In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA.

Origin of term

The term was adapted in 1920 by Hans Winkler, Professor of Botany at the University of Hamburg, Germany. In Greek, the word ''genome'' (γίνομαι) means "I become, I am born, to come into being". The Oxford English Dictionary suggests the name to be a blend of the words ''gene'' and ''chromosome''. A few related ''-ome'' words already existed, such as ''biome'' and ''rhizome'', forming a vocabulary into which ''genome'' fits systematically.

Overview

Some organisms have multiple copies of chromosomes, diploid, triploid, tetraploid and so on. In classical genetics, in a sexually reproducing organism (typically eukarya) the gamete has half the number of chromosomes of the somatic cell and the genome is a full set of chromosomes in a gamete. In haploid organisms, including cells of bacteria, archaea, and in organelles including mitochondria and chloroplasts, or viruses, that similarly contain genes, the single or set of circular and/or linear chains of DNA (or RNA for some viruses), likewise constitute the ''genome''. The term genome can be applied specifically to mean that stored on a complete set of ''nuclear DNA'' (i.e., the "nuclear genome") but can also be applied to that stored within organelles that contain their own DNA, as with the "mitochondrial genome" or the "chloroplast genome". Additionally, the genome can comprise nonchromosomal genetic elements such as viruses, plasmids, and transposable elements.

When people say that the genome of a sexually reproducing species has been "sequenced", typically they are referring to a determination of the sequences of one set of autosomes and one of each type of sex chromosome, which together represent both of the possible sexes. Even in species that exist in only one sex, what is described as "a genome sequence" may be a composite read from the chromosomes of various individuals. In general use, the phrase "genetic makeup" is sometimes used conversationally to mean the genome of a particular individual or organism. The study of the global properties of genomes of related organisms is usually referred to as genomics, which distinguishes it from genetics which generally studies the properties of single genes or groups of genes.

Both the number of base pairs and the number of genes vary widely from one species to another, and there is only a rough correlation between the two (an observation known as the C-value paradox). At present, the highest known number of genes is around 60,000, for the protozoan causing trichomoniasis (see List of sequenced eukaryotic genomes), almost three times as many as in the human genome.

An analogy to the human genome stored on DNA is that of instructions stored in a book:

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 fits into a cell nucleus the size of a pinpoint;

At least one copy of the book (all 23 chapters) is contained in most cells of our body. The only exception in humans is found in mature red blood cells which become enucleated during development and therefore lack a genome.

Types

Most biological entities that are more complex than a virus sometimes or always carry additional genetic material besides that which resides in their chromosomes. In some contexts, such as sequencing the genome of a pathogenic microbe, "genome" is meant to include information stored on this auxiliary material, which is carried in plasmids. In such circumstances then, "genome" describes all of the genes and information on non-coding DNA that have the potential to be present.

In eukaryotes such as plants, protozoa and animals, however, "genome" carries the typical connotation of only information on chromosomal DNA. So although these organisms contain chloroplasts and/or mitochondria that have their own DNA, the genetic information contained by DNA within these organelles is not considered part of the genome. In fact, 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".

Genomes and genetic variation

A genome does not capture the genetic diversity or the genetic polymorphism of a species. For example, the human genome sequence in principle could be determined from just half the information on the DNA of one cell from one individual. To learn what variations in genetic information underlie particular traits or diseases requires comparisons across individuals. This point explains the common usage of "genome" (which parallels a common usage of "gene") to refer not to the information in any particular DNA sequence, but to a whole family of sequences that share a biological context.

Although this concept may seem counter intuitive, it is the same concept that says there is no particular shape that is the shape of a cheetah. Cheetahs vary, and so do the sequences of their genomes. Yet both the individual animals and their sequences share commonalities, so one can learn something about cheetahs and "cheetah-ness" from a single example of either.

Sequencing and mapping

The Human Genome Project was organized to map and to sequence the human genome. Other genome projects include mouse, rice, the plant ''Arabidopsis thaliana'', the puffer fish, and bacteria like E. coli. 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 first DNA-genome project to be completed was the Phage Φ-X174, with only 5386 base pairs, which was sequenced by Fred Sanger in 1977. The first bacterial genome to be completed 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 the 16 chromosomes of budding yeast Saccharomyces cerevisiae being released as a result of a European-led effort begun in the mid-1980s.

