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In terms of modern molecular biology and genetics, a genome is the genetic material of an organism. It consists of DNA
DNA
(or RNA
RNA
in RNA viruses). The genome includes both the genes (the coding regions) and the noncoding DNA,[1] as well as the genetic material of the mitochondria[2] and chloroplasts.

Contents

1 Non-technical overview 2 Origin of term 3 Sequencing
Sequencing
and mapping 4 Viral genomes 5 Prokaryotic genomes 6 Eukaryotic
Eukaryotic
genomes

6.1 Coding sequences 6.2 Noncoding sequences

6.2.1 Tandem repeats 6.2.2 Transposable elements

6.2.2.1 Retrotransposons 6.2.2.2 DNA
DNA
transposons

7 Genome
Genome
size 8 Genomic alterations 9 Genome
Genome
evolution 10 In fiction 11 See also 12 References 13 Further reading 14 External links

Non-technical overview[edit] A genome is all the genetic information of an organism. For example, the human genome is analogous to the instructions stored in a cookbook. Just as a cookbook gives the instructions needed to make a range of meals including a holiday feast or a summer picnic, the human genome contains all the instructions needed to make the full range of human cell types including muscle cells or neurons.

The book (genome) would contain 23 chapters (chromosomes); Each chapter contains 48 to 250 million letters (A,C,G,T) without spaces; Hence, the book contains over 3.2 billion letters total; The book contains approximately 20,000 different recipes (genes), which together make up less than 2% of the letters in the book; Most cells carry two copies of the book; These books fit into a cell nucleus the size of a pinpoint; In meiosis, the genetic material of gametes is divided in half to create egg and sperm cells, which have only one copy of the book.[3]

Origin of term[edit] The term genome was created in 1920 by Hans Winkler,[4] professor of botany at the University of Hamburg, Germany. The Oxford Dictionary suggests the name is a blend of the words gene and chromosome.[5] However, see omics for a more thorough discussion. A few related -ome words already existed—such as biome, rhizome, forming a vocabulary into which genome fits systematically.[6] Sequencing
Sequencing
and mapping[edit] Further information: Genome
Genome
project A genome sequence is the complete list of the nucleotides (A, C, G, and T for DNA
DNA
genomes) that make up all the chromosomes 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.

