Genome

Editor-In-Chief: C. Michael Gibson, M.S., M.D. [1]

Overview

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 coined in 1920 by Hans Winkler, Professor of Botany at the University of Hamburg, Germany, as a portmanteau of the words gene and chromosome.

More precisely, the genome of an organism is a complete DNA sequence of 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 the complete set of nuclear DNA (i.e., the "nuclear genome") but can also be applied to 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 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 humans have.

The Human Genome is Like a Book: • The book is over one billion words long. • The book is bound in 5,000 300 page volumes (the equivalent to 800 bibles long) • The book fits into a cell nucleus the size of a pinpoint • A copy of the book (all 5000 volumes) is contained in every cell (except red blood cells) as a strand of DNA over two miles in length.

Types

Most biological entities 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 this auxiliary material, which is carried in plasmids. In such circumstances then, "genome" describes all of the genes and non-coding DNA that have the potential to be present.

In vertebrates such as sheep and other various animals however, "genome" carries the typical connotation of only chromosomal DNA. So although human mitochondria contain genes, these genes 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 DNA of one cell from one individual. To learn what variations in DNA 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 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

Further information: Genome project

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.[2] 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

Main article: Genome size

Organism	Genome size (base pairs)	Note
Virus, Bacteriophage MS2	3569	First sequenced RNA-genome
Virus, SV40	5224
Virus, Phage Φ-X174;	5386	First sequenced DNA-genome
Virus, Phage λ	5×104
Bacterium, Carsonella ruddii	1.6×105	Smallest non-viral genome, Feb 2007
Bacterium, Buchnera aphidicola	6×105
Bacterium, Wigglesworthia glossinidia	7×105
Bacterium, Escherichia coli	4×106
Amoeba, Amoeba dubia	6.7×1011	Largest known genome, Dec 2005
Plant, Arabidopsis thaliana	1.57×108	First plant genome sequenced, Dec 2000.
Plant, Genlisea margaretae	6.34×107	Smallest recorded flowering plant genome, 2006.
Plant, Fritillaria assyrica	1.3×1011
Plant, Populus trichocarpa	4.8×108	First tree genome, Sept 2006
Yeast,Saccharomyces cerevisiae	2×107
Fungus, Aspergillus nidulans	3×107
Nematode, Caenorhabditis elegans	9.8×107	First multicellular animal genome, December 1998
Insect, Drosophila melanogaster aka Fruit Fly	1.3×108
Insect, Bombyx mori aka Silk Moth	5.30×108
Insect, Apis mellifera aka Honey Bee	1.77×109
Fish, Tetraodon nigroviridis, type of Puffer fish	3.85×108	Smallest vertebrate genome known
Mammal, Homo sapiens	3.2×109
Fish, Protopterus aethiopicus aka Marbled lungfish	1.3×1011	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
• Genome project
• Human genome
• 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

• Benfey, P. (2004). Essentials of Genomics. Prentice Hall.
• Brown, Terence A. (2002). Genomes 2. Oxford: Bios Scientific Publishers. ISBN 978-1859960295.
• Gibson, Greg (2004). A Primer of Genome Science (Second Edition ed.). Sunderland, Mass: Sinauer Assoc. ISBN 0-87893-234-8. CS1 maint: Extra text (link)
• Gregory, T. Ryan (ed) (2005). The Evolution of the Genome. Elsevier. ISBN 0-12-301463-8.CS1 maint: Extra text: authors list (link)
• Reece, Richard J. (2004). Analysis of Genes and Genomes. Chichester: John Wiley & Sons. ISBN 0-470-84379-9.
• Saccone, Cecilia (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. PMID 14678738.
• Witzany, G. (2006). "Natural Genome Editing Competences of Viruses". Acta Biotheoretica. 54 (4): 235–253. PMID 17347785.

External links

• 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
• Software that maps an Artificial Genome sequence to a Network and to a Lineage tree
• IMG The Integrated Microbial Genomes system, for genome analysis by the DOE-JGI.