The development of new technologies has made it dramatically easier and cheaper to do sequencing, and the number of complete genome sequences is growing rapidly. Among many genome databases, the one maintained by the US National Institutes of Health is inclusive.

These new technologies open up the prospect of personal genome sequencing as an important diagnostic tool. A major step toward that goal was the completion of the decipherment of the full genome of DNA pioneer James D. Watson in 2007.

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. A fundamental step in the Human genome project was the release of a detailed genomic map by Jean Weissenbach and his team at the Genoscope in Paris

Comparison of different genome sizes

!Organism type	!Organism	!Genome size (base pairs)	!Genome size (in human-readable format)	Picogram>pg	Note
Virus	Bacteriophage MS2		3.5kb		First sequenced RNA-genome
Virus	SV40		5.2kb
Virus			5.3kb		First sequenced DNA-genome
Virus	HIV		9.7kb
Virus			48kb
Virus	Mimivirus		1.1Mb		Largest known viral genome
Bacterium	''Haemophilus influenzae''		1.8Mb		First genome of a living organism sequenced, July 1995
Bacterium	''Carsonella ruddii''		159kb		Smallest non-viral genome.
Bacterium	''Buchnera aphidicola''		600kb
Bacterium	''Wigglesworthia glossinidia''		700Kb
Bacterium	''Escherichia coli''		4.6Mb
Bacterium	''Solibacter usitatus'' (strain Ellin 6076)		9.9Mb		Largest known Bacterial genome
Amoeboid	''Polychaos dubium'' (''"Amoeba" dubia'')		670Gb (Disputed )		Largest known genome. (Disputed )
Plant	''Arabidopsis thaliana''		157Mb		First plant genome sequenced, December 2000.
Plant	''Genlisea margaretae''		63Mb		Smallest recorded flowering plant genome, 2006.
Plant	''Fritillaria assyrica''		130Gb
Plant			480Mb		First tree genome sequenced, September 2006
Plant	''Pieris japonica'' (Japanese-native, pale-petal)		150Gb		Largest plant genome known
Moss	''Physcomitrella patens''		480Mb		First genome of a bryophyte sequenced, January 2008.
Yeast	''Saccharomyces cerevisiae''		12.1Mb		First eukaryotic genome sequenced, 1996
Fungus	''Aspergillus nidulans''		30Mb
	''Caenorhabditis elegans''		100Mb		First multicellular animal genome sequenced, December 1998
	''Pratylenchus coffeae''		20Mb		Smallest animal genome known
Insect	''Drosophila melanogaster'' (fruit fly)		130Mb
Insect	''Bombyx mori'' (silk moth)		530Mb
Insect	''Apis mellifera'' (honey bee)		236Mb
Insect	''Solenopsis invicta'' (fire ant)		480Mb
Fish	''Tetraodon nigroviridis'' (type of puffer fish)		3.9Mb		Smallest vertebrate genome known
Mammal	''Homo sapiens''		3.2Gb
Fish	''Protopterus aethiopicus'' (marbled lungfish)		130Gb		Largest vertebrate genome known

''Note:'' The DNA from a single (diploid) human cell if the 46 chromosomes were connected end-to-end and straightened, would have a length of ~2 m and a width of ~2.4 nanometers.

Since genomes and their organisms 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 multicellular organisms (see Developmental biology). The work is both ''in vivo'' and ''in silico''.

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 ''chromosome number'' (karyotype), 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. Duplications may range from extension of short tandem repeats, to duplication of a cluster of genes, and all the way to duplications 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 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.

See also

Full genome sequencing

References

Further reading

External links

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

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.

Category:Genetic mapping Category:Genomics

ar:مجين ast:Xenoma bn:জিনোম zh-min-nan:Ki-in-thé bg:Геном ca:Genoma cv:Геном cs:Genom da:Arvemasse de:Genom et:Genoom el:Γονιδίωμα es:Genoma eo:Genaro eu:Genoma fa:ژنوم fr:Génome gl:Xenoma ko:게놈 hy:Գենոմ hr:Genom id:Genom ia:Genoma is:Erfðamengi it:Genoma he:גנום jv:Genom kn:ಜಿನೊಮ್‌ kk:Геном la:Genoma lv:Genoms lb:Genom lt:Genomas hu:Genom mk:Геном mr:जीनोम ms:Genom nl:Genoom ja:ゲノム no:Genom oc:Genòma pl:Genom pt:Genoma ro:Genom ru:Геном simple:Genome sk:Genóm sl:Dednina sr:Геном sh:Genom fi:Genomi sv:Genom ta:மரபணுத்தொகை th:จีโนม tr:Genom uk:Геном vi:Bộ gen zh:基因組