Part of DNA
DNA
sequence - prototypification of complete genome of virus

In 1976, Walter Fiers at the University of Ghent
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: Phage Φ-X174, of 5386 base pairs.[7] The first complete genome sequences among all three domains of life were released within a short period during the mid-1990s: The first bacterial genome to be sequenced was that of Haemophilus influenzae, completed by a team at The Institute for Genomic Research
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 archaeon, Methanococcus jannaschii, was completed in 1996, again by The Institute for Genomic Research. 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.[8] Among the thousands of completed genome sequencing projects include those for rice, a mouse, the plant Arabidopsis thaliana, the puffer fish, and the bacteria E. coli. In December 2013, scientists first sequenced the entire genome of a Neanderthal, an extinct species of humans. The genome was extracted from the toe bone of a 130,000-year-old Neanderthal
Neanderthal
found in a Siberian cave.[9][10] 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 full genome of James D. Watson, one of the co-discoverers of the structure of DNA.[11] Whereas a genome sequence lists the order of every DNA
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
Human Genome Project
was organized to map and to 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
Genoscope
in Paris.[12][13] Reference genome
Reference genome
sequences and maps continue to be updated, removing errors and clarifying regions of high allelic complexity.[14] The decreasing cost of genomic mapping has permitted genealogical sites to offer it as a service,[15] to the extent that one may submit one's genome to crowd sourced scientific endeavours such as DNA.LAND at the New York Genome
Genome
Center,[16] an example both of the economies of scale and of citizen science.[17] Viral genomes[edit] Viral genomes can be composed of either RNA
RNA
or DNA. The genomes of RNA viruses can be either single-stranded or double-stranded RNA, and may contain one or more separate RNA
RNA
molecules. DNA
DNA
viruses can have either single-stranded or double-stranded genomes. Most DNA
DNA
virus genomes are composed of a single, linear molecule of DNA, but some are made up of a circular DNA
DNA
molecule.[18] Prokaryotic genomes[edit] Prokaryotes and eukaryotes have DNA
DNA
genomes. Archaea
Archaea
have a single circular chromosome.[19] Most bacteria also have a single circular chromosome; however, some bacterial species have linear chromosomes[20] or multiple chromosomes.[21] If the DNA
DNA
is replicated faster than the bacterial cells divide, multiple copies of the chromosome can be present in a single cell. Most prokaryotes have very little repetitive DNA
DNA
in their genomes.[22] Some bacteria have auxiliary genetic material, which is carried in plasmids. Eukaryotic
Eukaryotic
genomes[edit] Eukaryotic
Eukaryotic
genomes are composed of one or more linear DNA
DNA
chromosomes. The number of chromosomes varies widely from Jack jumper ants and an asexual nemotode,[23] which each have only one pair, to a fern species that has 720 pairs.[24] A typical human cell has two copies of each of 22 autosomes, one inherited from each parent, plus two sex chromosomes, making it diploid. Gametes, 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
Mitochondria
are sometimes said to have their own genome often referred to as the "mitochondrial genome". The DNA
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, eukaryotes have exon-intron organization of protein coding genes and variable amounts of repetitive DNA. In mammals and plants, the majority of the genome is composed of repetitive DNA.[25] Coding sequences[edit] DNA
DNA
sequences that carry the instructions to make proteins are coding sequences. The proportion of the genome occupied by coding sequences varies widely. A bigger genome does not mean more genes, and the proportion of non-repetitive DNA
DNA
decreases along with increasing genome size in complex eukaryotes.[25] Most bacteria have little or no repetitive DNA, hence their typical protein coding capacity is in the range of 85-90%. However, some symbiotic bacteria (e.g. Serratia symbiotica) have reduced genomes and a high fraction of pseudogenes: only ~40% of their DNA
DNA
encodes proteins.[26][27] Simple eukaryotes such as C. elegans and fruit fly, possess more non-repetitive DNA
DNA
than repetitive DNA.[25][28] Higher eukaryotes tend to have more repetitive DNA
DNA
than non-repetitive ones.[29] In some plants and amphibians, the proportion of repetitive DNA
DNA
is more than 80%.[25] Similarly, only 2% of the human genome codes for proteins.

Composition of the human genome

Noncoding sequences[edit] Noncoding sequences include introns, 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
DNA
in the genome: tandem repeats and interspersed repeats.[30] Tandem repeats[edit] 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.[31] Tandom repeats can be functional. For example, telomeres 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 disease.[32] For example, the human gene huntingtin 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.[32] Tandem repeats are usually caused by slippage during replication, unequal crossing-over and gene conversion.[33] Transposable elements[edit] Transposable elements (TEs) are sequences of DNA
DNA
with a defined structure that are able to change their location in the genome.[31][22][34] TEs are categorized as either class I TEs, which replicate by a copy-and-paste mechanism, or class II TEs, which can be excised from the genome and inserted at a new location. 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.[35] Retrotransposons[edit] Retrotransposons can be transcribed into RNA, which are then duplicated at another site into the genome.[36] Retrotransposons can be divided into Long terminal repeats (LTRs) and Non-Long Terminal Repeats (Non-LTR).[35] 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.[34] 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.[37] Non-long terminal repeats (Non-LTRs) are classified as long interspersed elements (LINEs), short interspersed elements (SINEs), and Penelope-like elements. In Dictyostelium discoideum, there is another DIRS-like elements belong to Non-LTRs. Non-LTRs are widely spread in eukaryotic genomes.[38] 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.[39] 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.[40] The Alu element
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.[35] DNA
DNA
transposons[edit] DNA
DNA
transposons 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.[31] This cut-and-paste mechanism typically reinserts transposons near their original location (within 100kb).[35] DNA
DNA
transposons are found in bacteria and make up 3% of the human genome and 12% of the genome of the roundworm C. elegans.[35] Genome
Genome
size[edit]

