Difference between revisions of "Genome" - New World Encyclopedia

From New World Encyclopedia
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As nucleic acids, DNA and RNA contain numerous [[nucleotide]]s (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 [[Cell (biology)|cells]] is normally packaged in the form of one or more large macromolecules called chromosomes.
 
As nucleic acids, DNA and RNA contain numerous [[nucleotide]]s (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 [[Cell (biology)|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 (Cuthbert 2001). That it, a genome is the genetic content (DNA sequences) contained within one set of chromosomes in [[eukaryote]]s, or the single chromosome of [[prokaryote]]s. 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 (Mayr 2001).
+
Genome refers to the total DNA sequence that characterizes a species.<ref>A. W. Cuthbert, "Genome," in C. Blakemore and S. Jennett, ''The Oxford Companion to the Body'' (New York: Oxford University Press, 2001). ISBN 019852403X.</ref> That it, a genome is the genetic content (DNA sequences) contained within one set of chromosomes in [[eukaryote]]s, or the single chromosome of [[prokaryote]]s. 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.<ref name=Mayr2001>E. Mayr, ''What Evolution Is'' (New York: Basic Books, 2001). ISBN 0465044263.</ref>
  
 
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 '''''gen'''e'' and ''chromos'''ome'''''; however, many related ''-ome'' words already existed, such as ''[[biome]]'' and ''[[rhizome]]'', forming a vocabulary into which ''genome'' fits systematically (Lederberg and McCray 2001).
 
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 '''''gen'''e'' and ''chromos'''ome'''''; however, many related ''-ome'' words already existed, such as ''[[biome]]'' and ''[[rhizome]]'', forming a vocabulary into which ''genome'' fits systematically (Lederberg and McCray 2001).
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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 [[gene]]s or groups of genes.
 
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 [[gene]]s 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 (Mayr 2001).
+
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.<ref name=Mayr2001>
  
 
== Genomes of organelles ==
 
== Genomes of organelles ==
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== Genome determinations and species comparisons==
 
== Genome determinations and species comparisons==
  
−
Technology has developed whereby it is possible to determine the entire DNA sequence of an organism's genome. 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|bacteriophage MS2]]). The first DNA-genome project to be completed was the [[Phi-X174 phage|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. Genomes were subsequently elucidated for several bacteria (including ''Escherichia coli''), then [[yeast]] (''Saccharomyces), a plant (''Arabidopsis), and some animals (the [[nematode]] ''Caenorhabditis'' and the [[fruit fly]] ''Drosophila'') (Mayr 2001).  
+
Technology has developed whereby it is possible to determine the entire DNA sequence of an organism's genome. 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|bacteriophage MS2]]). The first DNA-genome project to be completed was the [[Phi-X174 phage|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. Genomes were subsequently elucidated for several bacteria (including ''Escherichia coli''), then [[yeast]] (''Saccharomyces), a plant (''Arabidopsis), and some animals (the [[nematode]] ''Caenorhabditis'' and the [[fruit fly]] ''Drosophila'').<ref name=Mayr2001>
  
−
The genome of numerous organisms has since been done. The [[Human Genome Project]] was organized to [[physical map|map]] and to [[sequencing|sequence]] the human genome. The completion of the essential sequence of the human genome was announced in June 2000 (Mayr 2001). Other genome projects include [[mus musculus|mouse]], [[rice]], and so forth, with the cost of sequencing continuing to drop and making the process more feasible. In May 2007, the full genome of DNA pioneer James D. Watson was recorded, perhaps a gateway to upcoming personalized genomic medicine (Wade 2007).  
+
The genome of numerous organisms has since been done. The [[Human Genome Project]] was organized to [[physical map|map]] and to [[sequencing|sequence]] the human genome. The completion of the essential sequence of the human genome was announced in June 2000.<ref name=Mayr2001> Other genome projects include [[mus musculus|mouse]], [[rice]], and so forth, with the cost of sequencing continuing to drop and making the process more feasible. In May 2007, the full genome of DNA pioneer James D. Watson was recorded, perhaps a gateway to upcoming personalized genomic medicine (Wade 2007).  
  
