Array ( [0] => {{Short description|All genetic material of an organism}} [1] => {{For multi|a non-technical introduction to the topic|Introduction to genetics|other uses}} [2] => [[File:Prokaryotic Cell Diagram.jpg|thumb|A label diagram explaining the different parts of a prokaryotic genome]] [3] => {{Use dmy dates|date=October 2021}} [4] => {{Genetics sidebar}} [5] => [6] => [[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).]] [7] => [8] => In the fields of [[molecular biology]] and [[genetics]], a '''genome''' is all the genetic information of an organism.{{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 }} 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.{{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}}{{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}} Almost all eukaryotes have [[mitochondrial DNA|mitochondria]] and a small [[mitochondrial genome]]. Algae and plants also contain [[chloroplast DNA|chloroplasts]] with a chloroplast genome. [9] => [10] => 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 [[Human Genome Project]] was started in October 1990, and then reported the sequence of the [[human genome]] in April 2003,{{Cite web |title=The Human Genome Project |url=https://www.genome.gov/human-genome-project |access-date=2023-04-29 |website=Genome.gov }} although the initial "finished" sequence was missing 8% of the genome consisting mostly of repetitive sequences.{{cite web |date=2022-04-11 |title=First complete sequence of a human genome |url=https://www.nih.gov/news-events/nih-research-matters/first-complete-sequence-human-genome#:~:text=This%20last%208%25%20of%20the,of%20each%20chromosome. |archive-url=https://web.archive.org/web/20230414170647/https://www.nih.gov/news-events/nih-research-matters/first-complete-sequence-human-genome#:~:text=This%20last%208%25%20of%20the,of%20each%20chromosome |archive-date=2023-04-14 |url-status=live |access-date=2023-04-29 |website=National Institutes of Health (NIH)}} [11] => [12] => With advancements in technology that could handle sequencing of the many repetitive sequences found in human DNA that were not fully uncovered by the original Human Genome Project study, scientists reported the first end-to-end human genome sequence in March 2022.{{cite web |last1=Hartley |first1=Gabrielle |title=The Human Genome Project pieced together only 92% of the DNA – now scientists have finally filled in the remaining 8% |url=https://theconversation.com/the-human-genome-project-pieced-together-only-92-of-the-dna-now-scientists-have-finally-filled-in-the-remaining-8-176138 |website=TheConversation.org |date=31 March 2022 |publisher=The Conversation US, Inc. |access-date=4 April 2022}} [13] => [14] => == Origin of the term == [15] => {{Wiktionary}} [16] => The term ''genome'' was created in 1920 by [[Hans Winkler]],{{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}} 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]]''.{{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}}{{Cite OED|genome}}{{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]]}}{{Cite OEtymD|genome}} 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.{{cite journal|last1=Lederberg |first1=Joshua |last2=McCray |first2=Alexa T. |name-list-style = vanc |title='Ome Sweet 'Omics – A Genealogical Treasury of Words |journal=The Scientist |volume=15 |issue=7 |date=2001 |url=http://lhncbc.nlm.nih.gov/lhc/docs/published/2001/pub2001047.pdf |url-status=dead |archive-url=https://web.archive.org/web/20060929175954/https://lhncbc.nlm.nih.gov/lhc/docs/published/2001/pub2001047.pdf |archive-date=29 September 2006 }} [17] => [18] => == Definition == [19] => {{Anchor|definition}} [20] => It's very difficult to come up with a precise definition of "genome." It usually refers to the DNA (or sometimes RNA) molecules that carry the genetic information in an organism but sometimes it is difficult to decide which molecules to include in the definition; 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. The definition of 'genome' that's commonly used in the scientific literature is usually restricted to the large chromosomal DNA molecules in bacteria.{{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 }} [21] => [22] => ===Nuclear genome=== [23] => 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.{{ cite book |vauthors = Brown, TA |date = 2018 |title = Genomes 4 |publisher = Garland Science |place = New York, NY, USA |isbn = 9780815345084}} This is the most common use of 'genome' in the scientific literature. [24] => [25] => ===Ploidy=== [26] => 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.{{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}} [27] => [28] => == Sequencing and mapping == [29] => {{Details|Whole genome sequencing|Genome project}} [30] => 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]] [31] => 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 Φ-X174]], of 5386 base pairs.{{cite web|url=http://www.beowulf.org.uk/|title=All about genes|website=beowulf.org.uk}} 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.{{cn|date=January 2023}} [32] => [33] => 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.{{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}} 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]].{{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}}{{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 }} [34] => [35] => New sequencing technologies, such as [[massive parallel sequencing]] have also opened up the prospect of personal genome sequencing as a diagnostic tool, as pioneered by [[Manteia Predictive Medicine]]. A major step toward that goal was the completion in 2007 of the [[human genome|full genome]] of [[James D. Watson]], one of the co-discoverers of the structure of DNA.{{cite news|url=https://www.nytimes.com/2007/05/31/science/31cnd-gene.html |work=The New York Times |title=Genome of DNA Pioneer Is Deciphered |first=Nicholas |last=Wade |name-list-style = vanc |date=2007-05-31 |access-date=2 April 2010}} [36] => [37] => 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. The [[Human Genome Project]] was organized to [[Physical map (genetics)#Linkage map|map]] and to [[sequencing|sequence]] the [[human genome]]. A fundamental step in the project was the release of a detailed genomic map by [[Jean Weissenbach]] and his team at the [[Genoscope]] in Paris.