Log-log
Log-log
plot of the total number of annotated proteins in genomes submitted to GenBank
GenBank
as a function of genome size.[41]

Genome size
Genome size
is the total number of DNA
DNA
base pairs in one copy of a haploid genome. In humans, the nuclear genome comprises approximately 3.2 billion nucleotides of DNA, divided into 24 linear molecules, the shortest 50 000 000 nucleotides in length and the longest 260 000 000 nucleotides, each contained in a different chromosome.[42] The genome size is positively correlated with the morphological complexity among prokaryotes and lower eukaryotes; however, after mollusks and all the other higher eukaryotes above, this correlation is no longer effective.[25][43] This phenomenon also indicates the mighty influence coming from repetitive DNA
DNA
on the genomes. 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.[44][45] Here is a table of some significant or representative genomes. See #See also for lists of sequenced genomes.

Organism type Organism Genome
Genome
size (base pairs) Approx. no. of genes Note

Virus Porcine circovirus
Porcine circovirus
type 1 1,759 1.8kb

Smallest viruses replicating autonomously in eukaryotic cells.[46]

Virus Bacteriophage MS2 3,569 3.5kb

First sequenced RNA-genome[47]

Virus SV40 5,224 5.2kb

[48]

Virus Phage Φ-X174 5,386 5.4kb

First sequenced DNA-genome[49]

Virus HIV 9,749 9.7kb

[50]

Virus Phage λ 48,502 48.5kb

Often used as a vector for the cloning of recombinant DNA. [51] [52] [53]

Virus Megavirus 1,259,197 1.3Mb

Until 2013 the largest known viral genome.[54]

Virus Pandoravirus salinus 2,470,000 2.47Mb

Largest known viral genome.[55]

Bacterium Nasuia deltocephalinicola (strain NAS-ALF) 112,091 112kb

Smallest non-viral genome.[56]

Bacterium Carsonella ruddii 159,662 160kb

Bacterium Buchnera aphidicola 600,000 600kb

[57]

Bacterium Wigglesworthia glossinidia 700,000 700Kb

Bacterium Haemophilus influenzae 1,830,000 1.8Mb

First genome of a living organism sequenced, July 1995[58]

Bacterium Escherichia coli 4,600,000 4.6Mb 4288 [59]

Bacterium Solibacter usitatus (strain Ellin 6076) 9,970,000 10Mb

[60]

Bacterium
Bacterium
– cyanobacterium Prochlorococcus spp. (1.7 Mb) 1,700,000 1.7Mb 1884 Smallest known cyanobacterium genome[61][62]

Bacterium
Bacterium
– cyanobacterium Nostoc punctiforme 9,000,000 9Mb 7432 7432 "open reading frames"[63]

Amoeboid Polychaos dubium ("Amoeba" dubia) 670,000,000,000 670Gb

Largest known genome.[64] (Disputed)[65]

Eukaryotic
Eukaryotic
organelle Human mitochondrion 16,569 16.6kb

[66]

Plant Genlisea tuberosa 61,000,000 61Mb

Smallest recorded flowering plant genome, 2014.[67]

Plant Arabidopsis thaliana 135,000,000[68] 135 Mb 27,655[69] First plant genome sequenced, December 2000.[70]

Plant Populus
Populus
trichocarpa 480,000,000 480Mb 73013 First tree genome sequenced, September 2006[71]

Plant Fritillaria assyrica 130,000,000,000 130Gb

Plant Paris japonica
Paris japonica
(Japanese-native, pale-petal) 150,000,000,000 150Gb

Largest plant genome known[72]

Plant
Plant
– moss Physcomitrella patens 480,000,000 480Mb

First genome of a bryophyte sequenced, January 2008.[73]

Fungus
Fungus
– yeast Saccharomyces cerevisiae 12,100,000 12.1Mb 6294 First eukaryotic genome sequenced, 1996[74]

