For a non-technical introduction to the topic, see Introduction to genetics.
For other uses, see Genome (disambiguation).
The study of the genome is called genomics.
Origin of term
However, see omics for a more thorough discussion.
Sequencing and mapping
Further information: Genome project
Within a species, the vast majority of nucleotides are identical between individuals, but sequencing multiple individuals is necessary to understand the genetic diversity.
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 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 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.
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.
Reference genome sequences and maps continue to be updated, removing errors and clarifying regions of high allelic complexity.
The decreasing cost of genomic mapping has permitted genealogical sites to offer it as a service, to the extent that one may submit one's genome to crowdsourced scientific endeavours such as DNA.LAND at the New York Genome Center, an example both of the economies of scale and of citizen science.
Viral genomes can be composed of either RNA or DNA.
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.There are also viral RNA called single stranded RNA: serves as template for mRNA synthesis and single stranded RNA: serves as template for DNA synthesis.
Viral envelope is a outer layer of membrane that viral genomes use to enter the host cell.
Some of the classes of viral DNA and RNA consists of a viral envelope while some do not.
|Single-stranded RNA: Serves as template for mRNA synthesis|
|Single-stranded RNA: serves as template for DNA synthesis|
Prokaryotes and eukaryotes have DNA genomes.
Archaea and most bacteria have a single circular chromosome, however, some bacterial species have linear or multiple chromosomes.
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.
Some bacteria have auxiliary genetic material, also part of their genome, which is carried in plasmids.
For this, the word genome should not be used as a synonym of chromosome.
See also: Eukaryotic chromosome fine structure
Eukaryotic genomes are composed of one or more linear DNA chromosomes.
Gametes, such as ova, sperm, spores, and pollen, are haploid, meaning they carry only one copy of each chromosome.
Mitochondria are sometimes said to have their own genome often referred to as the "mitochondrial genome".
The DNA found within the chloroplast may be referred to as the "plastome".
Like the bacteria they originated from, mitochondria and chloroplasts have a circular chromosome.
Unlike prokaryotes, 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.
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.
Main article: Non-coding DNA
See also: Intergenic region
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 in the genome: tandem repeats and interspersed repeats.
Short, non-coding sequences that are repeated head-to-tail are called tandem repeats.
Microsatellites consisting of 2-5 basepair repeats, while minisatellite repeats are 30-35 bp.
Tandem repeats make up about 4% of the human genome and 9% of the fruit fly genome.
Tandem 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.
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.
Tandem repeats are usually caused by slippage during replication, unequal crossing-over and gene conversion.
Transposable elements (TEs) are sequences of DNA with a defined structure that are able to change their location in the genome.
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.
Retrotransposons are found mostly in eukaryotes but not found in prokaryotes and retrotransposons form a large portion of genomes of many eukaryotes.
Retrotransposon is a transposable element that transpose through an RNA intermediate.
Retrotransposons 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.
Retrotransposons that carry reverse transcriptase in their gene can trigger its own transposition but the genes that lack the reverse transcriptase must use reverse transcriptase synthesized by another retrotransposon.
Retrotransposons can be transcribed into RNA, which are then duplicated at another site into the genome.
Retrotransposons can be divided into long terminal repeats (LTRs) and non-long terminal repeats (Non-LTRs).
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.
In Dictyostelium discoideum, there is another DIRS-like elements belong to Non-LTRs.
Non-LTRs are widely spread in eukaryotic genomes.
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.
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.
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.
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.
This cut-and-paste mechanism typically reinserts transposons near their original location (within 100kb).
DNA transposons are found in bacteria and make up 3% of the human genome and 12% of the genome of the roundworm C. . elegans
Genome size is the total number of DNA base pairs in one copy of a haploid genome.
Genome size varies widely across species.
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.
Genome size is largely a function of the expansion and contraction of repetitive DNA elements.
Since genomes are very complex, one research strategy is to reduce the number of genes in a genome to the bare minimum and still have the organism in question survive.
There is experimental work being done on minimal genomes for single cell organisms as well as minimal genomes for multi-cellular organisms (see Developmental biology).
Here is a table of some significant or representative genomes.
See #See also for lists of sequenced genomes.
