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[[Image:Legionella pneumophila-s.jpg|right|frame|''[[Legionella pneumophila]]'' are [[prokaryote|prokaryotic]] bacteria that can persist and reproduce inside [[phagocytic]] cells such as protists that have eaten them. They occasionally capture genes from their [[eukaryotic]] host cells, and are competent in [[transformation]].]]
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'''Horizontal gene transfer (HGT)''' (also called '''lateral gene transfer (LGT)''') is any process in which an [[organism]] transfers genetic material to another [[cell]] or organism that is ''not'' one of its own offspring. HGT is thus very different from common [[Biological inheritance|vertical gene transfer]] which involves simple inheritance of parental traits by the progeny as part of the normal organism's life cycle, be it a sexual fusion of [[gametes]] to form [[zygotes]] as in [[animals]] and [[plants]], or asexual propagation as in [[microorganism]]s such as [[bacteria]] and [[fungi]]. HGT occurs at a lower frequency than vertical gene transfer, so is not easily detected directly; its discovery depends on using special techniques to enable rare genetic events to be detected or inferred.
 
[[Image:Legionella pneumophila-s.jpg|right|frame|''[[Legionella pneumophila]]'' are [[prokaryote|prokaryotic]] bacteria that can survive and reproduce inside [[phagocytic]] cells such as protists that have eaten them. They are competent in DNA [[transformation]] and occasionally capture genes from their [[eukaryotic]] host cells.]]
 
'''Horizontal gene transfer''' occurs when an [[organism]] transfers its genetic material to a being ''other'' than one of its own offspring. The actual process of this transfer can be by any mechanism, but because genes are not passing by descent, horizontal gene transfer (abbreviated as HGT) is always very different from [[Biological inheritance|vertical gene transfer]]. In vertical descent, parental traits are inherited by progeny by one of two general methods: either (1) ''sexual reproduction'' in which [[gametes]] form [[zygotes]], a common method in higher animals and plants, or (2) by ''asexual reproduction'', where splitting of cells or an entire organism grows from a fragment, as is usual in [[bacteria]] and [[Fungus|fungi]], but which also happens in some animals and plants. HGT is a much more recently discovered route of passage for genetic material; it is relatively common in [[microorganism]]s, and to a lesser extent in plants. By HGT, genetic material can be shared between organisms without the immediate relatedness of mother cell to daughter cells, or parent organisms to offspring; indeed, by HGT material can pass between organismsthat are not even be of the same [[species]], [[genus]], sub-kingdom or kingdom of life form. HGT (sometimes called ''lateral'' gene transfer) is very much less common than vertical gene transfer, so its detection requires special techniques.


==Introduction==
==Introduction==
The advent of [[genomics|genome]] science and [[bioinformatics]] has provided abundant indirect evidence that extensive natural HGT occurs between diverse biological [[taxa]] that are widely separated in the [[phylogeny|phylogenetic]] tree. About 2% of core microbial genes arise from HGT, and this allows the the main lineages of microbial evolution to be treated as trees with HGT cobwebs (see figures). These transfers include gene movement between different microbial species and other microbial [[taxa]] such as protists, between different plant families, between different animals, and between bacteria and plants.
Evidence from [[genomics|genome]] science and [[bioinformatics]] shows that HGT has occurred between diverse biological [[taxa]] that are widely separated in the [[phylogeny|phylogenetic]] [http://www.tolweb.org/tree/ tree of life]. Known HGTs include movement of genetic material between different species of microbes and other microbial taxa such as protists, gene movement between different plant families, between different animals, and between bacteria and plants. [[Image:Cobwebsoflife.jpg|right|frame|HGT — gene exchange between non-related organisms —appears commonplace among bacteria, but contributes just small fragments of genetic information, leaving the traditional tree of life intact. From: [http://biology.plosjournals.org/perlserv/?request=slideshow&type=figure&doi=10.1371/journal.pbio.0030347&id=36052    Comparing Gene Trees and Genome Trees: A Cobweb of Life? PLoS Biol 3:e347]]]


[[Image:Cobwebsoflife.jpg|right|frame|HGT — gene exchange between non-related organisms —appears commonplace among bacteria, but contributes just small bits of genetic information, leaving the traditional tree of life intact. From: [http://biology.plosjournals.org/perlserv/?request=slideshow&type=figure&doi=10.1371/journal.pbio.0030347&id=36052  Comparing Gene Trees and Genome Trees: A Cobweb of Life? ''PLoS Biol'' '''3''' e347]]]
Microorganisms appear to be most affected by HGT, but even in microbes only about 2% of core genes are transferred laterally. Because this percentage is so low, the main lineages of microbial evolution can still be treated as 'trees' branched by vertical descent, with HGT included in the scheme only as 'cobwebs' (see figure at right).


