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Genome

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For other uses, see Genome (disambiguation).
For a non-technical introduction to the topic, see Introduction to genetics.
An image of multiple chromosomes, making up a genome

In classical genetics, the genome of a diploid organism including eukarya refers to a full set of chromosomes or genes in a gamete; thereby, a regular somatic cell contains two full sets of genomes. In a haploid organism, including bacteria, archaea, virus, and mitochondria, a cell contains only a single set of genome, usually in a single circular or contiguous linear DNA (or RNA for some viruses). In modern molecular biology the genome of an organism is its hereditary information encoded in DNA (or, for some viruses, RNA).

The genome 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.[1]

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 (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 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

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.[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

Main article: Genome size
Organism Genome size (base pairs) Note
Virus, Bacteriophage MS2 3,569 First sequenced RNA-genome[2]
Virus, SV40 5,224 [3]
Virus, Phage Φ-X174; 5,386 First sequenced DNA-genome[4]
Virus, Phage λ 50,000
Bacterium, Haemophilus influenzae 1,830,000 First genome of living organism, July 1995[5]
Bacterium, Carsonella ruddii 160,000 Smallest non-viral genome.[6]
Bacterium, Buchnera aphidicola 600,000
Bacterium, Wigglesworthia glossinidia 700,000
Bacterium, Escherichia coli 4,000,000 [7]
Amoeba, Amoeba dubia 670,000,000,000 Largest known genome.[8]
Plant, Arabidopsis thaliana 157,000,000 First plant genome sequenced, Dec 2000.[9]
Plant, Genlisea margaretae 63,400,000 Smallest recorded flowering plant genome, 2006.[9]
Plant, Fritillaria assyrica 130,000,000,000
Plant, Populus trichocarpa 480,000,000 First tree genome, Sept 2006
Yeast,Saccharomyces cerevisiae 20,000,000 [10]
Fungus, Aspergillus nidulans 30,000,000
Nematode, Caenorhabditis elegans 98,000,000 First multicellular animal genome, December 1998[11]
Insect, Drosophila melanogaster aka Fruit Fly 130,000,000 [12]
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

References

  1. ^ Joshua Lederberg and Alexa T. McCray (2001). "'Ome Sweet 'Omics -- A Genealogical Treasury of Words" (PDF). The Scientist. 15 (7).
  2. ^ Fiers W; et al. (1976). "Complete nucleotide-sequence of bacteriophage MS2-RNA - primary and secondary structure of replicase gene". Nature. 260: 500–507. doi:10.1038/260500a0. PMID 1264203. {{cite journal}}: Explicit use of et al. in: |author= (help)
  3. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  5. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  6. ^ Nakabachi A, Yamashita A, Toh H; et al. (2006). "The 160-kilobase genome of the bacterial endosymbiont Carsonella". Science (journal). 314 (5797): 267. doi:10.1126/science.1134196. PMID 17038615. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  7. ^ Frederick R. Blattner, Guy Plunkett III; et al. (1997). "The Complete Genome Sequence of Escherichia coli K-12". science. 277: 1453–1462. doi:10.1126/science.277.5331.1453. PMID 9278503. {{cite journal}}: Explicit use of et al. in: |author= (help)
  8. ^ Parfrey, L.W. (2008). "The Dynamic Nature of Eukaryotic Genomes". Molecular Biology and Evolution. 25 (4): 787. doi:10.1093/molbev/msn032. PMID 18258610. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  9. ^ 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: 770–777. doi:10.1055/s-2006-924101. PMID 17203433.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  10. ^ A. Goffeau; et al. (1996-10-25). "Life with 6000 genes". Science. 274: 546–567. doi:10.1126/science.274.5287.546. PMID 8849441. {{cite journal}}: Explicit use of et al. in: |author= (help)
  11. ^ 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. ISSN 0036-8075. PMID 9851916. {{cite journal}}: Unknown parameter |quotes= ignored (help)
  12. ^ Adams MD, Celniker SE, Holt RA; et al. (2000). "The genome sequence of Drosophila melanogaster". Science. 287 (5461): 2185–95. doi:10.1126/science.287.5461.2185. PMID 10731132. Retrieved 2007-05-25. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)

Further reading

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