−
One of the more interesting results from comparing the genomes of various organisms is the the basic genes of higher organism can be traced back to genes in bacteria (Mayr 2001).
+
One of the more interesting results from comparing the genomes of various organisms is the the basic genes of higher organism can be traced back to genes in bacteria.<ref name=Mayr2001>
  
−
In general, genome size is larger for organisms higher on the phylogenetic tree, with humans having a genome of about 3500 Mb and a bacterium only about 4 Mb (Mayr 2001). However, the presence of coding and non-coding DNA also is reflected in many organisms, such as [[lungfish]]es and [[salamander]]s, having unusually large genomes (Mayr 2001). The largest known genome belongs to an [[amoeba]] (''Amoeba dubia'') (Parfrey et al. 2008).
+
In general, genome size is larger for organisms higher on the phylogenetic tree, with humans having a genome of about 3500 Mb and a bacterium only about 4 Mb.<ref name=Mayr2001> However, the presence of coding and non-coding DNA also is reflected in many organisms, such as [[lungfish]]es and [[salamander]]s, having unusually large genomes.<ref name=Mayr2001> The largest known genome belongs to an [[amoeba]] (''Amoeba dubia'') (Parfrey et al. 2008).
  
 
=== Genomes of various species ===
 
=== Genomes of various species ===
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|[[Virus]], [[SV40]]
 
|[[Virus]], [[SV40]]
 
|5,224
 
|5,224
−
|<ref name=Fiers1978>W. Fiers, R. Contreras, G. Haegemann, R. Rogiers,, A. Van de Voorde, H. Van Heuverswyn, J. Van Herreweghe, G. Volckaert, and M. Ysebaert, [http://www.nature.com/nature/journal/v273/n5658/abs/273113a0.html "Complete nucleotide sequence of SV40 DNA,"] ''Nature'' 273(1978)(5658): 113–120. PMID 205802. Retrieved July 12, 2008.</ref>
+
|<ref name=Fiers1978>W. Fiers, R. Contreras, G. Haegemann, R. Rogiers,, A. Van de Voorde, H. Van Heuverswyn, J. Van Herreweghe, G. Volckaert, and M. Ysebaert, [http://www.nature.com/nature/journal/v273/n5658/abs/273113a0.html "Complete nucleotide sequence of SV40 DNA,"] ''Nature'' 273, no. 5658(1978): 113–120. PMID 205802. Retrieved July 12, 2008.</ref>
 
|-
 
|-
 
|[[Virus]], [[Phi-X174 phage|Phage Φ-X174;]]
 
|[[Virus]], [[Phi-X174 phage|Phage Φ-X174;]]
 
|5,386
 
|5,386
−
|First sequenced DNA-genome<ref name=Sanger1977>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, [http://www.nature.com/nature/journal/v265/n5596/abs/265687a0.html "Nucleotide sequence of bacteriophage phi X174 DNA,"] ''Nature'' 265(1977)(5596): 687–695. PMID 870828. Retrieved July 12, 2008.</ref>
+
|First sequenced DNA-genome<ref name=Sanger1977>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, [http://www.nature.com/nature/journal/v265/n5596/abs/265687a0.html "Nucleotide sequence of bacteriophage phi X174 DNA,"] ''Nature'' 265, no. 5596(1977): 687–695. PMID 870828. Retrieved July 12, 2008.</ref>
 
|-
 
|-
 
|[[Virus]], [[lambda phage|Phage λ]]
 
|[[Virus]], [[lambda phage|Phage λ]]
Line 71: Line 71:
 
|[[Bacterium]], ''[[Haemophilus influenzae]]''
 
|[[Bacterium]], ''[[Haemophilus influenzae]]''
 