Gene transfers between different biological [[domain]]s, such as between [[eukaryote|eukaryotic]] protists and [[bacteria]] <ref>Suwwan de Felipe K ''et al'' (2005) Evidence for acquisition of Legionella type IV secretion substrates via interdomain horizontal gene transfer ''J Bacteriol'' '''187''':7716-26</ref>
Gene transfers between different biological [[Three-domain system|sub-kingdoms]] (domains), such as between [[eukaryote|eukaryotic]] protists and bacteria, or between bacteria and insects are the most phylogenetically extreme cases of HGT. An example is bacterial 'rol' genes from ''Agrobacterium'' species which have been found in tobacco plants (''Nicotiniana'').<ref>de Felipe K ''et al.'' (2005) Evidence for acquisition of Legionella type IV secretion substrates via interdomain horizontal gene transfer. J Bacteriol [http://jb.asm.org/cgi/content/full/187/22/7716?view=long&pmid=16267296 187:7716-26]  PMID 16267296 (Open access)
, or between bacteria and insects <ref>Kondo N ''et al'' (2002) Genome fragment of ''Wolbachia'' endosymbiont transferred to X chromosome of host insect ''PNAS USA'' [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=137875 '''99''':14280-5]</ref> are the most phylogenetically extreme cases of HGT. Bacterial "rol" genes from ''Agrobacterium'' species have for instance been found in plants of the tobacco (''Nicotiniana'') genus. <ref>Intrieri MC, Buiatti M (2001) The horizontal transfer of Agrobacterium rhizogenes genes and the evolution of the genus Nicotiana ''Mol Phylogen Evol'' '''20''':100-10 PMID 11421651</ref>.
* Kondo N ''et al.'' (2002) Genome fragment of ''Wolbachia'' endosymbiont transferred to X chromosome of host insect. Proc Natl Acad Sci USA [http://www.pnas.org/cgi/content/full/99/22/14280 99:14280-5] PMID 12386340 (Open access)
* Intrieri MC, Buiatti M (2001) The horizontal transfer of ''Agrobacterium'' rhizogenes genes and the evolution of the genus ''Nicotiana''. Mol Phylogen Evol 20:100-10 PMID 11421651</ref>


HGT is closely connected with [[mobile DNA]] ("jumping genes", [[transposons]]) and the dynamic changes that occur during genome evolution caused by the DNA rearrangement and  [[transposition]] processes catalyzed by mobile DNA. Movement of mobile genes (such as [[transposons]]) within a genome, and between different parts of an organism's genome (that is, between the [[chromosomes]] of the [[nucleus]], the circular [[mitochondrion]] chromosome <ref>Adams KL ''et al''(2000) Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants ''Nature'' '''408''':354 PMID 11099041 </ref>, and the circular [[plastid]] ([[chloroplast]]) chromosome) are part of the mechanisms that enable horizontal gene transfer between different species.
HGT is just one of several processes that can cause rearrangement of genomes during evolution. The possibility of intracellular movement of genes between different parts of an organism's genome (that is, between the [[chromosomes]] of the [[nucleus]], the circular [[mitochondrion]] chromosome, or the circular [[plastid]] ([[chloroplast]]) chromosome) needs to be considered when evaluating HGT between different species.<ref>Timmis JN  ''et al.'' (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5:123-35  PMID 14735123</ref>