{{cite web|url=http://www.genomenewsnetwork.org/resources/whats_a_genome/Chp3_1.shtml |title=What's a Genome? |publisher=Genomenewsnetwork.org |date=2003-01-15 |access-date=27 January 2011}}{{cite web|author= |url=https://www.ncbi.nlm.nih.gov/About/primer/mapping.html |title=Mapping Factsheet |date=2004-03-29 |access-date=27 January 2011 |url-status=dead |archive-url=https://web.archive.org/web/20100719235548/http://www.ncbi.nlm.nih.gov/About/primer/mapping.html |archive-date=19 July 2010 }} [38] => [39] => [[Reference genome]] sequences and maps continue to be updated, removing errors and clarifying regions of high allelic complexity.{{cite web|author=Genome Reference Consortium |url=https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/ |title=Assembling the Genome |access-date=23 August 2016}} The decreasing cost of genomic mapping has permitted [[genealogy|genealogical]] sites to offer it as a service,{{cite news |url=https://www.washingtonpost.com/news/speaking-of-science/wp/2016/05/17/how-do-your-20000-genes-determine-so-many-wildly-different-traits-they-multitask/ |title=How do your 20,000 genes determine so many wildly different traits? They multitask. |newspaper=The Washington Post |date=2016-04-17 |access-date=2016-08-27 |author=Kaplan, Sarah}} to the extent that one may submit one's genome to [[crowdsourcing|crowdsourced]] scientific endeavours such as [[DNA.LAND]] at the [[New York Genome Center]],{{cite journal|last1=Check Hayden|first1=Erika|title=Scientists hope to attract millions to 'DNA.LAND'|url=https://www.nature.com/news/scientists-hope-to-attract-millions-to-dna-land-1.18514|journal=Nature|doi=10.1038/nature.2015.18514|year=2015|s2cid=211729308 }} an example both of the [[economies of scale]] and of [[citizen science]].{{cite web |url=https://www.statnews.com/feature/game-of-genomes/season-three/ |title=Game of Genomes, Episode 13: Answers and Questions |publisher=STAT |access-date=2016-08-27 |author=Zimmer, Carl|date=25 July 2016 }} [40] => [41] => == Viral genomes == [42] => [[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.{{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/}} [43] => [44] => == Prokaryotic genomes == [45] => Prokaryotes and eukaryotes have DNA genomes. Archaea and most bacteria have a single [[circular chromosome]],{{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 }} however, some bacterial species have linear or multiple chromosomes.{{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}}{{cite web|url=http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/chroms-genes-prots/chromosomes.html|title=Bacterial Chromosomes|website=Microbial Genetics|year=2002}} 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.{{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 }} However, some [[symbiotic bacteria]] (e.g. ''[[Serratia symbiotica]]'') have reduced genomes and a high fraction of pseudogenes: only ~40% of their DNA encodes proteins.{{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 }}{{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 }} [46] => [47] => 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''. [48] => [49] => == Eukaryotic genomes == [50] => {{See also|Eukaryotic chromosome fine structure}} [51] => [[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}}]] [52] => 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]],{{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}} which each have only one pair, to a [[Ophioglossum|fern species]] that has 720 pairs.{{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 }} 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 due to the fact that eukaryotic genomes show as much as 64,000-fold variation in their sizes. However, this special characteristic is caused by the presence of repetitive DNA, and transposable elements (TEs). [53] => [54] => 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. [55] => [56] => 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.{{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}} Genes in eukaryotic genomes can be annotated using FINDER.{{cite journal |vauthors = Banerjee S, Bhandary P, Woodhouse M, Sen TZ, Wise RP, Andorf CM |title = FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences |journal = BMC Bioinformatics |volume = 44 |issue = 9 |pages = e89 |date = Apr 2021 |pmid = 33879057 |doi = 10.1186/s12859-021-04120-9 |pmc = 8056616 |doi-access = free }} [57] => {{cite journal |last1=Harb |first1=Omar S. |last2=Boehme |first2=Ulrike |last3=Crouch |first3=Kathryn |last4=Ifeonu |first4=Olukemi O. |last5=Roos |first5=David S. |last6=Silva |first6=Joana C. |last7=Silva-Franco |first7=Fatima |last8=Svärd |first8=Staffan |last9=Tretina |first9=Kyle |last10=Weedall |first10=Gareth |title=Genomes |url=https://www.ncbi.nlm.nih.gov/books/NBK556349/#genomes.s1 |website=Molecular Parasitology: Protozoan Parasites and their Molecules |series=Wellcome Trust–Funded Monographs and Book Chapters |publisher=Springer |date=2016|pmid=32348078 }} [58] => [59] => === DNA sequencing === [60] => 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. [61] => [62] => === Coding sequences === [63] => 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.[[File:Components of the human genome.png|thumb|Composition of the human genome]] [64] => [65] => === Noncoding sequences === [66] => {{Main|Non-coding DNA}} [67] => {{See also|Intergenic region}} [68] => [69] => 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.{{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}} [70] => [71] => ==== Tandem repeats ==== [72] => 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.{{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 }} 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. [73] => [74] => In other cases, expansions in the number of tandem repeats in exons or introns can cause [[Trinucleotide repeat disorder|disease]].