|location=Chichester|date=2003|isbn=978-0-471-39128-9 }}
* {{cite journal |vauthors = Werner E |title = In silico multicellular systems biology and minimal genomes |journal = Drug Discovery Today |volume = 8 |issue = 24 |pages = 1121–27 |date = December 2003 |pmid = 14678738 |doi = 10.1016/S1359-6446(03)02918-0 }}

== External links ==
{{Wiktionary}}
{{wikiquote}}
* [http://genome.ucsc.edu UCSC Genome Browser] – view the genome and annotations for more than 80 organisms.
* [https://web.archive.org/web/20130809102814/http://www.genomecenter.howard.edu/ genomecenter.howard.edu] (archived 9 August 2013)
* [https://web.archive.org/web/20100609223959/http://learn.genetics.utah.edu/content/begin/dna/builddna/ Build a DNA Molecule] (archived 9 June 2010)
* [http://www.genomenewsnetwork.org/articles/02_01/Sizing_genomes.shtml Some comparative genome sizes]
* [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]
* [https://web.archive.org/web/20050901105257/http://www.rbgkew.org.uk/cval/homepage.html Plant genome size database] (archived 1 September 2005)
* [http://www.genomesonline.org/ GOLD:Genomes OnLine Database]
* [http://www.genomenewsnetwork.org/ The Genome News Network]
* [https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj NCBI Entrez Genome Project database]
* [https://www.ncbi.nlm.nih.gov/About/primer/genetics_genome.html NCBI Genome Primer]
* [https://www.genecards.org/ GeneCards]—an integrated database of human genes
* [http://news.bbc.co.uk/1/hi/sci/tech/4994088.stm BBC News – Final genome 'chapter' published]
* [http://img.jgi.doe.gov/ IMG] (The Integrated Microbial Genomes system)—for genome analysis by the DOE-JGI
* [https://web.archive.org/web/20120303111440/http://www.geknome.com/ GeKnome Technologies Next-Gen Sequencing Data Analysis]—next-generation sequencing data analysis for [[Illumina (company)|Illumina]] and [[454 Life Sciences|454]] Service from GeKnome Technologies (archived 3 March 2012)

{{Genetics}}
{{Genomics}}
{{Self-replicating organic structures}}

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[[Category:Genetic mapping]]
[[Category:Genomics]]
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[[Category:Methylation]]

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