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In the fields of
molecular biology Molecular biology is the branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, P ...
and
genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, ...

genetics
, a genome is all genetic information of an organism. It consists of nucleotide sequences of
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

DNA
(or
RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large molecules, or macromolecules, composed of many Re ...

RNA
in
RNA virus An RNA virus is a virus A virus is a submicroscopic infectious agent In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processe ...
es). The genome includes both the
gene In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mecha ...

gene
s (the
coding region The coding region of a gene, also known as the CDS (from ''coding sequence''), is the portion of a gene's DNA or RNA that codes for protein. Studying the length, composition, regulation, splicing, structures, and functions of coding regions compare ...
s) and the
noncoding DNA Non-coding DNA sequences are components of an organism's DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of ...
, as well as
mitochondrial DNA Mitochondrial DNA (mtDNA or mDNA) is the DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five car ...

mitochondrial DNA
and
chloroplast DNA Chloroplast DNA (cpDNA) is the DNA located in chloroplasts, which are photosynthetic organelles located within the cells of some eukaryotic organisms. Chloroplasts, like other types of plastid The plastid (Greek: πλαστός; plastós: formed ...
. The study of the genome is called
genomics Genomics is an interdisciplinary field of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interact ...
. The genome for several organisms have been sequenced and genes analyzed, the human genome project which sequenced the entire genome for ''Homo sapiens'' was successfully complete
in April 2003


Origin of term

The term ''genome'' was created in 1920 by
Hans Winkler Hans Karl Albert Winkler (23 April 1877 – 22 November 1945) was a German botanist. He was Professor of Botany Botany, also called , plant biology or phytology, is the science Science (from the Latin word ''scientia'', meaning "kn ...
, professor of
botany Botany, also called , plant biology or phytology, is the science of plant life and a branch of biology. A botanist, plant scientist or phytologist is a scientist who specialises in this field. The term "botany" comes from the Ancient Greek wo ...

botany
at the
University of Hamburg The University of Hamburg (german: Universität Hamburg, also referred to as UHH) is a university in Hamburg, Germany. It was founded on 28 March 1919 by combining the previous General Lecture System ('':de:Allgemeines Vorlesungswesen, Allgemei ...
, Germany. The Oxford Dictionary suggests the name is a blend of the words ''
gene In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mecha ...

gene
'' and ''
chromosome A chromosome is a long DNA molecule with part or all of the genome, genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called histones which, aided by Chaperone (protein), chaperone proteins, bind to and ...

chromosome
''. However, see
omics The branches of science Science (from the Latin word ''scientia'', meaning "knowledge") is a systematic enterprise that Scientific method, builds and Taxonomy (general), organizes knowledge in the form of Testability, testable explanations ...
for a more thorough discussion. A few related ''-ome'' words already existed, such as ''
biome A biome is a collection of plants Plants are predominantly photosynthetic Photosynthesis is a process used by plants and other organisms to Energy transformation, convert light energy into chemical energy that, through cellular respi ...
'' and ''
rhizome In botany Botany, also called , plant biology or phytology, is the science of plant life and a branch of biology. A botanist, plant scientist or phytologist is a scientist who specialises in this field. The term "botany" comes from the A ...

rhizome
'', forming a vocabulary into which ''genome'' fits systematically.


Sequencing and mapping

A genome sequence is the complete list of the
nucleotide Nucleotides are organic molecules , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, ...

nucleotide
s (A, C, G, and T for DNA genomes) that make up all the
chromosome A chromosome is a long DNA molecule with part or all of the genome, genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called histones which, aided by Chaperone (protein), chaperone proteins, bind to and ...

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. In 1976,
Walter Fiers Walter Fiers (31 January 1931 in Ypres, West Flanders – 28 July 2019 in Destelbergen) was a Belgian molecular biologist. He obtained a degree of Engineer for Chemistry and Agricultural Industries at the University of Ghent in 1954, and star ...
at the
University of Ghent Ghent University ( nl, Universiteit Gent, abbreviated as UGent) is a public research university A university ( la, universitas, 'a whole') is an educational institution, institution of higher education, higher (or Tertiary education, tertiary) ...
(Belgium) was the first to establish the complete nucleotide sequence of a viral RNA-genome (
Bacteriophage MS2 ''Escherichia virus MS2'' is an icosahedral, positive-sense single-stranded RNA virus that infects the bacterium ''Escherichia coli'' and other members of the Enterobacteriaceae. MS2 is a member of a family of closely related bacterial viruses t ...
). The next year,
Fred Sanger Frederick Sanger (; 13 August 1918 – 19 November 2013) was a British biochemist who twice won the Nobel Prize in Chemistry, one of only two people to have done so in the same category (the other is John Bardeen in physics), the fourth pe ...
completed the first DNA-genome sequence: Phage Φ-X174, of 5386 base pairs. 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 ''Haemophilus influenzae'' (formerly called Pfeiffer's bacillus or ''Bacillus influenzae'') is a Gram-negative, Coccobacillus, coccobacillary, facultative anaerobic organism, facultatively anaerobic Capnophile, capnophilic pathogenic bacteriu ...