{{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 }} 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. [75] => [76] => Tandem repeats are usually caused by slippage during replication, unequal crossing-over and gene conversion.{{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 }} [77] => [78] => ==== Transposable elements ==== [79] => Transposable elements (TEs) are sequences of DNA with a defined structure that are able to change their location in the genome.{{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 }} 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.{{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 }} [80] => [81] => 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.{{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 }} [82] => [83] => ===== Retrotransposons ===== [84] => [[Retrotransposon]]s{{Cite web|title=Transposon {{!}} genetics|url=https://www.britannica.com/science/transposon|access-date=2020-12-05|website=Encyclopedia Britannica}} 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{{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}} 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.{{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 }} Retrotransposons can be divided into [[long terminal repeat]]s (LTRs) and non-long terminal repeats (Non-LTRs). [85] => [86] => '''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. 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.{{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 }} [87] => [88] => '''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.{{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 }} [89] => [90] => 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.{{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 }} [91] => [92] => 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.{{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 }} 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. [93] => [94] => ===== DNA transposons ===== [95] => [[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. This cut-and-paste mechanism typically reinserts transposons near their original location (within 100 kb). 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'']]. [96] => [97] => == Genome size == [98] => [[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]] [99] => [[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.  Before this loss, DNA methylation allows the adequate expansion of the genome. [100] => [101] => 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.{{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 }} There is no clear and consistent correlation between morphological complexity and genome size in either [[bacterial genome size|prokaryotes]] or lower [[eukaryotes]].{{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 }} Genome size is largely a function of the expansion and contraction of repetitive DNA elements. [102] => [103] => 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]]''.{{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 }} [104] => {{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 }} [105] => [106] => === Genome size differences due to transposable elements === [107] => [[File:Genome sizes.png|thumb|Comparison among genome sizes]] [108] => [109] => 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. Eukaryote genomes often contain many thousands of copies of these elements, most of which have acquired mutations that make them defective. [110] => Here is a table of some significant or representative genomes. See [[#See also]] for lists of sequenced genomes. [111] => [112] => {|class="wikitable sortable" [113] => |- [114] => !Organism type [115] => !Organism [116] => !colspan="2"|Genome size
([[base pair]]s) [117] => !Approx. no. of genes [118] => !class="unsortable"|Note [119] => |- [120] => |[[Virus]] [121] => |[[Porcine circovirus]] type 1 [122] => |align="right"|1,759 [123] => |1.8 kB [124] => | [125] => |Smallest viruses replicating autonomously in [[eukaryotic]] cells{{cite book |chapter-url=http://www.horizonpress.com/avir|author=Mankertz P|date=2008|chapter=Molecular Biology of Porcine Circoviruses|title=Animal Viruses: Molecular Biology|publisher=Caister Academic Press |isbn = 978-1-904455-22-6 }} [126] => |- [127] => |[[Virus]] [128] => |[[Bacteriophage MS2]] [129] => |align="right"|3,569 [130] => |3.6 kB [131] => | [132] => |First sequenced RNA-genome{{cite journal |vauthors = Fiers W, Contreras R, Duerinck F, Haegeman G, Iserentant D, Merregaert J, Min Jou W, Molemans F, Raeymaekers A, Van den Berghe A, Volckaert G, Ysebaert M |title = Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene |journal = Nature |volume = 260 |issue = 5551 |pages = 500–07 |date = April 1976 |pmid = 1264203 |doi = 10.1038/260500a0 |bibcode = 1976Natur.260..500F |s2cid = 4289674 }} [133] => |- [134] => |[[Virus]] [135] => |[[SV40]] [136] => |align="right"|5,224 [137] => |5.2 kB [138] => | [139] => |{{cite journal |vauthors = 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 = 113–20 |date = May 1978 |pmid = 205802 |doi = 10.1038/273113a0 |bibcode = 1978Natur.273..113F |s2cid = 1634424 |url = https://biblio.ugent.be/publication/1926957/file/1929034 }} [140] => |- [141] => |[[Virus]] [142] => |[[Phi-X174 phage|Phage Φ-X174]] [143] => |align="right"|5,386 [144] => |5.4 kB [145] => | [146] => |First sequenced DNA-genome{{cite journal |vauthors = 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 = 687–95 |date = February 1977 |pmid = 870828 |doi = 10.1038/265687a0 |bibcode = 1977Natur.265..687S |s2cid = 4206886 }} [147] => |- [148] => |[[Virus]] [149] => |[[HIV]] [150] => |align="right"|9,749 [151] => |9.7 kB [152] => | [153] => |{{cite web|url=http://pathmicro.med.sc.edu/lecture/hiv9.htm |title=Virology – Human Immunodeficiency Virus And Aids, Structure: The Genome And Proteins of HIV |publisher=Pathmicro.med.sc.edu |date=2010-07-01 |access-date=27 January 2011}} [154] => |- [155] => |[[Virus]] [156] => |[[lambda phage|Phage λ]] [157] => |align="right"|48,502 [158] => |48.5 kB [159] => | [160] => |Often used as a vector for the cloning of recombinant DNA [161] => {{cite journal |vauthors = Thomason L, Court DL, Bubunenko M, Costantino N, Wilson H, Datta S, Oppenheim A |title = Recombineering: Genetic Engineering in Bacteria Using Homologous Recombination |s2cid = 490362 |journal = Current Protocols in Molecular Biology |volume = Chapter 1 |page = Unit 1.16 |date = April 2007 |pmid = 18265390 |doi = 10.1002/0471142727.mb0116s78 |isbn = 978-0-471-14272-0 }} [162] => {{cite journal |vauthors = Court DL, Oppenheim AB, Adhya SL |title = A new look at bacteriophage lambda genetic networks |journal = Journal of Bacteriology |volume = 189 |issue = 2 |pages = 298–304 |date = January 2007 |pmid = 17085553 |pmc = 1797383 |doi = 10.1128/JB.01215-06 }} [163] => {{cite journal |vauthors = Sanger F, Coulson AR, Hong GF, Hill DF, Petersen GB |title = Nucleotide sequence of bacteriophage lambda DNA |journal = Journal of Molecular Biology |volume = 162 |issue = 4 |pages = 729–73 |date = December 1982 |pmid = 6221115 |doi = 10.1016/0022-2836(82)90546-0 }} [164] => |- [165] => |[[Virus]] [166] => |[[Megavirus]] [167] => |align="right"|1,259,197 [168] => |1.3 MB [169] => | [170] => |Until 2013 the largest known viral genome{{cite journal |vauthors = Legendre M, Arslan D, Abergel C, Claverie JM |title = Genomics of Megavirus and the elusive fourth domain of Life |journal = Communicative & Integrative Biology |volume = 5 |issue = 1 |pages = 102–06 |date = January 2012 |pmid = 22482024 |pmc = 3291303 |doi = 10.4161/cib.18624 }} [171] => |- [172] => |[[Virus]] [173] => |''[[Pandoravirus salinus]]'' [174] => |style="text-align:right;"|2,470,000 [175] => |2.47 MB [176] => | [177] => |Largest known viral genome.{{cite journal |vauthors = Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C |s2cid = 16877147 |title = Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes |journal = Science |volume = 341 |issue = 6143 |pages = 281–86 |date = July 2013 |pmid = 23869018 |doi = 10.1126/science.1239181 |bibcode = 2013Sci...341..281P |url = https://hal-cea.archives-ouvertes.fr/cea-00862677/file/phi.pdf }} [178] => |- [179] => |[[Eukaryote|Eukaryotic]] [[organelle]] [180] => |Human [[mitochondrion]] [181] => |align="right"|16,569 [182] => |16.6 kB [183] => | [184] => |{{cite journal |vauthors = Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG |title = Sequence and organization of the human mitochondrial genome |journal = Nature |volume = 290 |issue = 5806 |pages = 457–65 |date = April 1981 |pmid = 7219534 |doi = 10.1038/290457a0 |bibcode = 1981Natur.290..457A |s2cid = 4355527 }} [185] => |- [186] => |[[Bacterium]] [187] => |''[[Nasuia deltocephalinicola]]'' (strain NAS-ALF) [188] => |align="right"|112,091 [189] => |112 kB [190] => |137 [191] => |Smallest known non-viral genome. Symbiont of [[leafhopper]]s.{{cite journal |vauthors = Bennett GM, Moran NA |title = Small, smaller, smallest: the origins and evolution of ancient dual symbioses in a Phloem-feeding insect |journal = Genome Biology and Evolution |volume = 5 |issue = 9 |pages = 1675–88 |date = 5 August 2013 |pmid = 23918810 |pmc = 3787670 |doi = 10.1093/gbe/evt118 }} [192] => |- [193] => |[[Bacterium]] [194] => |''[[Carsonella ruddii]]'' [195] => |align="right"|159,662 [196] => |160 kB [197] => | [198] => |An [[endosymbiont]] of [[psyllid]] insects [199] => |- [200] => |[[Bacterium]] [201] => |''[[Buchnera aphidicola]]'' [202] => |align="right"|600,000 [203] => |600 kB [204] => | [205] => |An endosymbiont of [[aphid]]s{{cite journal |vauthors = Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H |title = Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS |journal = Nature |volume = 407 |issue = 6800 |pages = 81–86 |date = September 2000 |pmid = 10993077 |doi = 10.1038/35024074 |bibcode = 2000Natur.407...81S |doi-access = free }} [206] => |- [207] => |[[Bacterium]] [208] => |''[[Wigglesworthia glossinidia]]'' [209] => |align="right"|700,000 [210] => |700 kB [211] => | [212] => |A symbiont in the gut of the [[tsetse fly]] [213] => |- [214] => |[[Bacterium]] – [[cyanobacterium]] [215] => |''[[Prochlorococcus]]'' spp. (1.7 Mb) [216] => |align="right"|1,700,000 [217] => |1.7 MB [218] => |1,884 [219] => |Smallest known cyanobacterium genome. One of the primary photosynthesizers on Earth. [220] => {{cite journal |vauthors = Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER, Chisholm SW |display-authors = 6 |title = Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation |journal = Nature |volume = 424 |issue = 6952 |pages = 1042–47 |date = August 2003 |pmid = 12917642 |doi = 10.1038/nature01947 |bibcode = 2003Natur.424.1042R |s2cid = 4344597 |doi-access = free }} [221] => {{cite journal |vauthors = Dufresne A, Salanoubat M, Partensky F, Artiguenave F, Axmann IM, Barbe V, Duprat S, Galperin MY, Koonin EV, Le Gall F, Makarova KS, Ostrowski M, Oztas S, Robert C, Rogozin IB, Scanlan DJ, Tandeau de Marsac N, Weissenbach J, Wincker P, Wolf YI, Hess WR |display-authors = 6 |title = Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome |journal = Proceedings of the National Academy of Sciences of the United States of America |volume = 100 |issue = 17 |pages = 10020–25 |date = August 2003 |pmid = 12917486 |pmc = 187748 |doi = 10.1073/pnas.1733211100 |bibcode = 2003PNAS..10010020D |doi-access = free }} [222] => |- [223] => |[[Bacterium]] [224] => |''[[Haemophilus influenzae]]'' [225] => |align="right"|1,830,000 [226] => |1.8 MB [227] => | [228] => |First genome of a living organism sequenced, July 1995{{cite journal |vauthors = Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM |s2cid = 10423613 |title = Whole-genome random sequencing and assembly of Haemophilus influenzae Rd |journal = Science |volume = 269 |issue = 5223 |pages = 496–512 |date = July 1995 |pmid = 7542800 |doi = 10.1126/science.7542800 |bibcode = 1995Sci...269..496F }} [229] => |- [230] => |[[Bacterium]] [231] => |''[[Escherichia coli]]'' [232] => |align="right"|4,600,000 [233] => |4.6 MB [234] => |4,288 [235] => |{{cite journal |vauthors = Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y |display-authors = 6 |title = The complete genome sequence of Escherichia coli K-12 |journal = Science |volume = 277 |issue = 5331 |pages = 1453–62 |date = September 1997 |pmid = 9278503 |doi = 10.1126/science.277.5331.1453 |doi-access = free }} [236] => |- [237] => |[[Bacterium]] – cyanobacterium [238] => |''[[Nostoc punctiforme]]'' [239] => |align="right"|9,000,000 [240] => |9 MB [241] => |7,432 [242] => |7432 [[open reading frame]]s [243] => {{cite journal |vauthors = Meeks JC, Elhai J, Thiel T, Potts M, Larimer F, Lamerdin J, Predki P, Atlas R |title = An overview of the genome of Nostoc punctiforme, a multicellular, symbiotic cyanobacterium |journal = Photosynthesis Research |volume = 70 |issue = 1 |pages = 85–106 |year = 2001 |pmid = 16228364 |doi = 10.1023/A:1013840025518 |s2cid = 8752382 }} [244] => |- [245] => |[[Bacterium]] [246] => |''[[Solibacter usitatus]]'' (strain Ellin 6076) [247] => |align="right"|9,970,000 [248] => |10 MB [249] => | [250] => |{{cite journal |vauthors = Challacombe JF, Eichorst SA, Hauser L, Land M, Xie G, Kuske CR |title = Biological consequences of ancient gene acquisition and duplication in the large genome of Candidatus Solibacter usitatus Ellin6076 |journal = PLOS ONE|volume = 6 |issue = 9 |page = e24882 |date = 15 September 2011 |pmid = 21949776 |pmc = 3174227 |doi = 10.1371/journal.pone.0024882 |editor1-last = Steinke |bibcode = 2011PLoSO...624882C |editor1-first = Dirk |doi-access = free }} [251] => |- [252] => |[[Amoeboid]] [253] => |''[[Polychaos dubium]]'' (''"Amoeba" dubia'') [254] => |align="right"|670,000,000,000 [255] => |670 GB [256] => | [257] => |Largest known genome.{{cite journal |vauthors = Parfrey LW, Lahr DJ, Katz LA |title = The dynamic nature of eukaryotic genomes |journal = Molecular Biology and Evolution |volume = 25 |issue = 4 |pages = 787–94 |date = April 2008 |pmid = 18258610 |pmc = 2933061 |doi = 10.1093/molbev/msn032 }} (Disputed)[http://news.sciencemag.org/sciencenow/2010/10/scienceshot-biggest-genome-ever.html ScienceShot: Biggest Genome Ever] {{webarchive|url=https://web.archive.org/web/20101011155609/http://news.sciencemag.org/sciencenow/2010/10/scienceshot-biggest-genome-ever.html |date=11 October 2010 }}, comments: "The measurement for Amoeba dubia and other protozoa which have been reported to have very large genomes were made in the 1960s using a rough biochemical approach which is now considered to be an unreliable method for accurate genome size determinations." [258] => |- [259] => |[[Plant]] [260] => |''[[Genlisea tuberosa]]'' [261] => |align="right"|61,000,000 [262] => |61 MB [263] => | [264] => |Smallest recorded [[flowering plant]] genome, 2014{{cite journal |vauthors = Fleischmann A, Michael TP, Rivadavia F, Sousa A, Wang W, Temsch EM, Greilhuber J, Müller KF, Heubl G |title = Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms |journal = Annals of Botany |volume = 114 |issue = 8 |pages = 1651–63 |date = December 2014 |pmid = 25274549 |pmc = 4649684 |doi = 10.1093/aob/mcu189 }} [265] => |- [266] => |[[Plant]] [267] => |''[[Arabidopsis thaliana]]'' [268] => |align="right"|135,000,000{{cite web |title = Genome Assembly |url = https://www.arabidopsis.org/portals/genAnnotation/gene_structural_annotation/agicomplete.jsp |work = The Arabidopsis Information Resource (TAIR) }} [269] => |135 MB [270] => |27,655{{cite web|url=http://plants.ensembl.org/Arabidopsis_thaliana/Info/Annotation/|title=Details - Arabidopsis thaliana - Ensembl Genomes 40|website=plants.ensembl.org}} [271] => |First plant genome sequenced, December 2000{{cite journal |vauthors = Greilhuber J, Borsch T, Müller K, Worberg A, Porembski S, Barthlott W |title = Smallest angiosperm genomes found in lentibulariaceae, with chromosomes of bacterial size |journal = Plant Biology |volume = 8 |issue = 6 |pages = 770–77 |date = November 2006 |pmid = 17203433 |doi = 10.1055/s-2006-924101 |bibcode = 2006PlBio...8..770G |s2cid = 260252929 }} [272] => |- [273] => |[[Plant]] [274] => |''[[Populus|Populus trichocarpa]]'' [275] => |align="right"|480,000,000 [276] => |480 MB [277] => |73,013 [278] => |First tree genome sequenced, September 2006{{cite journal |vauthors = Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D |display-authors = 6 |title = The genome of black cottonwood, Populus trichocarpa (Torr. & Gray) |journal = Science |volume = 313 |issue = 5793 |pages = 1596–604 |date = September 2006 |pmid = 16973872 |doi = 10.1126/science.1128691 |bibcode = 2006Sci...313.1596T |osti = 901819 |s2cid = 7717980 |url = https://digital.library.unt.edu/ark:/67531/metadc883930/m2/1/high_res_d/901819.pdf }} [279] => |- [280] => |[[Plant]] [281] => |''[[Pinus taeda]]'' (Loblolly pine) [282] => |align="right"|22,180,000,000 [283] => |22.18 GB [284] => |50,172 [285] => |[[Gymnosperm]]s generally have much larger genomes than [[angiosperm]]s{{cite journal|last1=Zimin|first1=Aleksey|last2=Stevens|first2=Kristian|display-authors=etal|title=Sequencing and Assembly of the 22-Gb Loblolly Pine Genome|journal=Genetics|date=Mar 2014|volume=196|issue=3|pages=875–890|doi=10.1534/genetics.113.159715|pmid=24653210|pmc=3948813 }}{{cite journal|last=Neale|first=David B|display-authors=etal|title=Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies|journal=Genome Biology|date=Mar 2014|volume=15|issue=3|pages=R59|doi=10.1186/gb-2014-15-3-r59|pmid=24647006|pmc=4053751 |doi-access=free }} [286] => |- [287] => |[[Plant]] [288] => |''[[Fritillaria assyriaca]]'' [289] => |align="right"|130,000,000,000 [290] => |130 GB [291] => | [292] => | [293] => |- [294] => |[[Plant]] [295] => |''[[Paris japonica]]'' (Japanese-native, order [[Liliales]]) [296] => |align="right"|150,000,000,000 [297] => |150 GB [298] => | [299] => |Largest plant genome known{{cite journal |last1 = Pellicer |first1 = Jaume |last2 = Fay |first2 = Michael F. |last3 = Leitch |first3 = Ilia J. |name-list-style = vanc |title=The largest eukaryotic genome of them all?