Name	J. Craig Venter
Birth date	October 14, 1946
Birth place	Salt Lake City, Utah, USA
Alma mater	University of California, San Diego
Work institution	State University of New York at Buffalo National Institutes of Health J. Craig Venter Institute
Occupation	BiologistEntrepreneur
Known for	DNAHuman genomeMetagenomicsSynthetic genomicsShotgun approach to genome sequencing
Awards	Kistler Prize (2008), ENI award (2008), National Medal of Science (2008)
Website	J. Craig Venter Institute }}

John Craig Venter (born October 14, 1946) is an American biologist and entrepreneur, most famous for his role in being one of the first to sequence the human genome and for his role in creating the first cell with a synthetic genome in 2010. Venter founded Celera Genomics, The Institute for Genomic Research and the J. Craig Venter Institute, now working at the latter to create synthetic biological organisms and to document genetic diversity in the world's oceans. He was listed on ''Time'' magazine's 2007 and 2008 Time 100 list of the most influential people in the world. In 2010, the British magazine ''New Statesman'' listed Craig Venter at 14th in the list of "The World's 50 Most Influential Figures 2010".

Early life

Venter was born in Salt Lake City, Utah. In his youth, he did not take his education seriously, preferring to spend his time on the water in boats or surfing. According to his biography, ''A Life Decoded'', he was said to never be a terribly engaged student, having Cs and Ds on his eighth-grade report cards.

Although he was against the Vietnam War, Venter was drafted and enlisted in the United States Navy where he worked in the intensive-care ward of a field hospital. While in Vietnam, he attempted to commit suicide by swimming out to sea, but changed his mind more than a mile out. Being confronted with wounded, maimed, and dying soldiers on a daily basis instilled in him a desire to study medicine — although he later switched to biomedical research.

Education

Venter graduated from Mills High School and began his college career at a community college, College of San Mateo in California. He received his B.S. degree in biochemistry in 1972, and his Ph.D. degree in physiology and pharmacology in 1975, both from the University of California, San Diego. At UCSD, he studied under biochemist Nathan O. Kaplan, and married former Ph.D. candidate Barbara Rae. After working as an associate professor, and later as full professor, at the State University of New York at Buffalo, he joined the National Institutes of Health in 1984. In Buffalo, he divorced Dr. Rae-Venter and married his student, Claire M. Fraser, remaining married to her until 2005.

Discovery

While at the NIH, Venter learned of a technique for rapidly identifying all of the mRNAs present in a cell and began to use it to identify human brain genes. The short cDNA sequence fragments discovered by this method are called expressed sequence tags (ESTs) a name coined by Anthony Kerlavage at The Institute for Genomic Research. The NIH initially led an effort to patent these gene fragments, in which Venter coincidentally and controversially became involved. The NIH later withdrew the patent applications, following public outcry. Subsequent court cases declared that ESTs were not directly patentable.

Human Genome Project

Venter was passionate about the power of genomics to radically transform healthcare. Venter believed that shotgun sequencing was the fastest and most effective way to get useful human genome data. The method was controversial, however, since some geneticists felt it would not be accurate enough for a genome as complicated as that of humans. Frustrated with what Venter viewed as the slow pace of progress in the Human Genome project, and unable to get funds for his ideas, he sought funding from the private sector to fund Celera Genomics. The goal of the company was to sequence the entire human genome and release it into the public domain for non-commercial use in much less time and for much less cost than the public human genome project. The company planned to monetize their work by creating a value-added database of genomic data to which users could subscribe for a fee. The goal consequently put pressure on the public genome program and spurred several groups to redouble their efforts to produce the full sequence. DNA from five demographically different individuals was used by Celera to generate the sequence of the human genome; one of the individuals was Venter himself. In 2000, Venter and Francis Collins of the National Institutes of Health and U.S. Public Genome Project jointly made the announcement of the mapping of the human genome, a full three years ahead of the expected end of the Public Genome Program. The announcement was made along with US President Bill Clinton, and U.K. Prime Minister Tony Blair. Venter and Collins thus shared an award for "Biography of the Year" from A&E; Network. Celera published the first Human Genome in the journal Science, and was soon followed by a Human Genome Project Publication in Nature. Despite some claims that shotgun sequencing was in some ways less accurate than the clone-by-clone method chosen by the Human Genome Project, the technique became widely accepted by the scientific community and is still the de facto standard used today.