|Organism type||Organism||Genome size||Approx. no. of genes||Note|
|Virus||Porcine circovirus type 1||1,759||1.8kb||Smallest viruses replicating autonomously in eukaryotic cells.|
|Virus||Bacteriophage MS2||3,569||3.5kb||First sequenced RNA-genome|
|Virus||Phage Φ-X174||5,386||5.4kb||First sequenced DNA-genome|
|Virus||Phage λ||48,502||48.5kb||Often used as a vector for the cloning of recombinant DNA.|
|Virus||Megavirus||1,259,197||1.3Mb||Until 2013 the largest known viral genome.|
|Virus||Pandoravirus salinus||2,470,000||2.47Mb||Largest known viral genome.|
|Eukaryotic organelle||Human mitochondrion||16,569||16.6kb|
|Bacterium||Nasuia deltocephalinicola (strain NAS-ALF)||112,091||112kb||137||Smallest known non-viral genome. Symbiont of leafhoppers.|
|Bacterium||Carsonella ruddii||159,662||160kb||An endosymbiont of psyllid insects|
|Bacterium||Buchnera aphidicola||600,000||600kb||An endosymbiont of aphids|
|Bacterium||Wigglesworthia glossinidia||700,000||700Kb||A symbiont in the gut of the tsetse fly|
|Bacterium – cyanobacterium||Prochlorococcus spp. (1.7 Mb)||1,700,000||1.7Mb||1,884||Smallest known cyanobacterium genome. One of the primary photosynthesizers on Earth.|
|Bacterium||Haemophilus influenzae||1,830,000||1.8Mb||First genome of a living organism sequenced, July 1995|
|Bacterium – cyanobacterium||Nostoc punctiforme||9,000,000||9Mb||7,432||7432 open reading frames|
|Bacterium||Solibacter usitatus (strain Ellin 6076)||9,970,000||10Mb|
|Amoeboid||Polychaos dubium ("Amoeba" dubia)||670,000,000,000||670Gb||Largest known genome. (Disputed)|
|Plant||Genlisea tuberosa||61,000,000||61Mb||Smallest recorded flowering plant genome, 2014.|
|Plant||Arabidopsis thaliana||135,000,000||135 Mb||27,655||First plant genome sequenced, December 2000.|
|Plant||Populus trichocarpa||480,000,000||480Mb||73,013||First tree genome sequenced, September 2006|
|Plant||Paris japonica (Japanese-native, pale-petal)||150,000,000,000||150Gb||Largest plant genome known|
|Plant – moss||Physcomitrella patens||480,000,000||480Mb||First genome of a bryophyte sequenced, January 2008.|
|Fungus – yeast||Saccharomyces cerevisiae||12,100,000||12.1Mb||6,294||First eukaryotic genome sequenced, 1996|
|Nematode||Pratylenchus coffeae||20,000,000||20Mb||Smallest animal genome known|
|Nematode||Caenorhabditis elegans||100,300,000||100Mb||19,000||First multicellular animal genome sequenced, December 1998|
|Insect||Drosophila melanogaster (fruit fly)||175,000,000||175Mb||13,600||Size variation based on strain (175-180Mb; standard y w strain is 175Mb)|
|Insect||Apis mellifera (honey bee)||236,000,000||236Mb||10,157|
|Insect||Bombyx mori (silk moth)||432,000,000||432Mb||14,623||14,623 predicted genes|
|Insect||Solenopsis invicta (fire ant)||480,000,000||480Mb||16,569|
|Mammal||Pan paniscus||3,286,640,000||3.3Gb||20,000||Bonobo - estimated genome size 3.29 billion bp|
|Mammal||Homo sapiens||3,000,000,000||3Gb||20,000||Homo sapiens genome size estimated at 3.2 Gbp in 2001
Initial sequencing and analysis of the human genome
|Fish||Tetraodon nigroviridis (type of puffer fish)||385,000,000||390Mb||Smallest vertebrate genome known estimated to be 340 Mb – 385 Mb.|
|Fish||Protopterus aethiopicus (marbled lungfish)||130,000,000,000||130Gb||Largest vertebrate genome known|
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.
In certain lymphocytes in the human immune system, V(D)J recombination generates different genomic sequences such that each cell produces a unique antibody or T cell receptors.
During meiosis, diploid cells divide twice to produce haploid germ cells.
During this process, recombination results in a reshuffling of the genetic material from homologous chromosomes so each gamete has a unique genome.
This pathway is employed in the erasure of CpG methylation (5mC) in primordial germ cells.
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).
Duplications play a major role in shaping the genome.
Such duplications are probably fundamental to the creation of genetic novelty.
Horizontal gene transfer is invoked to explain how there is often an extreme similarity between small portions of the genomes of two organisms that are otherwise very distantly related.
Horizontal gene transfer seems to be common among many microbes.
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.
Works of science fiction illustrate concerns about the availability of genome sequences.
A geneticist extracts dinosaur DNA from the blood of ancient mosquitoes and fills in the gaps with DNA from modern species to create several species of dinosaurs.
A chaos theorist is asked to give his expert opinion on the safety of engineering an ecosystem with the dinosaurs, and he repeatedly warns that the outcomes of the project will be unpredictable and ultimately uncontrollable.
These warnings about the perils of using genomic information are a major theme of the book.
The 1997 film Gattaca is set in a futurist society where genomes of children are engineered to contain the most ideal combination of their parents' traits, and metrics such as risk of heart disease and predicted life expectancy are documented for each person based on their genome.
People conceived outside of the eugenics program, known as "In-Valids" suffer discrimination and are relegated to menial occupations.
The protagonist of the film is an In-Valid who works to defy the supposed genetic odds and achieve his dream of working as a space navigator.
The film warns against a future where genomic information fuels prejudice and extreme class differences between those who can and can't afford genetically engineered children.
Credits to the contents of this page go to the authors of the corresponding Wikipedia page: en.wikipedia.org/wiki/Genome.