==Main features of HGT in nature==
==Main features of HGT in nature==
* '''A hallmark of HGT''' is the presence of the same gene in organisms that are only very distantly related. The frequent discovery of shared DNA sequences such as the ''mariner''class of [[transposons]], [[insertion sequence]] DNA, and [[retrovirus]] genes in diverse species, and shared mitochondrial genes in diverse flowering plants indicate that [[mobile DNA]] has natural pathways for movement between species. Close relatives ''mariner'' mobile DNA have been discovered in organisms as diverse as mites, flatworms, hydras, insects, nematodes, mammals and humans<ref> Robertson HM (1993) The ''mariner'' transposable element is widespread in insects ''Nature'' '''362''':241-5 PMID 8384700
* A hallmark of HGT is the presence of the same gene in organisms that are only very distantly related to each other. The frequent discovery of shared DNA sequences such as the ''mariner'' class of [[transposons]], [[insertion sequence]] DNA, [[retrovirus]] genes in diverse species and shared mitochondrial genes in diverse flowering plants indicate that [[mobile DNA]] has natural pathways for movement between species. (The name mariner for a class of related transposons is an allusion to ''The Rime of the Ancient Mariner'', meaning a traveller to distant lands.) Close relatives of ''mariner'' mobile DNA have been identified in organisms as diverse as mites, flatworms, hydras, insects, nematodes, mammals and humans.<ref>Robertson HM (1996) Reconstruction of the ancient ''mariners'' of humans. Nat Genet 12:360-1 PMID 8630486
*Robertson HM (1996) Reconstruction of the ancient ''mariners'' of humans ''Nature Genetics'' '''12''':360-1 PMID 8630486</ref>.
*[http://etext.virginia.edu/toc/modeng/public/Col2Mar.html ''The Rime of the Ancient Mariner'']Samuel Taylor Coleridge(1772-1834)</ref>
 
[[Image:Millet.jpg|right|frame|Millet. From: Jumping Genes Cross Plant Species Boundaries ''PLoS Biol'' [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040035 4(1) e35]. A genome-wide analysis of millet and rice revealed clear evidence for HGT between chromosomes in the nucleus of one plant to chromosomes in the nucleus of a reproductively isolated species]]


* ''Horizontal movement of genes'' is common among [[bacteria]] and is responsible for '''infectious multiple-antibiotic resistance''' in pathogenic bacteria, a major factor limiting the effectiveness of antibiotics. Inter-[[domain]] transfer of several genes, from the [[eukaryote]] domain to the [[bacteria|bacterial]] domain for instance, as represented by an "accidentally pathogenic"  bacterium (''[[Legionella pneumophila]]'', see illustration) that resides and replicates within a vacuole of [[protist]] and mammalian [[macrophage]] cells, has also been demonstrated <ref> de Felipe KS ''et al'' (2005) Evidence for acquisition of Legionella type IV secretion substrates via interdomain horizontal gene transfer ''J Bacteriol'' [http://jb.asm.org/cgi/content/full/187/22/7716?view=long&pmid=16267296 '''187''':7716-26]</ref>.
[[Image:Millet.jpg|right|frame|Millet. From: [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040035 ''Jumping Genes Cross Plant Species Boundaries.'']Analysis of the genomes of millet and rice revealed evidence for HGT between chromosomes in the nucleus of one plant to chromosomes in the nucleus of a reproductively isolated species]]
* HGT is common in diverse groups of unicellular [[protists]], which often contain several genes transferred from both [[prokaryotes]] and other protists <ref> Richards TA ''et al'' (2003) ''Protist'' '''1''':17–32 PMID 12812367
*Graham H ''et al'' (2003) The amitochondriate eukaryote ''Trichomonas vaginalis'' contains a divergent thioredoxin-linked peroxiredoxin antioxidant system ''JBC'' [http://www.jbc.org/cgi/reprint/M304359200v1.pdf M304359200
*Andersson JO ''et al'' (2006) Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes ''BMC Evol Biol'' [http://www.biomedcentral.com/content/pdf/1471-2148-6-27.pdf '''6''':27]
*de Koning AP ''et al'' (2000) Lateral gene transfer and metabolic adaptation in the human parasite ''Trichomonas vaginalis''. ''Mol Biol Evol'' [http://mbe.oxfordjournals.org/cgi/content/full/17/11/1769?ijkey=9c802283c2061444eef49daaf216d2461b23859f&keytype2=tf_ipsecsha '''17''':1769-73]
*Loftus B ''et al'' (2005) The genome of the protist parasite  ''Entamoeba histolytica''. ''Nature'' '''433''':865-8 PMID 15729342
*Huang J ''et al'' (2004) Phylogenomic evidence supports past [[endosymbiosis]], intracellular and horizontal gene transfer in ''Cryptosporidium parvum''. ''Genome Biol'' [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15535864 '''5''':R88]</ref>.