| 1,830,000
 
| 1,830,000
−
|First genome of living organism, July 1995<ref name=Fleichmann_1995>R. Fleischmann, M. Adams, O.  White, R. Clayton, E. Kirkness, A. Kerlavage, C. Bult, J. Tomb, B. Dougherty, and J. Merrick. 1995. [http://www.sciencemag.org/cgi/content/abstract/269/5223/496 "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd,"] ''Science'' 269(1995)(5223): 496–512. PMID 7542800. Retrieved July 12, 2008.</ref>  
+
|First genome of living organism, July 1995<ref name=Fleichmann_1995>R. Fleischmann, M. Adams, O.  White, R. Clayton, E. Kirkness, A. Kerlavage, C. Bult, J. Tomb, B. Dougherty, and J. Merrick. 1995. [http://www.sciencemag.org/cgi/content/abstract/269/5223/496 "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd,"] ''Science'' 269, no. 5223(1995): 496–512. PMID 7542800. Retrieved July 12, 2008.</ref>  
 
|-
 
|-
 
|[[Bacterium]], ''[[Carsonella ruddii]]''
 
|[[Bacterium]], ''[[Carsonella ruddii]]''
 
|160,000
 
|160,000
−
|Smallest non-viral genome.<ref>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(2006)(5797): 267. PMID 17038615. Retrieved July 12, 2008.</ref>
+
|Smallest non-viral genome.<ref>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.</ref>
 
|-
 
|-
 
|[[Bacterium]], ''[[Buchnera aphidicola]]''
 
|[[Bacterium]], ''[[Buchnera aphidicola]]''
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|[[Amoeba]],  ''[[Amoeba dubia]]''
 
|[[Amoeba]],  ''[[Amoeba dubia]]''
 
|670,000,000,000
 
|670,000,000,000
−
|Largest known genome.<ref name=Parfrey2008>L. W. Parfrey, D. J. G. Lahr, and L. A. Katz, [http://www.ncbi.nlm.nih.gov/pubmed/18258610 "The dynamic nature of eukaryotic genomes,"] ''Molecular Biology and Evolution'' 25(2008)(4): 787-794. PMID 18258610. Retrieved July 12, 2008.</ref>
+
|Largest known genome.<ref name=Parfrey2008>L. W. Parfrey, D. J. G. Lahr, and L. A. Katz, [http://www.ncbi.nlm.nih.gov/pubmed/18258610 "The dynamic nature of eukaryotic genomes,"] ''Molecular Biology and Evolution'' 25, no. 4(2008): 787-794. PMID 18258610. Retrieved July 12, 2008.</ref>
 
|-
 
|-
 
|[[Plant]],  ''[[Arabidopsis thaliana]]''
 
|[[Plant]],  ''[[Arabidopsis thaliana]]''
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|[[Nematoda|Nematode]], ''[[Caenorhabditis elegans]]''
 
|[[Nematoda|Nematode]], ''[[Caenorhabditis elegans]]''
 
|98,000,000
 
|98,000,000
−
|First multicellular animal genome, December 1998<ref>The ''C. elegans'' Sequencing Consortium, [http://www.sciencemag.org/cgi/content/abstract/282/5396/2012 "Genome sequence of the nematode ''C. elegans'': A platform for investigating biology,"] ''Science'' 282(1998)(5396): 2012–2018. PMID 9851916. Retrieved July 12, 2008.</ref>
+
|First multicellular animal genome, December 1998<ref>The ''C. elegans'' Sequencing Consortium, [http://www.sciencemag.org/cgi/content/abstract/282/5396/2012 "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.</ref>
 
|-
 
|-
 
|[[Insect]], ''[[Drosophila melanogaster]]'' aka Fruit Fly
 
|[[Insect]], ''[[Drosophila melanogaster]]'' aka Fruit Fly
 
|130,000,000
 
|130,000,000
−
|<ref name=Adams_2000>M. D. Adams, S. E. Celniker R. A. Holt, et al., [http://www.sciencemag.org/cgi/content/abstract/287/5461/2185 "The genome sequence of ''Drosophila melanogaster'',"] ''Science'' 287(2000)(5461): 2185–2195. PMID 10731132. Retrieved July 12, 2008.</ref>
+
|<ref name=Adams_2000>M. D. Adams, S. E. Celniker R. A. Holt, et al., [http://www.sciencemag.org/cgi/content/abstract/287/5461/2185 "The genome sequence of ''Drosophila melanogaster'',"] ''Science'' 287, no. 5461(2000): 2185–2195. PMID 10731132. Retrieved July 12, 2008.</ref>
 