|journal=Botanical Journal of the Linnean Society|date=15 September 2010|volume=164|issue=1|pages=10–15|doi=10.1111/j.1095-8339.2010.01072.x|doi-access=free}} [300] => |- [301] => |[[Plant]] – [[moss]] [302] => |''[[Physcomitrella patens]]'' [303] => |align="right"|480,000,000 [304] => |480 MB [305] => | [306] => |First genome of a [[bryophyte]] sequenced, January 2008{{cite journal |vauthors = Lang D, Zimmer AD, Rensing SA, Reski R |title = Exploring plant biodiversity: the Physcomitrella genome and beyond |journal = Trends in Plant Science |volume = 13 |issue = 10 |pages = 542–49 |date = October 2008 |pmid = 18762443 |doi = 10.1016/j.tplants.2008.07.002 }} [307] => |- [308] => |[[Fungus]] – [[yeast]] [309] => |''[[Saccharomyces cerevisiae]]'' [310] => |align="right"|12,100,000 [311] => |12.1 MB [312] => |6,294 [313] => |First eukaryotic genome sequenced, 1996{{cite web|url=http://www.yeastgenome.org/ |title=Saccharomyces Genome Database |publisher=Yeastgenome.org |access-date=27 January 2011}} [314] => |- [315] => |[[Fungus]] [316] => |''[[Aspergillus nidulans]]'' [317] => |align="right"|30,000,000 [318] => |30 MB [319] => |9,541 [320] => |{{cite journal |vauthors = Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Baştürkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D'Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Peñalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren BW |display-authors = 6 |title = Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae |journal = Nature |volume = 438 |issue = 7071 |pages = 1105–15 |date = December 2005 |pmid = 16372000 |doi = 10.1038/nature04341 |bibcode = 2005Natur.438.1105G |doi-access = free }} [321] => |- [322] => |[[Nematoda|Nematode]] [323] => |''[[Pratylenchus coffeae]]'' [324] => |align="right"|20,000,000 [325] => |20 MB [326] => | [327] => |{{cite journal |vauthors = Leroy S, Bouamer S, Morand S, Fargette M |year = 2007 |title = Genome size of plant-parasitic nematodes |journal = Nematology |volume = 9 |issue = 3|pages = 449–50 |doi=10.1163/156854107781352089}} Smallest animal genome known{{cite web |vauthors = Gregory TR |date=2005 |title=Animal Genome Size Database |publisher= Gregory, T.R. (2016). Animal Genome Size Database. |url=http://www.genomesize.com/statistics.php?stats=entire#stats_top}} [328] => |- [329] => |[[Nematoda|Nematode]] [330] => |''[[Caenorhabditis elegans]]'' [331] => |align="right"|100,300,000 [332] => |100 MB [333] => |19,000 [334] => |First multicellular animal genome sequenced, December 1998{{cite journal |author = The ''C. elegans'' Sequencing Consortium |s2cid = 16873716 |title = Genome sequence of the nematode C. elegans: a platform for investigating biology |journal = Science |volume = 282 |issue = 5396 |pages = 2012–18 |date = December 1998 |pmid = 9851916 |doi = 10.1126/science.282.5396.2012 |bibcode = 1998Sci...282.2012. }} [335] => |- [336] => |[[Insect]] [337] => |''[[Belgica antarctica]]'' (Antarctic midge) [338] => |align="right"|99,000,000 [339] => |99 MB [340] => | [341] => |Smallest insect genome sequenced thus far, likely an adaptation to an extreme environment{{Cite journal |last1=Kelley |first1=Joanna L. |last2=Peyton |first2=Justin T. |last3=Fiston-Lavier |first3=Anna-Sophie |last4=Teets |first4=Nicholas M. |last5=Yee |first5=Muh-Ching |last6=Johnston |first6=J. Spencer |last7=Bustamante |first7=Carlos D. |last8=Lee |first8=Richard E. |last9=Denlinger |first9=David L. |date=2014-08-12 |title=Compact genome of the Antarctic midge is likely an adaptation to an extreme environment |journal=Nature Communications |volume=5 |pages=4611 |doi=10.1038/ncomms5611 |issn=2041-1723 |pmc=4164542 |pmid=25118180|bibcode=2014NatCo...5.4611K }} [342] => |- [343] => |[[Insect]] [344] => |''[[Drosophila melanogaster]]'' (fruit fly) [345] => |align="right"|175,000,000 [346] => |175 MB [347] => |13,600 [348] => |Size variation based on strain (175–180 Mb; standard ''y w'' strain is 175 Mb){{cite journal |vauthors = Ellis LL, Huang W, Quinn AM, Ahuja A, Alfrejd B, Gomez FE, Hjelmen CE, Moore KL, Mackay TF, Johnston JS, Tarone AM |title = Intrapopulation genome size variation in D. melanogaster reflects life history variation and plasticity |journal = PLOS Genetics |volume = 10 |issue = 7 |page = e1004522 |date = July 2014 |pmid = 25057905 |pmc = 4109859 |doi = 10.1371/journal.pgen.1004522 |doi-access = free }} [349] => |- [350] => |[[Insect]] [351] => |''[[Apis mellifera]]'' (honey bee) [352] => |align="right"|236,000,000 [353] => |236 MB [354] => |10,157 [355] => |{{cite journal |author = Honeybee Genome Sequencing Consortium |title = Insights into social insects from the genome of the honeybee Apis mellifera |journal = Nature |volume = 443 |issue = 7114 |pages = 931–49 |date = October 2006 |pmid = 17073008 |pmc = 2048586 |doi = 10.1038/nature05260 |bibcode = 2006Natur.443..931T }} [356] => |- [357] => |[[Insect]] [358] => |''[[Bombyx mori]]'' (silk moth) [359] => |align="right"|432,000,000 [360] => |432 MB [361] => |14,623 [362] => |14,623 predicted genes{{cite journal |title = The genome of a lepidopteran model insect, the silkworm Bombyx mori |journal = Insect Biochemistry and Molecular Biology |volume = 38 |issue = 12 |pages = 1036–45 |date = December 2008 |pmid = 19121390 |doi = 10.1016/j.ibmb.2008.11.004 |last1 = The International Silkworm Genome }} [363] => |- [364] => |[[Insect]] [365] => |''[[Solenopsis invicta]]'' (fire ant) [366] => |align="right"|480,000,000 [367] => |480 MB [368] => |16,569 [369] => |{{cite journal |vauthors = Wurm Y, Wang J, Riba-Grognuz O, Corona M, Nygaard S, Hunt BG, Ingram KK, Falquet L, Nipitwattanaphon M, Gotzek D, Dijkstra MB, Oettler J, Comtesse F, Shih CJ, Wu WJ, Yang CC, Thomas J, Beaudoing E, Pradervand S, Flegel V, Cook ED, Fabbretti R, Stockinger H, Long L, Farmerie WG, Oakey J, Boomsma JJ, Pamilo P, Yi SV, Heinze J, Goodisman MA, Farinelli L, Harshman K, Hulo N, Cerutti L, Xenarios I, Shoemaker D, Keller L |display-authors = 6 |title = The genome of the fire ant Solenopsis invicta |journal = Proceedings of the National Academy of Sciences of the United States of America |volume = 108 |issue = 14 |pages = 5679–84 |date = April 2011 |pmid = 21282665 |pmc = 3078418 |doi = 10.1073/pnas.1009690108 |bibcode = 2011PNAS..108.5679W |doi-access = free }} [370] => |- [371] => |[[Crustacean]] [372] => |[[Antarctic krill]] [373] => |48,010,000,000 [374] => |48 GB [375] => |23,000 [376] => |70-92% repetitive DNA{{Cite journal |last1=Shao |first1=Changwei |last2=Sun |first2=Shuai |last3=Liu |first3=Kaiqiang |last4=Wang |first4=Jiahao |last5=Li |first5=Shuo |last6=Liu |first6=Qun |last7=Deagle |first7=Bruce E. |last8=Seim |first8=Inge |last9=Biscontin |first9=Alberto |last10=Wang |first10=Qian |last11=Liu |first11=Xin |last12=Kawaguchi |first12=So |last13=Liu |first13=Yalin |last14=Jarman |first14=Simon |last15=Wang |first15=Yue |date=2023-03-16 |title=The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights |journal=Cell Glish |volume=186 |issue=6 |pages=1279–1294.e19 |doi=10.1016/j.cell.2023.02.005 |issn=0092-8674 |pmid=36868220|s2cid=257286259 |doi-access=free |hdl=11577/3472081 |hdl-access=free }} [377] => |- [378] => |[[Amphibian]] [379] => |''[[Neuse River waterdog]]'' [380] => |align="right"|118,000,000,000 [381] => |118 GB [382] => | [383] => |Largest tetrapod genome sequenced as of 2022{{cite web |title=Junk DNA Deforms Salamander Bodies |website=[[Scientific American]] |date=February 2022 |archive-url=https://web.archive.org/web/20230522140405/https://www.scientificamerican.com/article/junk-dna-deforms-salamander-bodies/ |archive-date=2023-05-22 |url-status=live |url=https://www.scientificamerican.com/article/junk-dna-deforms-salamander-bodies/}} [384] => |- [385] => |[[Amphibian]] [386] => |''[[Ornate burrowing frog]]'' [387] => |align="right"|1,060,000,000 [388] => |1.06 GB [389] => | [390] => |Smallest known frog genome[https://www.pnas.org/doi/10.1073/pnas.2011649118 A bird-like genome from a frog - PNAS] [391] => |- [392] => |[[Mammal]] [393] => |''[[Mus musculus]]'' [394] => |align="right"|2,700,000,000 [395] => |2.7 GB [396] => |20,210 [397] => |{{cite journal |vauthors = Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, Bult CJ, Agarwala R, Cherry JL, DiCuccio M, Hlavina W, Kapustin Y, Meric P, Maglott D, Birtle Z, Marques AC, Graves T, Zhou S, Teague B, Potamousis K, Churas C, Place M, Herschleb J, Runnheim R, Forrest D, Amos-Landgraf J, Schwartz DC, Cheng Z, Lindblad-Toh K, Eichler EE, Ponting CP |display-authors = 6 |title = Lineage-specific biology revealed by a finished genome assembly of the mouse |journal = PLOS Biology |volume = 7 |issue = 5 |page = e1000112 |date = May 2009 |pmid = 19468303 |pmc = 2680341 |doi = 10.1371/journal.pbio.1000112 |editor1-last = Roberts |editor1-first = Richard J |doi-access = free }} [398] => |- [399] => |[[Mammal]] [400] => |''[[Pan paniscus]]'' [401] => |align="right"|3,286,640,000 [402] => |3.3 GB [403] => |20,000 [404] => |Bonobo – estimated genome size 3.29 billion bp{{cite web|url=https://www.ncbi.nlm.nih.gov/genome/10729 |title=Pan paniscus (pygmy chimpanzee) |publisher=nih.gov |access-date=30 June 2016 }} [405] => |- [406] => |[[Mammal]] [407] => |''[[Homo sapiens]]'' [408] => |align="right"|3,117,000,000 [409] => |3.1 GB [410] => |20,000 [411] => |''Homo sapiens'' genome size estimated at 3.12 Gbp in 2022 [412] => Initial sequencing and analysis of the human genome{{cite journal |vauthors = Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X |display-authors = 6 |title = The sequence of the human genome |journal = Science |volume = 291 |issue = 5507 |pages = 1304–51 |date = February 2001 |pmid = 11181995 |doi = 10.1126/science.1058040 |bibcode = 2001Sci...291.1304V |author-link1 = Craig Venter |doi-access = free }} [413] => |- [414] => |[[Bird]] [415] => |''[[Red junglefowl|Gallus gallus]]'' [416] => |align="right"|1,043,000,000 [417] => |1.0 GB [418] => |20,000 [419] => |{{Cite journal|date=December 2004|title=Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution|journal=Nature|volume=432|issue=7018|pages=695–716|doi=10.1038/nature03154|pmid=15592404|issn=0028-0836|author1=International Chicken Genome Sequencing Consortium|bibcode=2004Natur.432..695C|doi-access=free}} [420] => |- [421] => |[[Fish]] [422] => |''[[Tetraodon nigroviridis]]'' (type of puffer fish) [423] => |align="right"|385,000,000 [424] => |390 MB [425] => | [426] => |Smallest vertebrate genome known, estimated to be 340 Mb{{cite journal |vauthors = Roest Crollius H, Jaillon O, Dasilva C, Ozouf-Costaz C, Fizames C, Fischer C, Bouneau L, Billault A, Quetier F, Saurin W, Bernot A, Weissenbach J |title = Characterization and repeat analysis of the compact genome of the freshwater pufferfish Tetraodon nigroviridis |journal = Genome Research |volume = 10 |issue = 7 |pages = 939–49 |date = July 2000 |pmid = 10899143 |pmc = 310905 |doi = 10.1101/gr.10.7.939 }}{{cite journal |vauthors = Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biémont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigó R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quétier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Roest Crollius H |display-authors = 6 |title = Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype |journal = Nature |volume = 431 |issue = 7011 |pages = 946–57 |date = October 2004 |pmid = 15496914 |doi = 10.1038/nature03025 |bibcode = 2004Natur.431..946J |doi-access = free }} – 385 Mb{{cite web|title=Tetraodon Project Information|url=http://www.broadinstitute.org/annotation/tetraodon/background.html|access-date=17 October 2012|url-status=dead|archive-url=https://web.archive.org/web/20120926160058/http://www.broadinstitute.org/annotation/tetraodon/background.html|archive-date=26 September 2012}} [427] => |- [428] => |[[Fish]] [429] => |''[[Protopterus aethiopicus]]'' (marbled lungfish) [430] => |align="right"|130,000,000,000 [431] => |130 GB [432] => | [433] => |Largest vertebrate genome known [434] => |} [435] => [436] => == Genomic alterations == [437] => 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.{{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 }} 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. [438] => [439] => 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. [440] => [441] => === Genome-wide reprogramming === [442] => 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.{{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 }} 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]].{{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 }} [443] => [444] => == Genome evolution == [445] => 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). [446] => [447] => [[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. [448] => [449] => [[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. [450] => [451] => == In fiction == [452] => Works of science fiction illustrate concerns about the availability of genome sequences. [453] => [454] => 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. [455] => [456] => 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.