* '''HGT occurs globally''' on a massive scale among marine microorganisms, and viruses, at total numbers near 10<sup>29</sup> being the most common biological entities in the sea, are a major pathway for inter-species gene movement in the ocean. The estimated virus-mediated gene transfer events in the Mediterranean sea are 10<sup>13</sup> per year <ref>Weinbauer MG ''et al'' (2004) Are viruses driving microbial diversification and diversity? ''Envir Microbiol'' [http://www.blackwell-synergy.com/links/doi/10.1046/j.1462-2920.2003.00539.x/full/ 6:1-11]
* Horizontal movement of genes is common among bacteria, and is a major factor in accelerating the rate of their evolution. HGT is involved in multiple-antibiotic resistance in pathogenic bacteria, and this is a major factor that is limiting the effectiveness of antibiotics. Inter-domain (sub-kingdom) transfer of several genes from eukaryotes to bacteria for instance, has occurred in the 'accidentally pathogenic' bacterium (''Legionella pneumophila'', see illustration) that lives within vacuoles of [[protist]] and mammalian [[macrophage]] cells.<ref>Jain R ''et al.'' (2003) Horizontal gene transfer accelerates genome innovation and evolution. Mol Biol Evol [http://mbe.oxfordjournals.org/cgi/content/full/20/10/1598 20:1598-602] PMID 12777514 (Open access)
*Paul JH (1999) Microbial gene transfer ''J Mol Microbiol Biotechnol'' '''1''':45–50
* de Felipe KS ''et al.'' (2005) Evidence for acquisition of ''Legionella'' type IV secretion substrates via interdomain horizontal gene transfer. J Bacteriol[http://jb.asm.org/cgi/content/full/187/22/7716?view=long&pmid=16267296 187:7716-26] PMID 16267296 (Open access) </ref>
*Fuhrman JA (1999) Marine viruses and their biogeochemical and ecological effects ''Nature'' '''399''':541–8 PMID 10376593</ref>. [[Endosymbiosis]] with an alga is identified as a route for HGT in marine dinoflagellates, the organisms that cause 'red tides' <ref>Yoon HS ''et al'' (2005) Tertiary endosymbiosis driven genome evolution in dinoflagellate algae ''Mol Biol Evol'' [http://mbe.oxfordjournals.org/cgi/content/full/22/5/1299 '''22''':1299-308]</ref>.


* '''Mechanisms for HGT''' in  flowering plants involving parasitic plants such as dodder or endophytes such as mosses (which facilitate inter-species gene transfer by being in intimate cell-to-cell contact with their host plants) are now well established (see [[Horizontal gene transfer in plants]]).  
* HGT is documented in diverse unicellular protists, which can contain several genes transferred from both [[prokaryotes]] and other protists.<ref>Andersson JO ''et al.'' (2006) Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes.[http://www.biomedcentral.com/1471-2148/6/27  BMC Evol Biol]  PMID 16551352 (Open access)
* Loftus B ''et al.'' (2005) The genome of the protist parasite ''Entamoeba histolytica''. Nature 433:865-8  PMID 15729342</ref>