|-
 
|-
 
|[[Insect]], ''[[Bombyx mori]]'' aka Silk Moth
 
|[[Insect]], ''[[Bombyx mori]]'' aka Silk Moth
Line 150: Line 150:
  
 
== Genome evolution ==
 
== Genome evolution ==
−
Genomes are more than the sum of an organism's genes and have traits that may be [[Measurement|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).   
+
Genomes are more than the sum of an organism's genes and have traits that may be [[Measurement|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.   
  
 
[[gene duplication|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 [[polyploidy|entire genomes]].  Such duplications are probably fundamental to the creation of genetic novelty.
 
[[gene duplication|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 [[polyploidy|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 [[microbe]]s. Also, [[Eukaryote|eukaryotic cells]] seem to have experienced a transfer of some genetic material from their [[chloroplast]] and [[mitochondria]]l genomes to their nuclear chromosomes.
+
[[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 [[microbe]]s. Also acquisition of entire sets of genes, even whole genomes of organisms, has been postulated as a major source of transmitted variation in organisms.<ref>L. Margulis and D. Sagan, ''Acquiring Genomes'' (New York: Basic Books, 2002). ISBN 0465043917.</ref>And [[Eukaryote|eukaryotic cells]] seem to have experienced a transfer of some genetic material from their [[chloroplast]] and [[mitochondria]]l genomes to their nuclear chromosomes.
−
 
 
−
==See also==
 
−
<div style="-moz-column-count:3; column-count:3;">
 
−
*[[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]]
 
−
</div>
 
  
 
==Notes==
 
==Notes==
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==References==
 
==References==
−
* Cuthbert, A. W. 2001. Genome. In C. Blakemore and S. Jennett, ''The Oxford Companion to the Body''. New York: Oxford University Press. ISBN 019852403X.
+
 
  
 
* {{cite book|last=Benfey|first=P.|coauthors=Protopapas, A.D.|authorlink=|title=Essentials of Genomics|edition=|publisher=Prentice Hall|location=|year=2004|isbn=|series=}}
 
* {{cite book|last=Benfey|first=P.|coauthors=Protopapas, A.D.|authorlink=|title=Essentials of Genomics|edition=|publisher=Prentice Hall|location=|year=2004|isbn=|series=}}
Line 186: Line 167:
 
* {{cite book|last=Gregory|first=T. Ryan (ed)|coauthors=|authorlink=|title=[[The Evolution of the Genome]]|edition=|publisher=Elsevier|location=|year=2005|isbn=0-12-301463-8|series=}}
 
* {{cite book|last=Gregory|first=T. Ryan (ed)|coauthors=|authorlink=|title=[[The Evolution of the Genome]]|edition=|publisher=Elsevier|location=|year=2005|isbn=0-12-301463-8|series=}}
  
−
* Mayr, 2001.
+
 
  
 
<ref>{{cite journal |author = Joshua Lederberg and Alexa T. McCray | title='Ome Sweet 'Omics — A Genealogical Treasury of Words | journal=The Scientist | volume=15 | issue=7 | year=2001 | url=http://lhncbc.nlm.nih.gov/lhc/docs/published/2001/pub2001047.pdf}}</ref>
 
<ref>{{cite journal |author = Joshua Lederberg and Alexa T. McCray | title='Ome Sweet 'Omics — A Genealogical Treasury of Words | journal=The Scientist | volume=15 | issue=7 | year=2001 | url=http://lhncbc.nlm.nih.gov/lhc/docs/published/2001/pub2001047.pdf}}</ref>

Revision as of 00:42, 13 July 2008

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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