Haemophilus influenzae
, completed by a team at
The Institute for Genomic Research 200px, Educational Bus near J. Craig Venter Institute in Rockville, Maryland The J. Craig Venter Institute (JCVI) is a Non-profit organization, non-profit genomics research institute founded by Craig Venter, J. Craig Venter, Ph.D. ...
in 1995. A few months later, the first eukaryotic genome was completed, with sequences of the 16 chromosomes of budding yeast ''
Saccharomyces cerevisiae ''Saccharomyces cerevisiae'' () is a species of yeast Yeasts are eukaryotic Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are ...

Saccharomyces cerevisiae
'' published as the result of a European-led effort begun in the mid-1980s. The first genome sequence for an
archaeon Archaea ( ; singular archaeon ) constitute a domain Domain may refer to: Mathematics *Domain of a function, the set of input values for which the (total) function is defined **Domain of definition of a partial function **Natural domain of a pa ...

archaeon
, ''
Methanococcus jannaschii ''Methanocaldococcus jannaschii'' (formerly ''Methanococcus jannaschii'') is a thermophilic methanogen Methanogens are microorganisms that produce methane Methane ( or ) is a chemical compound with the chemical formula (one atom of carbon ...
'', 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 The National Institutes of Health (NIH) () is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late 1880s and is now part of the United States Department of Health an ...
maintains one of several comprehensive databases of genomic information. Among the thousands of completed genome sequencing projects include those for
rice Rice is the seed A seed is an embryonic ''Embryonic'' is the twelfth studio album by experimental rock band the Flaming Lips released on October 13, 2009, on Warner Bros. Records, Warner Bros. The band's first double album, it was relea ...

rice
, a
mouse A mouse, plural mice, is a small mammal Mammals (from Latin language, Latin , 'breast') are a group of vertebrate animals constituting the class (biology), class Mammalia (), and characterized by the presence of mammary glands which ...
, the plant ''
Arabidopsis thaliana ''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small flowering plant Flowering plants include multiple members of the clade Angiospermae (), commonly called angiosperms. The term "angiosperm" is derived from ...

Arabidopsis thaliana
'', the
puffer fish Tetraodontidae is a family In human society, family (from la, familia) is a group of people related either by consanguinity (by recognized birth) or affinity (by marriage or other relationship). The purpose of families is to maintain ...

puffer fish
, and the bacteria
E. coli
E. coli
. In December 2013, scientists first sequenced the entire ''genome'' of a
Neanderthal Neanderthals (, also Neandertals, ''Homo neanderthalensis'' or ''Homo sapiens neanderthalensis'') are an extinct species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an org ...
, an extinct species of
humans Humans (''Homo sapiens'') are the most abundant and widespread species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A speci ...
. The genome was extracted from the toe bone of a 130,000-year-old Neanderthal found in a Siberian cave. New sequencing technologies, such as
massive parallel sequencingMassive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes a ...
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
full genome
of James D. Watson, one of the co-discoverers of the structure of DNA. 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 The Human Genome Project (''HGP'') was an international scientific research The scientific method is an Empirical evidence, empirical method of acquiring knowledge that has characterized the development of science since at least the 17th cen ...
was organized to
map A map is a symbol A symbol is a mark, sign, or that indicates, signifies, or is understood as representing an , , or . Symbols allow people to go beyond what is n or seen by creating linkages between otherwise very different s and s. A ...
and to
sequence In mathematics Mathematics (from Greek: ) includes the study of such topics as numbers (arithmetic and number theory), formulas and related structures (algebra), shapes and spaces in which they are contained (geometry), and quantities and t ...