* Not all of the '''vehicles by which HGT occurs''' are fully characterized, but some are clearly identified. HGT is difficult to detect directly, as it occurs at lower frequencies than with normal sexual reproduction within the species. Modern techniques of DNA analysis, by providing detailed comparison of [[genomics|genome]]s, provide much of the evidence for HGT. In insects, mites and viruses are probable vectors for HGT. In bacteria, surface appendages called [[Pilus|pili]] have various roles in DNA uptake, DNA secretion and DNA transfer which have been extensively analyzed; HGT in bacteria includes [[plasmid]]-mediated promiscuous mating by bacteria, for instance by the crown-gall bacterium ''[[Agrobacterium tumefaciens]]''<ref>*  Zhu J ''et al'' (2000) The bases of crown gall tumorigenesis ''J Bacteriol'' [http://jb.asm.org/cgi/content/full/182/14/3885?ijkey=6a7ba9226010373f50ec7c74aeb4e433fb5a3da5&keytype2=tf_ipsecsha '''182''':3885-95] This article describes the biology of crown-gall bacterium, and the mechanism of DNA injection by this bacterium, and explains how genes can move between bacterial species and from bacteria to eukaryotic organisms, and illustrates the extent to which different species can [[co-evolution|co-evolve]]</ref>, and carriage of genes between species by [[viruses]]<ref> Weinbauer, ''et al'' (2004) Are viruses driving microbial diversification and diversity? ''Envir Microbiol'' [http://www.blackwell-synergy.com/links/doi/10.1046/j.1462-2920.2003.00539.x/full/ '''6''':1-11]
* HGT occurs globally on a massive scale among marine microorganisms. Viruses, which, at total numbers near 10<sup>29</sup> are the most common biological entities in the sea, are a major pathway for gene movement between different species. It has been estimated that, on average, 10<sup>13</sup> virus-mediated gene transfer events occur in the Mediterranean sea each year. [[Endosymbiosis]] with an alga is identified as a route for HGT in marine [[dinoflagellates]], the organisms that cause 'red tides'.<ref>Fuhrman JA (1999) Marine viruses and their biogeochemical and ecological effects. Nature 399:541–8  PMID 10376593
*Amoils S (2005) Analysing incompatibility — Wolbachia on the couch ''Nature Rev Microbiol'' [http://www.nature.com/nrmicro/journal/v3/n9/pdf/nrmicro1242.pdf  '''3''':667]
*Yoon HS ''et al.'' (2005) Tertiary endosymbiosis driven genome evolution in dinoflagellate algae. Mol Biol Evol [http://mbe.oxfordjournals.org/cgi/content/full/22/5/1299 22:1299-308]  PMID 15746017 (Open access)</ref>
*Besser TE ''et al'' (2006) Greater diversity of Shiga toxin-encoding bacteriophage insertion sites among ''Escherichia coli'' O157:H7 isolates from cattle than from humans ''Appl Environ Microbiol'' PMID 17142358</ref>. Direct DNA uptake as another transfer mechanism is illustrated by ''Legionella'' bacteria, which are naturally competent for DNA uptake.
* Interspecies gene movement by cross-hybridization is common in flowering plants. Mechanisms for HGT in flowering plants between more distant taxa involving parasitic plants such as dodder and endophytes (such as mosses, which are in intimate cell-to-cell contact with their host plants) are also well established (see [[Horizontal gene transfer in plants]]). Plant mitochondria can be unusually active in HGT.
* Not all of the ways in which HGT occurs are fully characterized, but some have been identified. HGT is hard to detect directly, as it is relatively rare within a species, but can be detected by modern DNA analysis which can enable detailed comparison of [[genomics|genome]]s. In insects, mites and viruses are probably vectors for HGT. In certain bacteria, surface appendages called [[Pilus|pili]] have various roles in DNA uptake, DNA secretion and DNA transfer which have been extensively analyzed; HGT in bacteria includes [[plasmid]]-mediated promiscuous mating by bacteria (for instance by the crown-gall bacterium ''Agrobacterium tumefaciens'') and carriage of genes between species by viruses. Direct DNA uptake is another transfer mechanism, as illustrated by ''Legionella'' bacteria, which are naturally competent for DNA uptake.


==Prokaryotes==
==Prokaryotes==
:''See main article [[Horizontal gene transfer in prokaryotes]]''
:''See main article [[Horizontal gene transfer in prokaryotes|HGT in prokaryotes]]''
:''The three main mechanisms of HGT in [[bacteria]] and [[archaea]] which this article discusses are:''
:''The three main mechanisms of HGT in bacteria and archaea discussed here are:''
:* '''''Bacterial [[Transformation (genetics)|Transformation]]''' or direct uptake of extracellular DNA.''
:* '''''Bacterial [[Transformation (genetics)|Transformation]]''' or direct uptake of extracellular DNA.''
:* '''''[[Transduction (genetics)|Transduction]]''' of genes by bacterial viruses.''
:* '''''[[Transduction (genetics)|Transduction]]''' of genes by bacterial viruses.''
:* '''''[[Bacterial conjugation]]''', a gene transfer process carried out by [[plasmids]] and conjugative [[transposons]].''
:* '''''[[Bacterial conjugation]]''', a gene transfer process carried out by plasmids and conjugative transposons.''


