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An image of the 46 chromosomes making up the diploid genome of a human male. (The mitochondrial chromosome is not shown.)

In the fields of molecular biology and genetics, a genome is the genetic material of an organism. It consists of DNA (or RNA in RNA viruses). The genome includes both the genes (the coding regions) and the noncoding DNA,^[1] as well as mitochondrial DNA^[2] and chloroplast DNA. The study of the genome is called genomics.

Origin of term

The term genome was created in 1920 by Hans Winkler,^[3] professor of botany at the University of Hamburg, Germany. The Oxford Dictionary suggests the name is a blend of the words gene and chromosome.^[4] 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.^[5]

Sequencing and mapping

A genome sequence is the complete list of the nucleotides (A, C, G, and T for 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 sequence - prototypification of complete genome of virus

In 1976, Walter Fiers at the University of Ghent (Belgium) was the first to establish the complete nucleotide sequence of a viral RNA-genome (Bacteriophage MS2). The next year, Fred Sanger completed the first DNA-genome sequence: Phage Φ-X174, of 5386 base pairs.^[6] 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 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.^[7] 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 found in a Siberian cave.^[8][9]

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.^[10]

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 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 in Paris.^[11][12]

Reference genome sequences and maps continue to be updated, removing errors and clarifying regions of high allelic complexity.^[13] The decreasing cost of genomic mapping has permitted genealogical sites to offer it as a service,^[14] to the extent that one may submit one's genome to crowdsourced scientific endeavours such as DNA.LAND at the New York Genome Center,^[15] an example both of the economies of scale and of citizen science.^[16]

Viral genomes

Viral genomes can be composed of either 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 molecules. 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.^[17]

Prokaryotic genomes

Prokaryotes and eukaryotes have DNA genomes. Archaea have a single circular chromosome.^[18] Most bacteria also have a single circular chromosome; however, some bacterial species have linear chromosomes^[19] or multiple chromosomes.^[20] If the 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 in their genomes.^[21] However, some symbiotic bacteria (e.g. Serratia symbiotica) have reduced genomes and a high fraction of pseudogenes: only ~40% of their DNA encodes proteins.^[22][23]

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.

Eukaryotic genomes

Eukaryotic genomes are composed of one or more linear DNA chromosomes. The number of chromosomes varies widely from Jack jumper ants and an asexual nemotode,^[24] which each have only one pair, to a fern species that has 720 pairs.^[25] 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 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.^[26]

Coding sequences

DNA sequences that carry the instructions to make proteins are 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.^[26]

Simple eukaryotes such as C. elegans and fruit fly, have more non-repetitive DNA than repetitive DNA,^[26][27] while the genomes of more complex eukaryotes tend to be composed largely of repetitive DNA.^[28] In some plants and amphibians, the proportion of repetitive DNA is more than 80%.^[26] Similarly, only 2% of the human genome codes for proteins.

Composition of the human genome

Noncoding sequences

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.^[29]

Tandem repeats

Short, non-coding sequences that are repeated head-to-tail are called tandem repeats. Microsatellites consisting of 2-5 basepair repeats, while minisatellite repeats are 30-35 bp. Tandem repeats make up about 4% of the human genome and 9% of the fruit fly genome.^[30] 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.^[31] 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.^[31]

Tandem repeats are usually caused by slippage during replication, unequal crossing-over and gene conversion.^[32]

Transposable elements

Transposable elements (TEs) are sequences of DNA with a defined structure that are able to change their location in the genome.^[30][21][33] 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.^[34]

Retrotransposons

Retrotransposons can be transcribed into RNA, which are then duplicated at another site into the genome.^[35] Retrotransposons can be divided into Long terminal repeats (LTRs) and Non-Long Terminal Repeats (Non-LTR).^[34]

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.^[33] 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.^[36]

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.^[37]

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.^[38]

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.^[39] 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.^[34]

DNA transposons

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.^[30] This cut-and-paste mechanism typically reinserts transposons near their original location (within 100kb).^[34] DNA transposons are found in bacteria and make up 3% of the human genome and 12% of the genome of the roundworm C. elegans.^[34]

Genome size

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

Genome size is the total number of 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.^[40] 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.^[26][41] This phenomenon also indicates the mighty influence coming from repetitive 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.^[42][43]

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.^[89] In certain lymphocytes in the human immune system, V(D)J recombination generates different genomic sequences such that each cell produces a unique antibody or T cell receptors.

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

Genome evolution

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 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 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.^[90]

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

The 1997 film Gattaca is set in a futurist society where genomes of children are engineered to contain the most ideal combination of their parents' traits, and metrics such as risk of heart disease and predicted life expectancy are documented for each person based on their genome. People conceived outside of the eugenics program, known as "In-Valids" suffer discrimination and are relegated to menial occupations. The protagonist of the film is an In-Valid who works to defy the supposed genetic odds and achieve his dream of working as a space navigator. The film warns against a future where genomic information fuels prejudice and extreme class differences between those who can and can't afford genetically engineered children.^[91]

See also

References

Further reading

• 
  Benfey P, Protopapas AD (2004). Essentials of Genomics. Prentice Hall.
  


• 
  Brown TA (2002). Genomes 2. Oxford: Bios Scientific Publishers. ISBN 978-1-85996-029-5.
  


• 
  Gibson G, Muse SV (2004). A Primer of Genome Science (Second ed.). Sunderland, Mass: Sinauer Assoc. ISBN 978-0-87893-234-4.
  


• 
  Gregory TR (2005). The Evolution of the Genome. Elsevier. ISBN 978-0-12-301463-4.
  


• 
  Reece RJ (2004). Analysis of Genes and Genomes. Chichester: John Wiley & Sons. ISBN 978-0-470-84379-6.
  


• 
  Saccone C, Pesole G (2003). Handbook of Comparative Genomics. Chichester: John Wiley & Sons. ISBN 978-0-471-39128-9.
  


• 
  Werner E (December 2003). "In silico multicellular systems biology and minimal genomes". Drug Discovery Today. 8 (24): 1121–27. doi:10.1016/S1359-6446(03)02918-0. PMID 14678738.
  

External links

Wikiquote has quotations related to: Genome

• 
  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


• Plant genome size database


• GOLD:Genomes OnLine Database


• The Genome News Network


• NCBI Entrez Genome Project database


• NCBI Genome Primer


• 
  GeneCards—an integrated database of human genes


• 
  Visualization of nucleotide sequence - prototypification of complete genome of virus, sequence of 5418 nucleotides


• 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 and 454 Service from GeKnome Technologies.