Although Celera was originally set to sequence a composite of DNA samples, partway through the sequencing, Venter switched the samples for his own DNA.

After contributing to the Human Genome, and its release into the public domain, Venter was fired by Celera in early 2002. According to his biography, Venter was ready to leave Celera, and was fired due to conflict with the main investor, Tony White, that had existed since day one of the project. Venter writes that his main goal was always to accelerate science and thereby discovery, and he only sought help from the corporate world when he couldn't find funding in the public sector.

Ocean sampling

The Global Ocean Sampling Expedition (GOS) is an ocean exploration genome project with the goal of assessing the genetic diversity in marine microbial communities and to understand their role in nature's fundamental processes. Begun as a Sargasso Sea pilot sampling project in August 2003,Craig Venter announced the full Expedition on 4 March 2004. The project, which used Craig Venter's personal yacht, ''Sorcerer II'', started in Halifax,Canada, circumnavigated the globe and returned to the U.S. in January 2006.

Current work

Venter is currently the president of the J. Craig Venter Institute, which conducts research in synthetic biology. In June 2005, he co-founded Synthetic Genomics, a firm dedicated to using modified microorganisms to produce clean fuels and biochemicals. In July 2009, ExxonMobil announced a $600 million collaboration with Synthetic Genomics to research and develop next-generation biofuels.

Venter is a member of the USA Science and Engineering Festival's Advisory Board.

Media coverage

Venter has been the subject of articles in several magazines, including ''Wired'', ''The Economist'', Australian science magazine ''Cosmos'', and ''The Atlantic''. Additionally, he was featured on ''The Colbert Report'' on both February 27, 2007, and October 30, 2007.

Venter appeared in the "Evolution" episode of the documentary television series ''Understanding''.

On May 16, 2004, Venter gave the commencement speech at Boston University.

In a 2007 interview with ''New Scientist'' when asked "Assuming you can make synthetic bacteria, what will you do with them?", Venter replied:

Furthermore it suggests that one of the main purposes for creating synthetic bacteria would be to reduce the dependence on fossil fuels through bioremediation.

On May 10, 2007, Venter was awarded an honorary doctorate from Arizona State University., and on October 24 of the same year, he received an honorary doctorate from Imperial College London.

He was on the 2007 Time 100 most influential people in the world list made by Time magazine. In 2007 he also received the Golden Eurydice Award for contributions to Biophilosophy.

On September 4, 2007, a team led by Venter published the first complete (six-billion-letter) genome of an individual human — Venter's own DNA sequence. When on BBC News on October 22, 2007, when asked about his religious view he replied that he thought that a true scientist could not believe in supernatural explanations.

On December 4, 2007, Venter gave the Dimbleby lecture for the BBC in London. He outlined his current work and future developments in genetics.

In February 2008, he gave a speech about his current work at the TED conference.

Venter delivered the 2008 convocation speech for Faculty of Science honours and specialization students at the University of Alberta. A transcription of the speech is available here.

Dr. Venter was featured in Time Magazine's "The Top 10 Everything of 2008" article. Number three in 2008's Top 10 Scientific Discoveries was a piece outlining his work stitching together the 582,000 base pairs necessary to invent the genetic information for a whole new bacterium.

Dr. Venter took part in the inaugural San Diego Science Festival and spoke at its press conference on February 26, 2009.

On April 6, 2009, Venter gave a speech at Arizona State University as part of the Origins Symposium.

For an episode aired on July 27, 2009, Venter was interviewed on his boat by BBC One for the first episode of TV show Bang Goes the Theory.

On May 8, 2010, Venter received an honorary doctor of science degree from Clarkson University for his work on the human genome.

On May 20, 2010, Venter announced the creation of first self-replicating semi-synthetic bacterial cell.

On November 21, 2010 Steve Kroft profiled J. Craig Venter and his research on 60 minutes.

On April 21, 2011, Venter received the 2011 Benjamin Rush Medal from William & Mary School of Law.

In the June 2011 issue of Men's Journal, Ventner was featured as the "Survival Skills" celebrity of the month. He shared various anecdotes, and advice, including stories of his time in Vietnam, as well as mentioning a bout with melanoma upon his back, which subsequently resulted in "giving a pound of flesh" to surgery.