Fungus Aspergillus nidulans 30,000,000 30Mb 9541 [75]

Nematode Pratylenchus coffeae 20,000,000 20Mb

[76] Smallest animal genome known[77]

Nematode Caenorhabditis elegans 100,300,000 100Mb 19000 First multicellular animal genome sequenced, December 1998[78]

Insect Drosophila melanogaster
Drosophila melanogaster
(fruit fly) 175,000,000 175Mb 13600 Size variation based on strain (175-180Mb; standard y w strain is 175Mb)[79]

Insect Apis mellifera
Apis mellifera
(honey bee) 236,000,000 236Mb 10157 [80])

Insect Bombyx mori
Bombyx mori
(silk moth) 432,000,000 432Mb 14623 14,623 predicted genes[81]

Insect Solenopsis invicta
Solenopsis invicta
(fire ant) 480,000,000 480Mb 16569 [82]

Mammal Mus musculus 2,700,000,000 2.7Gb 20210 [83]

Mammal Homo sapiens 3,289,000,000 3.3Gb 20000 Homo sapiens
Homo sapiens
estimated genome size 3.2 billion bp[84] Initial sequencing and analysis of the human genome[85]

Mammal Pan paniscus 3,286,640,000 3.3Gb 20000 Bonobo - estimated genome size 3.29 billion bp[86]

Fish Tetraodon nigroviridis
Tetraodon nigroviridis
(type of puffer fish) 385,000,000 390Mb

Smallest vertebrate genome known estimated to be 340 Mb[87][88] – 385 Mb.[89]

Fish Protopterus aethiopicus
Protopterus aethiopicus
(marbled lungfish) 130,000,000,000 130Gb

Largest vertebrate genome known

Genomic alterations[edit] 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
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.[90] In certain lymphocytes in the human immune system, V(D)J recombination
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
Genome
evolution[edit] Genomes are more than the sum of an organism's genes and have traits that may be measured and studied without reference to the details of any particular genes and their products. Researchers compare traits such as karyotype (chromosome number), genome size, gene order, codon usage bias, and GC-content
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). 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 entire genomes. Such duplications are probably fundamental to the creation of genetic novelty. Horizontal gene transfer
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 microbes. Also, eukaryotic cells seem to have experienced a transfer of some genetic material from their chloroplast and mitochondrial 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.[91] In fiction[edit] Works of science fiction illustrate concerns about the availability of genome sequences. Michael Crichton's 1990 novel Jurassic Park and the subsequent 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
DNA
from the blood of ancient mosquitoes and fills in the gaps with DNA
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
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 can't afford genetically engineered children.[92] See also[edit]

Bacterial genome size Cryoconservation of animal genetic resources Genome
Genome
Browser Genome
Genome
Compiler Genome
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 Sequenceome Whole genome sequencing

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Further reading[edit]

Benfey, P.; Protopapas, A.D. (2004). Essentials of Genomics. Prentice Hall.  Brown, Terence A. (2002). Genomes 2. Oxford: Bios Scientific Publishers. ISBN 978-1-85996-029-5.  Gibson, Greg; Muse, Spencer V. (2004). A Primer of Genome
Genome
Science (Second ed.). Sunderland, Mass: Sinauer Assoc. ISBN 0-87893-234-8.  Gregory (2005). T. Ryan, ed. The Evolution
Evolution
of the Genome. Elsevier. ISBN 0-12-301463-8.  Reece, Richard J. (2004). Analysis of Genes and Genomes. Chichester: John Wiley & Sons. ISBN 0-470-84379-9.  Saccone, Cecilia; Pesole, Graziano (2003). Handbook of Comparative Genomics. Chichester: John Wiley & Sons. ISBN 0-471-39128-X.  Werner, E. (2003). " In silico
In silico
multicellular systems biology and minimal genomes". Drug Discov Today. 8 (24): 1121–1127. doi:10.1016/S1359-6446(03)02918-0. PMID 14678738. 

External links[edit]

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