sequence
the
human genome The human genome is a complete set of nucleic acid sequence A nucleic acid sequence is a succession of bases signified by a series of a set of five different letters that indicate the order of nucleotides Nucleotides are organic molecules c ...

human genome
. A fundamental step in the project was the release of a detailed genomic map by
Jean Weissenbach Jean Weissenbach (born 13 February 1946) is a French biologist. He is the current director of the Genoscope. He is one of the pioneers of the DNA sequencing, sequencing and analysis of the genomes. Publications * * * * * * References

L ...
and his team at the
Genoscope The French National Sequencing Center (Genoscope) was created in 1996 in Évry, Essonne, Évry, France. It has been involved in the DNA sequencing, sequencing of the human genome. Details The Genoscope is a member of the Commissariat à l'énergi ...

Genoscope
in Paris.
Reference genome A reference genome (also known as a reference assembly) is a digital nucleic acid sequence A nucleic acid sequence is a succession of bases signified by a series of a set of five different letters that indicate the order of nucleotides forming al ...
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 Genealogy (from el, γενεαλογία ' "the making of a pedigree") is the study of families, family history, and the tracing of their lineages. Genealogists use oral interviews, historical records, genetic analysis, and other records to ob ...

genealogical
sites to offer it as a service, to the extent that one may submit one's genome to
crowdsourced Crowdsourcing is a wikt:sourcing, sourcing model in which individuals or organizations obtain goods and services , goods or services, including ideas, voting, micro-tasks and finances, from a large, relatively open and often rapidly evolving g ...

crowdsourced
scientific endeavours such as DNA.LAND at the
New York Genome Center The New York Genome Center (NYGC) is an independent 501(c)(3) nonprofit academic research institution in New York, New York New York City (NYC), often simply called New York, is the List of United States cities by population, most populou ...
, an example both of the
economies of scale In microeconomics Microeconomics is a branch of mainstream economics Mainstream economics is the body of knowledge, theories, and models of economics, as taught by universities worldwide, that are generally accepted by economists as a basis ...

economies of scale
and of
citizen science Citizen science (CS; also known as community science, crowd science, crowd-sourced science, civic science, or volunteer monitoring) is scientific research conducted, in whole or in part, by amateur (or nonprofessional) scientists. Citizen scienc ...
.


Viral genomes

Viral genomes
Viral genomes
can be composed of either RNA or DNA. The genomes of
RNA virus An RNA virus is a virus A virus is a submicroscopic infectious agent In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processe ...
es can be either single-stranded RNA or
double-stranded RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek '' poly-'', "many" + '' -mer'', "part") is a substance or material consisting of very large molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of ...
, 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. 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. The viral envelope is an 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.


Prokaryotic genomes

Prokaryotes and eukaryotes have DNA genomes. Archaea and most bacteria have a single
circular chromosome A circular chromosome is a chromosome in bacteria, archaea, Mitochondrial DNA#Genome structure and diversity, mitochondria, and Chloroplast DNA#Molecular structure, chloroplasts, in the form of a molecule of circular DNA, unlike the linear chromoso ...
, 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. However, some
symbiotic bacteria Symbiotic bacteria are bacteria living in symbiosis Symbiosis (from Greek#REDIRECT Greek Greek may refer to: Greece Anything of, from, or related to Greece Greece ( el, Ελλάδα, , ), officially the Hellenic Republic, is a country l ...
(e.g. '' Serratia symbiotica'') have reduced genomes and a high fraction of pseudogenes: only ~40% of their DNA encodes proteins. Some bacteria have auxiliary genetic material, also part of their genome, which is carried in
plasmid A plasmid is a small, extrachromosomal DNA Extrachromosomal DNA (abbreviated ecDNA) is any DNA that is found off the chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. Most eukaryo ...
s. For this, the word ''genome'' should not be used as a synonym of ''chromosome''.