{{cite web |title = Gattaca (movie) |url = https://www.rottentomatoes.com/m/gattaca/ |work = Rotten Tomatoes |date = 24 October 1997 }} [457] => [458] => == See also == [459] => {{col div|colwidth=20em}} [460] => * [[Bacterial genome size]] [461] => * [[Cryoconservation of animal genetic resources]] [462] => * [[UCSC Genome Browser|Genome Browser]] [463] => * [[Genome Compiler]] [464] => * [[Circuit topology|Genome topology]] [465] => * [[Genome-wide association study]] [466] => * [[List of sequenced animal genomes]] [467] => * [[List of sequenced archaeal genomes]] [468] => * [[List of sequenced bacterial genomes]] [469] => * [[List of sequenced eukaryotic genomes]] [470] => * [[List of sequenced fungi genomes]] [471] => * [[List of sequenced plant genomes]] [472] => * [[List of sequenced plastomes]] [473] => * [[List of sequenced protist genomes]] [474] => * [[Metagenomics]] [475] => * [[Microbiome]] [476] => * [[Molecular epidemiology]] [477] => * [[Molecular pathological epidemiology]] [478] => * [[Molecular pathology]] [479] => * [[Nucleic acid sequence]] [480] => * [[Pan-genome]] [481] => * [[Precision medicine]] [482] => * [[Regulator gene]] [483] => * [[Whole genome sequencing]] [484] => {{_colend}} [485] => [486] => == References == [487] => {{reflist}} [488] => [489] => == Further reading == [490] => * {{cite book |vauthors = Benfey P, Protopapas AD|title=Essentials of Genomics|publisher=Prentice Hall|date=2004}} [491] => * {{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 }} [492] => * {{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}} [493] => * {{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 }} [494] => * {{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}} [495] => * {{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 }} [496] => * {{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 }} [497] => [498] => == External links == [499] => {{wikiquote}} [500] => * [http://genome.ucsc.edu UCSC Genome Browser] – view the genome and annotations for more than 80 organisms. [501] => * [https://web.archive.org/web/20130809102814/http://www.genomecenter.howard.edu/ genomecenter.howard.edu] (archived 9 August 2013) [502] => * [https://web.archive.org/web/20100609223959/http://learn.genetics.utah.edu/content/begin/dna/builddna/ Build a DNA Molecule] (archived 9 June 2010) [503] => * [http://www.genomenewsnetwork.org/articles/02_01/Sizing_genomes.shtml Some comparative genome sizes] [504] => * [http://www.dnai.org/ DNA Interactive: The History of DNA Science] [505] => * [http://www.dnaftb.org/ DNA From The Beginning] [506] => * [http://www.genome.gov/10001772 All About The Human Genome Project]—from Genome.gov [507] => * [http://www.genomesize.com/ Animal genome size database] [508] => * [https://web.archive.org/web/20050901105257/http://www.rbgkew.org.uk/cval/homepage.html Plant genome size database] (archived 1 September 2005) [509] => * [http://www.genomesonline.org/ GOLD:Genomes OnLine Database] [510] => * [http://www.genomenewsnetwork.org/ The Genome News Network] [511] => * [https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj NCBI Entrez Genome Project database] [512] => * [https://www.ncbi.nlm.nih.gov/About/primer/genetics_genome.html NCBI Genome Primer] [513] => * [https://www.genecards.org/ GeneCards]—an integrated database of human genes [514] => * [http://news.bbc.co.uk/1/hi/sci/tech/4994088.stm BBC News – Final genome 'chapter' published] [515] => * [http://img.jgi.doe.gov/ IMG] (The Integrated Microbial Genomes system)—for genome analysis by the DOE-JGI [516] => * [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) [517] => [518] => {{Genetics}} [519] => {{Genomics}} [520] => {{Self-replicating organic structures}} [521] => [522] => {{Authority control}} [523] => [524] => {{Portal bar|Astronomy|Biology|Evolutionary biology|Paleontology|Science}} [525] => [526] => [[Category:Genetic mapping]] [527] => [[Category:Genomics]] [528] => [[ur:موراثہ]] [] => )
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Genome

The Wikipedia page for "Genome" provides a comprehensive overview of what a genome is, its structure, function, and significance. A genome refers to the complete set of genetic instructions present in the DNA of an organism.

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A genome refers to the complete set of genetic instructions present in the DNA of an organism. It consists of genes, along with non-coding sequences, which hold information necessary for various biological processes. The page details the structure of a genome and mentions that it can be organized into different levels, including chromosomes, genes, and nucleotides. It also explores the concept of a haploid genome, which contains a single set of chromosomes, and a diploid genome, which contains two sets of chromosomes. The functions of the genome are explained, including coding for proteins, regulating gene expression, and determining the physical characteristics and traits of an organism. The page further discusses the concept of gene expression and explores how alterations in the genome contribute to the development of various diseases. The significance of understanding genomes in various fields, such as medicine, agriculture, and evolutionary biology, is also highlighted. Genetic sequencing techniques, such as Sanger sequencing and next-generation sequencing, are discussed as crucial tools in studying genomes. In addition, the page provides examples of various genome projects, such as the Human Genome Project, which sought to sequence and map the entire human genome. It also mentions the importance of comparative genomics, which involves comparing different genomes to identify similarities, differences, and evolutionary relationships between species. Overall, the Wikipedia page for "Genome" serves as a valuable resource for gaining a comprehensive understanding of the structure, function, and significance of genomes in the field of genetics.

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