Genome

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An image of multiple chromosomes, making up a genome

Genome is one complete set of hereditary information that characterizes an organism, as encoded in the DNA (or, for some viruses, RNA). That is, a genome is equivalent to the complete genetic sequence on one of the two sets of chromosomes of the somatic cells of a diploid individual, or the total genetic sequence in the single chromosome of a bacteria, or the sequence of RNA in an RNA virus. The genome includes both the genes and the non-coding sequences of DNA.

In eukaryotes, the term genome can be applied specifically to mean that genetic content 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.

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.

Overview

The units of heredity in living organisms are encoded in an organism's genetic material, DNA. The nucleic acid DNA (deoxyribonucleic acid) contains the genetic instructions used in the development and functioning of all known living organisms. (Some viruses utilize RNA, but are not universally considered living organisms.) The main role of DNA molecules is the long-term storage of information. DNA teams with the nucleic acid RNA (ribonucleic acid) to together oversee and carry out the construction of the tens of thousands of protein molecules needed by living organisms.

As nucleic acids, DNA and RNA contain numerous nucleotides (each composed of a phosphate unit, a sugar unit, and a "base" unit) linked recursively through the sugar and phosphate units to form a long chain with base units protruding from it. Nucleic acids carry the coded genetic information of life according to the order of the base units extending along the length of the molecule. The DNA which carries genetic information in cells is normally packaged in the form of one or more large macromolecules called chromosomes.

Genome refers to the total DNA sequence that characterizes a species.[1] That it, a genome is the genetic content (DNA sequences) contained within one set of chromosomes in eukaryotes, or the single chromosome of prokaryotes. For those viruses that utilize only RNA as hereditary material, genome is equivalent to the RNA sequence. Genome includes not only the coding genes of a chromosome but also the non-coding sequences, sometimes referred to as "junk DNA." In humans, this non-coding DNA may be as much as 97% of the total DNA.[2]

The term genome 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 (Lederberg and McCray 2001).

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.

The size of genomes is measured in terms of the number of base pairs, although the large numbers mean that the unit used is megabases (Mb), corresponding to 1,000 base pairs.Cite error: Closing </ref> missing for <ref> tag |- |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 Honeybee |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 meters (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. 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.

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 acquisition of entire sets of genes, even whole genomes of organisms, has been postulated as a major source of transmitted variation in organisms.[13]And eukaryotic cells seem to have experienced a transfer of some genetic material from their chloroplast and mitochondrial genomes to their nuclear chromosomes.

Notes

  1. ↑ A. W. Cuthbert, "Genome," in C. Blakemore and S. Jennett, The Oxford Companion to the Body (New York: Oxford University Press, 2001). ISBN 019852403X.
  2. ↑ E. Mayr, What Evolution Is (New York: Basic Books, 2001). ISBN 0465044263.
  3. ↑ W. Fiers, R. Contreras, G. Haegemann, R. Rogiers,, A. Van de Voorde, H. Van Heuverswyn, J. Van Herreweghe, G. Volckaert, and M. Ysebaert, "Complete nucleotide sequence of SV40 DNA," Nature 273, no. 5658(1978): 113–120. PMID 205802. Retrieved July 12, 2008.
  4. ↑ F. Sanger, G. M. Air, B. G. Barrell, N. L. Brown, A. R. Coulson, C. A. Fiddes, C. A. Hutchison, P. M. Slocombe, and M. Smith, "Nucleotide sequence of bacteriophage phi X174 DNA," Nature 265, no. 5596(1977): 687–695. PMID 870828. Retrieved July 12, 2008.
  5. ↑ R. Fleischmann, M. Adams, O. White, R. Clayton, E. Kirkness, A. Kerlavage, C. Bult, J. Tomb, B. Dougherty, and J. Merrick. 1995. "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd," Science 269, no. 5223(1995): 496–512. PMID 7542800. Retrieved July 12, 2008.
  6. ↑ A. Nakabachi, A. Yamashita, H. Toh, et al., ["http://www.ncbi.nlm.nih.gov/pubmed/17038615 The 160-kilobase genome of the bacterial endosymbiont Carsonella,"] Science 314, no. 5797(2006): 267. PMID 17038615. Retrieved July 12, 2008.
  7. ↑ F. R. Blattner, G. Plunkett, C. A. Bloch, et al., "The complete genome sequence of Escherichia coli K-12," Science 277(1997): 1453–1462. PMID 9278503. Retrieved July 12, 2008.
  8. ↑ L. W. Parfrey, D. J. G. Lahr, and L. A. Katz, "The dynamic nature of eukaryotic genomes," Molecular Biology and Evolution 25, no. 4(2008): 787-794. PMID 18258610. Retrieved July 12, 2008.
  9. ↑ 9.0 9.1 J. Greilhuber, T. Borsch, K. Müller, A. Worberg, S. Porembski, and W. Barthlott, W. "Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size," Plant Biology 8(2006): 770=777. PMID 17203433. Retrieved July 12, 2008.
  10. ↑ A. Goffeau, B. G. Barrell, H. Bussey, et al., "Life with 6000 genes," Science 274(1996): 546–567. PMID 8849441. Retrieved July 12, 2008.
  11. ↑ The C. elegans Sequencing Consortium, "Genome sequence of the nematode C. elegans: A platform for investigating biology," Science 282, no. 5396(1998): 2012–2018. PMID 9851916. Retrieved July 12, 2008.
  12. ↑ M. D. Adams, S. E. Celniker R. A. Holt, et al., "The genome sequence of Drosophila melanogaster," Science 287, no. 5461(2000): 2185–2195. PMID 10731132. Retrieved July 12, 2008.
  13. ↑ L. Margulis and D. Sagan, Acquiring Genomes (New York: Basic Books, 2002). ISBN 0465043917.

References
ISBN links support NWE through referral fees

  • 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. 


[1]

  • 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. 

[1] By NICHOLAS WADE Published: May 31, 2007


  • 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

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  1. ↑ Joshua Lederberg and Alexa T. McCray (2001). 'Ome Sweet 'Omics — A Genealogical Treasury of Words. The Scientist 15 (7).
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