Genome

For a non-technical introduction to the topic, see Introduction to genetics.

For other uses, see Genome (disambiguation).

Part of a series on
Genetics
Key components
Chromosome DNA • RNA Genome Heredity Mutation Nucleotide Variation
Glossary Index Outline
History and topics
Introduction History
Evolution • Molecular Population genetics Mendelian inheritance Quantitative genetics Molecular genetics
Research
DNA sequencing Genetic engineering Genomics • Topics Medical genetics
Branches in genetics
Biology portal •v · d · e

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

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.^[1]

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.^[2]

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.^[3]

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

For more details on this topic, see 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, 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.^[4]

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.^[5]

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 ^[6][7].

Comparison of different genome sizes

Main article: Genome size

Organism type	Organism	Genome size (base pairs)	Genome size (in human-readable format)	mass - in pg	Note
Virus	Bacteriophage MS2	3,569	3.5kb	0.000002	First sequenced RNA-genome[8]
Virus	SV40	5,224	5.2kb		[9]
Virus	Phage Φ-X174	5,386	5.4kb		First sequenced DNA-genome[10]
Virus	HIV	9,749	9.7kb		[11]
Virus	Phage λ	48,502	48kb
Virus	Mimivirus	1,181,404	1.2Mb		Largest known viral genome
Bacterium	Haemophilus influenzae	1,830,000	1.8Mb		First genome of a living organism sequenced, July 1995[12]
Bacterium	Carsonella ruddii	159,662	160kb		Smallest non-viral genome.[13]
Bacterium	Buchnera aphidicola	600,000	600kb
Bacterium	Wigglesworthia glossinidia	700,000	700Kb
Bacterium	Escherichia coli	4,600,000	4.6Mb		[14]
Bacterium	Solibacter usitatus (strain Ellin 6076)	9,970,000	10Mb		Largest known Bacterial genome
Amoeboid	Polychaos dubium ("Amoeba" dubia)	670,000,000,000	670Gb	737	Largest known genome.[15] (Disputed [16])
Plant	Arabidopsis thaliana	157,000,000	157Mb		First plant genome sequenced, December 2000.[17]
Plant	Genlisea margaretae	63,400,000	63Mb		Smallest recorded flowering plant genome, 2006.[17]
Plant	Fritillaria assyrica	130,000,000,000	130Gb
Plant	Populus trichocarpa	480,000,000	480Mb		First tree genome sequenced, September 2006
Plant	Paris japonica (Japanese-native, pale-petal)	150,000,000,000	150Gb	152.23	Largest plant genome known
Moss	Physcomitrella patens	480,000,000	480Mb		First genome of a bryophyte sequenced, January 2008.[18]
Yeast	Saccharomyces cerevisiae	12,100,000	12.1Mb		First eukaryotic genome sequenced, 1996[19]
Fungus	Aspergillus nidulans	30,000,000	30Mb
Nematode	Caenorhabditis elegans	100,300,000	100Mb		First multicellular animal genome sequenced, December 1998[20]
Nematode	Pratylenchus coffeae	20,000,000	20Mb		Smallest animal genome known[21]
Insect	Drosophila melanogaster (fruit fly)	130,000,000	130Mb		[22]
Insect	Bombyx mori (silk moth)	530,000,000	530Mb
Insect	Apis mellifera (honey bee)	236,000,000	236Mb
Insect	Solenopsis invicta (fire ant)	480,000,000	480Mb		[23]
Fish	Tetraodon nigroviridis (type of puffer fish)	385,000,000	390Mb		Smallest vertebrate genome known
Mammal	Homo sapiens	3,200,000,000	3.2Gb	3
Fish	Protopterus aethiopicus (marbled lungfish)	130,000,000,000	130Gb	143	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.^[24][25]

