Genome

For other uses, see Genome (disambiguation).

In biology the genome of an organism is its whole hereditary information and is encoded in the DNA (or, for some viruses, RNA).

This includes both the genes and the non-coding sequences of the DNA. The term was adapted in 1920 by Hans Winkler, Professor of Botany at the University of Hamburg, Germany. The Oxford English Dictionary suggests the name to be a portmanteau of the words gene and chromosome, however, many related -ome words already existed, such as biome and rhizome, forming a vocabulary into which genome fits systematically.

More precisely, the genome of an organism is a complete genetic sequence on one set of chromosomes; for example, one of the two sets that a diploid individual carries in every somatic cell. 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. 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 little connection between the two. 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 is over one billion words long;
• The book is bound 5000 volumes, each 300 pages long;
• The book fits into a cell nucleus the size of a pinpoint;
• A copy of the book (all 5000 volumes) is contained in almost every cell;

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 mitochondria that have their own DNA, the genes in this mitochondrial DNA are not considered part of the genome. In fact, mitochondria are sometimes said to have their own genome, often referred to as the "mitochondrial genome".

Genomes and genetic variation

Note that 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.

Genome projects

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, bacteria like E. coli, etc. 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 5368 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.

In May 2007, the New York Times announced that the full genome of DNA pioneer James D. Watson had been recorded.[1] The article noted that some scientists believe this to be the gateway to upcoming personalized genomic medicine.

Many genomes have been sequenced by various genome projects. The cost of sequencing continues to drop.

Comparison of different genome sizes

Organism	Genome size (base pairs)	Note
Virus, Bacteriophage MS2	3,569	First sequenced RNA-genome
Virus, SV40	5,224
Virus, Phage Φ-X174;	5,386	First sequenced DNA-genome
Virus, Phage λ	50,000
Bacterium, Haemophilus influenzae	1,830,000	First genome of living organism, July 1995
Bacterium, Carsonella ruddii	160,000	Smallest non-viral genome.
Bacterium, Buchnera aphidicola	600,000
Bacterium, Wigglesworthia glossinidia	700,000
Bacterium, Escherichia coli	4,000,000
Amoeba, Amoeba dubia	670,000,000,000	Largest known genome.
Plant, Arabidopsis thaliana	157,000,000	First plant genome sequenced, Dec 2000.
Plant, Genlisea margaretae	63,400,000	Smallest recorded flowering plant genome, 2006.
Plant, Fritillaria assyrica	130,000,000,000
Plant, Populus trichocarpa	480,000,000	First tree genome, Sept 2006
Yeast,Saccharomyces cerevisiae	20,000,000
Fungus, Aspergillus nidulans	30,000,000
Nematode, Caenorhabditis elegans	98,000,000	First multicellular animal genome, December 1998
Insect, Drosophila melanogaster aka Fruit Fly	130,000,000
Insect, Bombyx mori aka Silk Moth	530,000,000
Insect, Apis mellifera aka Honey Bee	1,770,000,000
Fish, Tetraodon nigroviridis, type of Puffer fish	385,000,000	Smallest vertebrate genome known
Mammal, Homo sapiens	3,200,000,000
Fish, Protopterus aethiopicus aka Marbled lungfish	130,000,000,000	Largest vertebrate genome known

Note: The DNA from a single human cell has a length of ~1.8 m (but at 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

• gene
• gene family
• Genome Comparison
• Human genome
• Human microbiome project
• List of omics topics in biology
• List of sequenced eukaryotic genomes
• List of sequenced prokaryotic genomes
• List of sequenced archeal genomes
• Minimal Genome Project
• Mitochondrial genome
• molecular systematics
• molecular evolution
• Honey Bee Genome Sequencing Consortium
• National Human Genome Research Institute

References

ISBN links support NWE through referral fees

• Cuthbert, A. W. 2001. Genome. In C. Blakemore and S. Jennett, The Oxford Companion to the Body. New York: Oxford University Press. ISBN 019852403X.

• Benfey, P. and Protopapas, A.D. (2004). Essentials of Genomics. Prentice Hall. 
• Brown, Terence A. (2002). Genomes 2. Oxford: Bios Scientific Publishers. ISBN 978-1859960295. 
• Gibson, Greg and Muse, Spencer V. (2004). A Primer of Genome Science, Second Edition, Sunderland, Mass: Sinauer Assoc. ISBN 0-87893-234-8. 
• Gregory, T. Ryan (ed) (2005). The Evolution of the Genome. Elsevier. ISBN 0-12-301463-8. 
• Reece, Richard J. (2004). Analysis of Genes and Genomes. Chichester: John Wiley & Sons. ISBN 0-470-84379-9. 
• Saccone, Cecilia and Pesole, Graziano (2003). Handbook of Comparative Genomics. Chichester: John Wiley & Sons. ISBN 0-471-39128-X. 
• Werner, E. (2003). In silico multicellular systems biology and minimal genomes. Drug Discov Today 8 (24): 1121–1127.
• Witzany, G. (2006). Natural Genome Editing Competences of Viruses. Acta Biotheoretica 54 (4): 235–253.

External links

• Genomics Directory: A genomics and biotechnology database for scientists and students
• 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
• BBC News - Final genome 'chapter' published
• The Plant Genome
• IMG The Integrated Microbial Genomes system, for genome analysis by the DOE-JGI.
• CAMERA Cyberinfrastructure for Metagenomics, data repository and bioinformatics tools for metagenomic research
• GeneCards an integrated database of human genes.

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