Eukaryotic genomes

Eukaryotic genomes are composed of one or more linear DNA chromosomes. The number of chromosomes varies widely from
Jack jumper ant The jack jumper ant (''Myrmecia pilosula''), also known as the jack jumper, jumping jack, hopper ant, or jumper ant, is a species of venomous ant native to Australia. Most frequently found in Tasmania and southeast mainland Australia, it is a ...
s and an asexual nemotode, which each have only one pair, to a fern species that has 720 pairs. 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). A typical human cell has two copies of each of 22
autosome An autosome is any chromosome that is not a sex chromosome (an allosome). The members of an autosome pair in a diploid cell have the same morphology, unlike those in allosome pairs which may have different structures. The DNA in autosomes is coll ...
s, one inherited from each parent, plus two
sex chromosome A sex chromosome (also referred to as an allosome, heterotypical chromosome, gonosome, heterochromosome, or idiochromosome) is a chromosome that differs from an ordinary autosome in form, size, and behavior. The human sex chromosomes, a typical p ...
s, making it diploid.
Gamete A gamete ( /ˈɡæmiːt/; from Ancient Greek Ancient Greek includes the forms of the Greek language Greek ( el, label=Modern Greek Modern Greek (, , or , ''Kiní Neoellinikí Glóssa''), generally referred to by speakers simply ...
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 Chloroplasts are organelles that conduct photosynthesis, where the photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in the energy-storage molecules Adenosine triphosphate, ATP and NADPH while fr ...

chloroplasts
and
mitochondria A mitochondrion (; ) is a double-membrane A membrane is a selective barrier; it allows some things to pass through but stops others. Such things may be molecules, ions, or other small particles. Biological membranes include cell membranes ...

mitochondria
have their own DNA. Mitochondria are sometimes said to have their own genome often referred to as the "
mitochondrial genome Mitochondrial DNA (mtDNA or mDNA) is the DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five car ...
". The DNA found within the chloroplast may be referred to as the "
plastome Chloroplast Chloroplasts are organelles that conduct photosynthesis, where the photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in the energy-storage molecules Adenosine triphosphate, ATP and ...
". 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. Genes in eukaryotic genomes can be annotated using FINDER.


Coding sequences

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


Noncoding sequences

Noncoding sequences include
intron An intron (for ''intragenic region'') is any Nucleic acid sequence, nucleotide sequence within a gene that is removed by RNA splicing during Post-transcriptional modification, maturation of the final RNA product. In other words, introns are non-c ...

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 Tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other. Several protein domains also form tandem repeats within their amino acid primary structure, such as armadil ...
and interspersed repeats.


Tandem repeats

Short, non-coding sequences that are repeated head-to-tail are called
tandem repeats Tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other. Several protein domains also form tandem repeats within their amino acid primary structure, such as armadil ...
. 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,
telomere A telomere ( or , from and ) is a region of repetitive nucleotide Nucleotides are organic molecules , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-h ...

telomere
s are composed of the tandem repeat TTAGGG in mammals, and they play an important role in protecting the ends of the chromosome. In other cases, expansions in the number of tandem repeats in exons or introns can cause
disease A disease is a particular abnormal condition that negatively affects the structure A structure is an arrangement and organization of interrelated elements in a material object or system A system is a group of Interaction, interactin ...
. 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 Huntington's disease (HD), also known as Huntington's chorea, is a neurodegenerative disease that is mostly Genetic disorder#Autosomal dominant, inherited. The earliest symptoms are often subtle problems with mood or mental abilities. A gener ...
, 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

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 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. 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

=
Retrotransposon Retrotransposons (also called Class I transposable elements or transposons via RNA intermediates) are a type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through ...

Retrotransposon
s 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 Ribonucleic acid (RNA) is a polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large molecules, or macromolecules, composed of many Re ...

RNA
intermediate. Retrotransposons are composed of
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

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.
Retrotransposon Retrotransposons (also called Class I transposable elements or transposons via RNA intermediates) are a type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through ...

Retrotransposon
s can be transcribed into RNA, which are then duplicated at another site into the genome. Retrotransposons can be divided into
long terminal repeat A long terminal repeat (LTR) is a pair of identical sequences of DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear ch ...
s (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. Non-long terminal repeats (Non-LTRs) are classified as
long interspersed nuclear element Long interspersed nuclear elements (LINEs) (also known as long interspersed nucleotide elements or long interspersed elements) are a group of non-LTR ( long terminal repeat) retrotransposons that are widespread in the genome of many eukaryotes. Th ...
s (LINEs),
short interspersed nuclear element Short interspersed nuclear elements (SINEs) are non-autonomous, non-coding Non-coding DNA sequences are components of an organism's DNA that do not encode protein Proteins are large biomolecules or macromolecules that are comprised of one or ...
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. 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 An Alu element is a short stretch of DNA originally characterized by the action of the '' Arthrobacter luteus (Alu)'' restriction endonuclease A restriction enzyme, restriction endonuclease, or '' restrictase '' is an enzyme Enzymes () are ...
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

=
DNA transposon DNA transposons are DNA sequences, sometimes referred to "jumping genes", that can move and integrate to different locations within the genome. They are class II transposable elements (TEs) that move through a DNA intermediate, as opposed to class I ...