==Eukaryotes==
==Eukaryotes==
: ''See also [[Endosymbiotic theory]]''
===Protists===
===Protists===
Analysis of the complete genome sequence of the protist ''Entamoeba histolytica'' indicates 96 cases of relatively recent horizontal gene transfer from prokaryotes <ref>Loftus B ''et al'' (2005) The genome of the protist parasite ''Entamoeba histolytica''. ''Nature'' '''433''':865-8</ref>, whereas similar analysis of the complete genome sequence of the protist "Cryptosporidium parvum"  reveal 24 candidates of horizontal gene transfer from bacteria <ref>Huang J ''et al'' (2004) Phylogenomic evidence supports past [[endosymbiosis]], intracellular and horizontal gene transfer in ''Cryptosporidium parvum''. ''Genome Biol'' '''5''':R88</ref>.There is convincing evidence also that a bacterial gene for a biosynthetic enzyme has been recruited by the protist ''Trichomonas vaginalis'' from bacteria related to the ancestors of ''Pasteurella'' bacteria.<ref> de Koning ''et al'' (2000)  Lateral gene transfer and metabolic adaptation in the human parasite ''Trichomonas vaginalis''. ''Mol Biol Evol'' [http://mbe.oxfordjournals.org/cgi/content/full/17/11/1769 '''17''':1769-73]</ref> These results fit the idea that "you are what you eat". That is, with unicellular grazing organisms, foreign genetic material is constantly entering the cell and occasionally the genome from food organisms <ref>Doolittle WF (1998) You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes ''Trends Genet'' '''14''':307-11 PMID 9724962</ref>
Analysis of the complete genome sequence of the protist ''Entamoeba histolytica'' indicates 96 cases of relatively recent HGT from prokaryotes. There is also convincing evidence that a bacterial gene for a biosynthetic enzyme has been recruited by the protist ''Trichomonas vaginalis'' from bacteria related to the ancestors of ''Pasteurella'' bacteria. Similar analysis of the protist ''Cryptosporidium parvum'' reveals 24 candidates of HGT from bacteria. These results fit the idea that 'you are what you eat'. That is, in unicellular grazing organisms, foreign genetic material is constantly entering the cell from food organisms, and occasionally some of this material enters the genome.<ref>Loftus B ''et al.'' (2005) The genome of the protist parasite ''Entamoeba histolytica''. Nature 433:865-8  PMID 15729342
* Doolittle WF (1998) You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends in Genetics 14:307-11 PMID 9724962</ref>


===Fungi===
===Fungi===
Comparison of the genome sequences of two fungi, the yeast ''Saccharomyces cerevisiae'' and ''Ashbya gossypii'', has revealed that baker's yeast ''Saccharomyces'' has received two genes from bacteria by HGT. One codes for an enzyme that allows baker's yeast to make pyrimidine nucleotide bases anaerobically, and the other allows usage of sulfur from several organic sulfur sources.<ref> Hall CS ''et al''(2005) Contribution of horizontal gene transfer to the evolution of ''Saccharomyces cerevisiae''. ''Eukaryot Cell'' [http://ec.asm.org/cgi/content/abstract/4/6/1102?ijkey=c901c5b18b97e28f1dd1d811d53d3c5ec8dd469c&keytype2=tf_ipsecsha '''4''':1102-1115]</ref>. Other work with yeasts suggests that eight genes from ''Yarrowia lipolytica'', five from ''Kluyveromyces lactis'', and one  from ''Debaryomyces hansenii'' are horizontally transferred. <ref>Dujon B ''et al'' {2004) Genome evolution in yeasts ''Nature'' '''430''':35-44 PMID 15229592</ref>
Comparison of the genome sequences of two fungi, baker's yeast (''Saccharomyces cerevisiae'') and ''Ashbya gossypii'', has shown that ''Saccharomyces'' has received two genes from bacteria by HGT. One of these genes codes for an enzyme that allows baker's yeast to make pyrimidine nucleotide bases anaerobically, and the other allows usage of sulfur from several organic sulfur sources. Other work with yeasts suggests that eight genes from ''Yarrowia lipolytica'', five from ''Kluyveromyces lactis'', and one  from ''Debaryomyces hansenii'' are horizontally transferred.<ref>Dujon B ''et al.'' {2004) Genome evolution in yeasts. Nature 430:35-44 PMID 15229592</ref>


===Other eukaryotes===
===Other eukaryotes===
Analysis of [[DNA sequence]]s suggests that HGT has also occurred within multicellular [[eukaryote]]s, by a route that involves transfer of genes from  chloroplast and mitochondrial genomes to the nuclear genomes <ref>Gray MW (1993) Origin and evolution of organelle genomes ''Curr Opin Genet Dev'' 3:884-90</ref>. According to the [[endosymbiotic theory]], chloroplasts and mitochondria originated as the bacterial [[endosymbiont]]s of a progenitor to the eukaryotic cell.
Analysis of [[DNA sequence]]s suggests that HGT has also occurred within multicellular eukaryotes, by a route that involves transfer of genes from  chloroplast and mitochondrial genomes to the nuclear genomes.<ref>Adams KL Palmer JD (2003) Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol 29:380–95  PMID 14615181</ref> According to the [[endosymbiotic theory]], chloroplasts and mitochondria originated as the bacterial [[endosymbiont]]s of a progenitor to the eukaryotic cell, and endosymbiosis can be considered to be a special case of HGT.