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

1. ^ Ridley, M. (2006). Genome. New York, NY: Harper Perennial. ISBN 0-06-019497-9
2. ^ Joshua Lederberg and Alexa T. McCray (2001). "'Ome Sweet 'Omics -- A Genealogical Treasury of Words". The Scientist 15 (7). http://lhncbc.nlm.nih.gov/lhc/docs/published/2001/pub2001047.pdf. 
3. ^ Madigan M, Martinko J (editors) (2006). Brock Biology of Microorganisms (11th ed.). Prentice Hall. ISBN 0-13-144329-1. 
4. ^ "Genome Home". 2010-12-08. http://www.ncbi.nlm.nih.gov/sites/entrez?db=Genome&itool=toolbar. Retrieved 2011-01-27. 
5. ^ Wade, Nicholas (2007-05-31). "Genome of DNA Pioneer Is Deciphered". The New York Times. http://www.nytimes.com/2007/05/31/science/31cnd-gene.html?em&ex=1180843200&en=19e1d55639350b73&ei=5087%0A. Retrieved 2010-04-02. 
6. ^ "What's a Genome?". Genomenewsnetwork.org. 2003-01-15. http://www.genomenewsnetwork.org/resources/whats_a_genome/Chp3_1.shtml. Retrieved 2011-01-27. 
7. ^ NCBI_user_services (2004-03-29). "Mapping Factsheet". http://www.ncbi.nlm.nih.gov/About/primer/mapping.html. Retrieved 2011-01-27. 
8. ^ Fiers W, et al. (1976). "Complete nucleotide-sequence of bacteriophage MS2-RNA - primary and secondary structure of replicase gene". Nature 260 (5551): 500–507. Bibcode 1976Natur.260..500F. doi:10.1038/260500a0. PMID 1264203. http://www.nature.com/nature/journal/v260/n5551/abs/260500a0.html. 
9. ^ Fiers W, Contreras R, Haegemann G, Rogiers R, Van de Voorde A, Van Heuverswyn H, Van Herreweghe J, Volckaert G, Ysebaert M (1978). "Complete nucleotide sequence of SV40 DNA". Nature 273 (5658): 113–120. doi:10.1038/273113a0. PMID 205802. http://www.nature.com/nature/journal/v273/n5658/abs/273113a0.html. 
10. ^ Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M (1977). "Nucleotide sequence of bacteriophage phi X174 DNA". Nature 265 (5596): 687–695. doi:10.1038/265687a0. PMID 870828. http://www.nature.com/nature/journal/v265/n5596/abs/265687a0.html. 
11. ^ "Virology - Human Immunodeficiency Virus And Aids, Structure: The Genome And Proteins Of HIV". Pathmicro.med.sc.edu. 2010-07-01. http://pathmicro.med.sc.edu/lecture/hiv9.htm. Retrieved 2011-01-27. 
12. ^ Fleischmann R, Adams M, White O, Clayton R, Kirkness E, Kerlavage A, Bult C, Tomb J, Dougherty B, Merrick J (1995). "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd". Science 269 (5223): 496–512. doi:10.1126/science.7542800. PMID 7542800. http://www.sciencemag.org/cgi/content/abstract/269/5223/496. 
13. ^ Nakabachi A, Yamashita A, Toh H, et al. (October 2006). "The 160-kilobase genome of the bacterial endosymbiont Carsonella". Science 314 (5797): 267. doi:10.1126/science.1134196. PMID 17038615. 
14. ^ Frederick R. Blattner, Guy Plunkett III, et al. (1997). "The Complete Genome Sequence of Escherichia coli K-12". Science 277 (5331): 1453–1462. doi:10.1126/science.277.5331.1453. PMID 9278503. http://www.sciencemag.org/cgi/content/abstract/277/5331/1453. 
15. ^ Parfrey LW, Lahr DJG, Katz LA (2008). "The Dynamic Nature of Eukaryotic Genomes". Molecular Biology and Evolution 25 (4): 787–94. doi:10.1093/molbev/msn032. PMC 2933061. PMID 18258610. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2933061. 
16. ^ ScienceShot: Biggest Genome Ever, comments: "The measurement for Amoeba dubia and other protozoa which have been reported to have very large genomes were made in the 1960s using a rough biochemical approach which is now considered to be an unreliable method for accurate genome size determinations."
17. ^ ^{a b} Greilhuber J, Borsch T, Müller K, Worberg A, Porembski S, and Barthlott W (2006). "Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size". Plant Biology 8 (6): 770–777. doi:10.1055/s-2006-924101. PMID 17203433. 
18. ^ Lang D, Zimmer AD, Rensing SA, Reski R (October 2008). "Exploring plant biodiversity: the Physcomitrella genome and beyond". Trends Plant Sci 13 (10): 542–549. doi:10.1016/j.tplants.2008.07.002. PMID 18762443. 
19. ^ "Saccharomyces Genome Database". Yeastgenome.org. http://www.yeastgenome.org/. Retrieved 2011-01-27. 
20. ^ The C. elegans Sequencing Consortium (1998). "Genome sequence of the nematode C. elegans: a platform for investigating biology". Science 282 (5396): 2012–2018. doi:10.1126/science.282.5396.2012. PMID 9851916. http://www.sciencemag.org/cgi/content/abstract/282/5396/2012. 
21. ^ Gregory TR (2005). "Animal Genome Size Database". http://www.genomesize.com. http://www.genomesize.com/statistics.php?stats=entire#stats_top. 
22. ^ Adams MD, Celniker SE, Holt RA, et al. (2000). "The genome sequence of Drosophila melanogaster". Science 287 (5461): 2185–95. Bibcode 2000Sci...287.2185.. doi:10.1126/science.287.5461.2185. PMID 10731132. http://www.sciencemag.org/cgi/content/abstract/287/5461/2185. Retrieved 2007-05-25. 
23. ^ Wurm Y et al. (2011). "The genome of the fire ant Solenopsis invicta". PNAS 108 (14): 5679–5684. doi:10.1073/pnas.1009690108. PMC 3078418. PMID 21282665. http://www.pnas.org/content/early/2011/01/24/1009690108.abstract. Retrieved 2011-02-01. 
24. ^ Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M, Hutchison CA 3rd, Smith HO, Venter JC (2006). "Essential genes of a minimal bacterium". Proc Natl Acad Sci USA 103 (2): 425–30. doi:10.1073/pnas.0510013103. PMC 1324956. PMID 16407165. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1324956. 
25. ^ Forster AC, Church GM (2006). "Towards synthesis of a minimal cell". Mol Syst Biol. 2:45 (1): 45. doi:10.1038/msb4100090. PMC 1681520. PMID 16924266. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1681520. 

Further reading

• Benfey, P.; Protopapas, A.D. (2004). Essentials of Genomics. Prentice Hall. 
• Brown, Terence A. (2002). Genomes 2. Oxford: Bios Scientific Publishers. ISBN 978-1859960295. 
• Gibson, Greg; Muse, Spencer V. (2004). A Primer of Genome Science (Second ed.). 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; 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. doi:10.1016/S1359-6446(03)02918-0. PMID 14678738. 

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.