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 100kb). DNA transposons are found in bacteria and make up 3% of the human genome and 12% of the genome of the roundworm .


Genome size

Genome size Genome size is the total amount of DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A ...
is the total number of the DNA base pairs in one copy of a
haploid Ploidy () is the number of complete sets of chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called histones which, aided by ...
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. 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. There is no clear and consistent correlation between morphological complexity and genome size in either
prokaryotes A prokaryote () is a single-celled organism A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contig ...
or lower
eukaryotes Eukaryotes () are organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system that embodies the Life#Biology, properties of life. It is a synonym for "Outline ...
. 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 Developmental biology is the study of the process by which animal Animals (also called Metazoa) are multicellular A multicellular organism is an organism In biology, an organism () is any organic, life, living system that fu ...
). The work is both ''
in vivo Studies Study or studies may refer to: General * Education **Higher education * Clinical trial * Experiment * Observational study * Research * Study skills, abilities and approaches applied to learning Other * Study (art), a drawing or series ...
'' and ''
in silico In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanisms ...
''.


Genome size due to transposable elements

There are many enormous differences in size in genomes, specially mentioned before in the multicellular eukaryotic genomes. The main reason why there is such a big variety of sizes is due to the presence of transposable elements. TEs are known to contribute to a significant change in a cell's mass of DNA. This process is correlated to their long-term accommodation in the host genome, and therefore, to the expansion of the genome size. Here is a table of some significant or representative genomes. See #See also for lists of sequenced genomes.


Genomic alterations

All the cells of an organism originate from a single cell, so they are expected to have identical genomes; however, in some cases, differences arise. Both the process of copying DNA during cell division and exposure to environmental mutagens can result in mutations in somatic cells. In some cases, such mutations lead to cancer because they cause cells to divide more quickly and invade surrounding tissues. In certain lymphocytes in the human immune system,
V(D)J recombination V(D)J recombination is the mechanism of somatic recombination that occurs only in developing lymphocyte A lymphocyte is a type of white blood cell in the immune system The immune system is a network of biological processes that protects an ...
generates different genomic sequences such that each cell produces a unique antibody or T cell receptors. During
meiosis Meiosis (; , because it is a reductional division) is a special type of of in organisms used to produce the , such as or . It involves two rounds of division that ultimately result in four cells with only one copy of each (). Additionall ...

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


Genome-wide reprogramming

Genome-wide reprogramming in mouse primordial germ cells involves
epigenetic In biology, epigenetics is the study of heritability, heritable phenotype changes that do not involve alterations in the DNA sequence. The Ancient Greek, Greek prefix ''wikt:epi-, epi-'' ( "over, outside of, around") in ''epigenetics'' implies f ...
imprint erasure leading to
totipotency Cell potency is a Cell (biology), cell's ability to Cellular differentiation, differentiate into other cell types. The more cell types a cell can differentiate into, the greater its potency. Potency is also described as the gene activation potentia ...
. Reprogramming is facilitated by active
DNA demethylation For molecular biology in mammals, DNA demethylation causes replacement of 5-methylcytosine (5mC) in a DNA sequence by cytosine (C) (see figure of 5mC and C). DNA demethylation can occur by an active process at the site of a 5mC in a DNA sequence ...
, a process that entails the DNA
base excision repair Base excision repair (BER) is a cellular mechanism, studied in the fields of biochemistry Biochemistry or biological chemistry, is the study of es within and relating to living s. A sub-discipline of both and , biochemistry may be divided ...
pathway. This pathway is employed in the erasure of (5mC) in primordial germ cells. The erasure of 5mC occurs via its conversion to (5hmC) driven by high levels of the ten-eleven dioxygenase enzymes TET1 and TET2.