===Plants===
===Plants===
Line 60: Line 60:
:''See [[Transgenic plant]] for hybridization by cross-pollination and artificial horizontal gene transfer in [[biotechnology]].''  
:''See [[Transgenic plant]] for hybridization by cross-pollination and artificial horizontal gene transfer in [[biotechnology]].''  


Plant genes have also been discovered to be able to move to endophyte fungi that grow on them. Several plant endophyte fungi that grow on taxol producing yew trees have gained ability to make taxol themselves <ref>Shrestha K ''et al'' (2001) Evidence for paclitaxel from three new endophytic fungi of Himalayan yew of Nepal ''Planta Med'' '''67''':374-6</ref>. (Taxol is an anti-cancer drug also called paclitaxel found in yew trees.)
It has also been discovered that plant genes can move to endophyte fungi that grow on them. Several plant endophyte fungi that grow on taxol-producing yew trees have gained the ability to make taxol themselves.<ref>Shrestha K ''et al.'' (2001) Evidence for paclitaxel from three new endophytic fungi of Himalayan yew of Nepal. Planta Med 67:374-6 PMID 11458463</ref> (Taxol, also called paclitaxel, is an anti-cancer drug found in yew trees.)


===Animals===
===Animals===
[[Junk DNA]] is the most obvious general evidence of HGT in eukaryotes. Such seemingly non-functional repetitive DNA contitutes a major portion of many genomes of plants and animals. This DNA usually includes multiple copies of various "[[Jumping genes]]" which can proliferate within a genome after they have been transferred from another species. Examples in the human of such horizontally transferred mobile elements are 'Hsmar1' and 'Hsmar2' which are related to the widely studied 'mariner' transposon. Close relatives of mariner mobile DNA have been discovered in organisms as diverse as mites, flatworms, hydras, insects, nematodes, mammals and humans <ref>Robertson HM (1996) Reconstruction of the ancient 'mariners' of humans ''Nature Genetics'' '''12''':360-361</ref>.[[Retroviruses]] and [[retrotransposons]] are other examples of mobile horizontally transferred DNA found in animals.
[[Junk DNA]] is the most obvious general evidence of HGT in eukaryotes. Junk DNA is the name given to the seemingly non-functional repetitive DNA sequences that are a major portion of the genomes of many plants and animals. This DNA usually includes multiple copies of various '[[Jumping genes]]' which can proliferate within a genome after they have been transferred from another species. Examples in the human of such mobile elements are 'Hsmar1' and 'Hsmar2' which are related to the widely studied 'mariner' transposon. Close relatives of mariner mobile DNA have been discovered in organisms as diverse as mites, flatworms, hydras, insects, nematodes, mammals and humans.<ref>Robertson HM ''et al.'' (1996) Reconstruction of the ancient 'mariners' of humans. Nat Genet 12:360-361 PMID 8630486</ref> [[Retroviruses]] and [[retrotransposons]] are other examples of mobile horizontally transferred DNA found in animals.


The adzuki bean beetle, ''Callosobruchus chinensis'', is infected with several strains of bacterial ''Wolbachia'' [[endosymbiont]]s. A genome fragment of one of these endosymbionts has been found transferred to the X chromosome of the host insect <ref>Kondo N ''et al'' (2002) Genome fragment of ''Wolbachia'' endosymbiont transferred to X chromosome of host insect ''PNAS USA''  [http://www.pnas.org/cgi/content/full/99/22/14280 '''99''':14280-5]</ref>.
The adzuki bean beetle ''Callosobruchus chinensis'' is infected with several strains of bacterial ''Wolbachia'' [[endosymbiont]]s. A genome fragment of one of these endosymbionts has been found transferred to the X chromosome of the host insect.<ref>Kondo N ''et al.'' (2002)Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect.Proc Natl Acad Sci USA   [http://www.pnas.org/cgi/content/full/99/22/14280 99:14280-5] PMID 12386340 (Open access)</ref>