Individual human genome sequenced

On September 4, 2007, a team led by Sam Levy published the first complete (six-billion-letter) genome of an individual human—Venter's own DNA sequence. Some of the sequences in Venter's genome are associated with wet earwax, increased risk of antisocial behavior, Alzheimer's and cardiovascular diseases. This publication was especially interesting since it contained a diploid instead of a haploid genome and shows promise for personalized medicine via genotyping. This genome, rather immodestly dubbed HuRef by Levy and others., was a landmark accomplishment and as of mid-2010 is probably the highest quality personal genome sequence yet completed.

The Human Reference Genome Browser is a web application for the navigation and analysis of Venter's recently published genome. The HuRef database consists of approximately 32 million DNA reads sequenced using microfluidic Sanger sequencing, assembled into 4,528 scaffolds and 4.1 million DNA variations identified by genome analysis. These variants include single-nucleotide polymorphisms (SNPs), block substitutions, short and large indels, and structural variations like insertions, deletions, inversions and copy number changes.

The browser enables scientists to navigate the HuRef genome assembly and sequence variations, and to compare it with the NCBI human build 36 assembly in the context of the NCBI and Ensembl annotations. The browser provides a comparative view between NCBI and HuRef consensus sequences, the sequence multi-alignment of the HuRef assembly, Ensembl and dbSNP annotations, HuRef variants, and the underlying variant evidence and functional analysis. The interface also represents the haplotype blocks from which diploid genome sequence can be inferred and the relation of variants to gene annotations. The display of variants and gene annotations are linked to external public resources including dbSNP, Ensembl, Online Mendelian Inheritance in Man (OMIM) and Gene Ontology (GO).

Users can search the HuRef genome using HUGO gene names, Ensembl and dbSNP identifiers, HuRef contig or scaffold locations, or NCBI chromosome locations. Users can then easily and quickly browse any genomic region via the simple and intuitive pan and zoom controls; furthermore, data relevant to specific loci can be exported for further analysis.

''Mycoplasma laboratorium''

Venter is seeking to patent the first life form created by humanity, possibly to be named ''Mycoplasma laboratorium''. There is speculation that this line of research could lead to producing bacteria that have been engineered to perform specific reactions, for example, produce fuels, make medicines, combat global warming, and so on.

In May 2010, a team of scientists led by Venter became the first to successfully create what was described as "synthetic life". This was done by synthesizing a very long DNA molecule containing an entire bacterium genome, and introducing this into another cell, analogous to the accomplishment of Eckard Wimmer's group, who synthesized and ligated an RNA virus genome and "booted" it in cell lysate. The single-celled organism contains four "watermarks" written into its DNA to identify it as synthetic and to help trace its descendants. The watermarks include # Code table for entire alphabet with punctuations # Names of 46 contributing scientists # Three quotations # The web address for the cell.

Selected bibliography

Venter is an ISI highly cited researcher and has authored over 200 publications in scientific journals.

See also

Artificial gene synthesis

Full genome sequencing

Genetic testing

''Genome: The Autobiography of a Species in 23 Chapters''

Metagenomics

Personal genomics

Pharmacogenomics

Predictive medicine

References

Further reading

External links

J. Craig Venter Institute

Sorcerer II Expedition

Synthetic Genomics

The Institute for Genomic Research (TIGR)

HuRef Genome Browser

Media

Cracking the code to life, ''The Guardian'', October 8, 2007

Craig Venter interview, ''Wired Science'', December 2007 (video)

Radio interview on Philosophy Talk

Video of interview/discussion with Craig Venter by Carl Zimmer on Bloggingheads.tv

Craig Venter: A voyage of DNA, genes and the sea – TED (Technology Entertainment Design) conference (video)

Webcast of Venter talk 'Genomics: From humans to the environment' at The James Martin 21st Century School

The Richard Dimbleby Lecture 2007 – Dr. J. Craig Venter – A DNA Driven World

A short course on synthetic genomics. Edge Master Class 2009

Category:1946 births Category:Members of the United States National Academy of Sciences Category:Living people Category:United States Navy sailors Category:University of California, San Diego alumni Category:University at Buffalo faculty Category:American atheists Category:American military personnel of the Vietnam War Category:American geneticists Category:Biotechnologists Category:Personal genome sequenced

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