Genome evolution

Genomes are more than the sum of an organism's
gene In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mecha ...

gene
s and have traits that may be and studied without reference to the details of any particular genes and their products. Researchers compare traits such as
karyotype A karyotype is a preparation of the complete set of metaphase Metaphase () is a stage of mitosis In cell biology Cell biology (also cellular biology or cytology) is a branch of biology Biology is the natural science that studies ...

karyotype
(chromosome number),
genome size Genome size is the total amount of DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A ...
, gene order,
codon usage bias Codon usage bias refers to differences in the frequency of occurrence of synonymous A synonym is a word, morpheme, or phrase that means exactly or nearly the same as another word, morpheme, or phrase in a given language. For example, in the Eng ...
, and
GC-content In molecular biology Molecular biology is the branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, mo ...
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 A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each ...
, 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 (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient G ...
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 A microorganism, or microbe,, ''mikros'', "small") and ''organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes ...
s. Also,
eukaryotic cells Eukaryotes () are organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interact ...

eukaryotic cells
seem to have experienced a transfer of some genetic material from their
chloroplast A chloroplast is a type of membrane-bound organelle In cell biology, an organelle is a specialized subunit, usually within a cell (biology), cell, that has a specific function. The name ''organelle'' comes from the idea that these structure ...

chloroplast
and
mitochondria A mitochondrion (; ) is a double-membrane A membrane is a selective barrier; it allows some things to pass through but stops others. Such things may be molecules, ions, or other small particles. Biological membranes include cell membranes ...

mitochondria
l genomes to their nuclear chromosomes. Recent empirical data suggest an important role of viruses and sub-viral RNA-networks to represent a main driving role to generate genetic novelty and natural genome editing.


In fiction

Works of science fiction illustrate concerns about the availability of genome sequences. Michael Crichton's 1990 novel ''Jurassic Park'' and the subsequent
film A film, also called a movie, motion picture or moving picture, is a work of visual art The visual arts are art forms such as painting Painting is the practice of applying paint Paint is any pigmented liquid, liquefiable, ...
tell the story of a billionaire who creates a theme park of cloned dinosaurs on a remote island, with disastrous outcomes. A geneticist extracts dinosaur DNA from the blood of ancient mosquitoes and fills in the gaps with DNA from modern species to create several species of dinosaurs. A chaos theorist is asked to give his expert opinion on the safety of engineering an ecosystem with the dinosaurs, and he repeatedly warns that the outcomes of the project will be unpredictable and ultimately uncontrollable. These warnings about the perils of using genomic information are a major theme of the book. The 1997 film ''
Gattaca ''Gattaca'' is a 1997 American dystopian science fiction film Science fiction (or sci-fi) is a film genre A film, also called a movie, motion picture or moving picture, is a work of visual art used to simulate experiences that commun ...

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.


See also

* Bacterial genome size *
Cryoconservation of animal genetic resources Cryoconservation of animal genetic resources is a strategy wherein samples of animal genetic materials are preserved cryogenics, cryogenically."Cryoconservation of Animal Genetic Resources", Rep. Rome: Food and Agriculture Organization of the Uni ...
*
Genome BrowserIn bioinformatics, a genome browser is a graphical interface for display of information from a biological database for genomic data. Genome browsers enable researchers to visualize and browse entire genomes with annotated data including gene predict ...
* Genome Compiler * *
Genome-wide association study In genetics Genetics is a branch of biology concerned with the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) Though heredity had been observed for millennia, Gregor Mendel, Moravia, Moravian scientist a ...
*
List of sequenced animal genomes This list of sequenced animal genomes contains animal species for which complete genome sequences have been assembled, annotated and published. Substantially complete draft genomes are included, but not partial genome sequences or organelle-only se ...
* List of sequenced archaeal genomes * List of sequenced bacterial genomes * List of sequenced eukaryotic genomes * List of sequenced fungi genomes * List of sequenced plant genomes * List of sequenced plastomes * List of sequenced protist genomes * Metagenomics * Microbiome * Molecular epidemiology * Molecular pathological epidemiology * Molecular pathology * Nucleic acid sequence * Pan-genome * Precision medicine * Regulator gene * Whole genome sequencing


References


Further reading

* * * * * * *


External links


UCSC Genome Browser
– view the genome and annotations for more than 80 organisms.
genomecenter.howard.edu

Build a DNA Molecule

Some comparative genome sizes

DNA Interactive: The History of DNA Science

DNA From The Beginning

All About The Human Genome Project
from Genome.gov
Animal genome size database



GOLD:Genomes OnLine Database

The Genome News Network

NCBI Entrez Genome Project database



GeneCards
an integrated database of human genes
BBC News – Final genome 'chapter' published

IMG
(The Integrated Microbial Genomes system)—for genome analysis by the DOE-JGI
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. {{Portal bar, Astronomy, Biology, Evolutionary biology, Paleontology, Science Genetic mapping Genomics