==History of discovery of HGT==
==History of discovery of HGT==
Line 76: Line 76:
:*''HGT and genetic engineering''
:*''HGT and genetic engineering''


==Evolutionary theory==
==Decoding the tree of life from genomes scrambled by HGT==
"Sequence comparisons suggest recent horizontal transfer of many [[gene]]s among diverse [[species]] including across the boundaries of [[phylogenetic]] "domains". Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes." <ref>[http://opbs.okstate.edu/~melcher/MG/MGW3/MG334.html Horizontal Gene Transfer, Oklahoma State]</ref>
: ''For more information, see Citizendium's article on [[Prokaryote phylogeny and evolution]]''


HGT is thus a potential [[Lurking variable|confounding factor]] in inferring [[phylogenetic tree]]s based on the [[sequence]] of one [[gene]]. For example, given two distantly related bacteria that have exchanged a gene, a [[phylogenetic tree]] including those species will show them to be closely related because that gene is the same, even though most other genes have diverged substantially. For this reason it is often ideal to use other information to infer phylogenies, such as the presence or absence of genes, or, more commonly, to include as wide a range of genes for analysis as possible.  
Because each organism carries a record of its ancestry in its DNA, methods for rapid gene isolation and analysis of DNA encoded sequences - which can extract the information from this ancestral archive - have been important for answering questions about evolution, and they have enabled rapid expansion of the field of biological [[systematics]] known as [[Molecular phylogeny|phylogenetic inference]]. Comparison of related ([[homologous]]) gene sequences from different organisms has made it possible to reconstruct the history of many evolutionary lineages.<ref>Steenkamp ET ''et al.'' (2006) The protistan origins of animals and fungi. Mol Biol Evol [http://mbe.oxfordjournals.org/cgi/content/full/23/1/93 23:93-106] PMID 16151185 (Open access)</ref>
Many issues about evolution have been clarifed by comparing homologous genes from different species, genera, families, and phyla. Unfortunately, HGT complicates the picture, because HGT 'scrambles' the evidence needed to deduce the branching patterns of evolutionary trees. One area of current research in phylogenetic inference, and arguably one of the most challenging problems in evolutionary theory, is the early stages in the [http://tolweb.org/Life_on_Earth/1 evolution of life]. This quandary about the origins of different cell types provides a good illustration of the complications introduced by HGT into the reconstruction of evolutionary history.  


The most common gene to be used for constructing phylogenetic relationships in [[prokaryote]]s is the small subunit ribosomal [[RNA]] (SSU rRNA, [[16s rRNA]]) gene, since its sequences tend to be conserved among members with close phylogenetic distances, but variable enough that differences can be measured <ref>{{cite journal | author = Woese C ''et al''| title = Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya| url=http://www.pnas.org/cgi/reprint/87/12/4576| journal = PNAS USA| volume = 87 | pages = 4576-9 | year = 1990 | id = PMID 2112744}}
The main early branches of the tree of life have been intensively studied by [[Microorganism|microbiologists]] because the first organisms were microrganisms. A gene very often used for constructing phylogenetic relationships in microorganisms is the small ribosomal subunit ribosomal RNA (SSU rRNA) gene, as its sequences tend to be conserved among members with close phylogenetic distances, yet it is variable enough that differences can be measured.<ref>Woese C ''et al.'' (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA [http://www.pnas.org/cgi/reprint/87/12/4576 87:4576-9PMID 2112744 (Open access)
*{{cite journal | author = Woese C, Fox G | title = Phylogenetic structure of the prokaryotic domain: the primary kingdoms|journal = PNAS USA |volume = 74 |pages = 5088-90 | year = 1977 | id = PMID 270744}}</ref>. The small subunit ribosomal [[RNA]] as a measure of evolutionary distances was pioneered by [[Carl Woese]] when formulating the first modern "tree of life", and his research results with SSU rRNA led him to propose the [[Archaea]] as a third domain of [[life]].) However, recently it has been argued that small subunit ribosomal RNA genes can also be horizontally transferred. Although this may be rare, this possiblity is forcing scrutiny of the validity of phylogenetic trees based on these small subunit ribosomal RNAs.
*Woese C, Fox G (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=270744 74:5088-90] PMID 270744</ref> The use of SSU rRNA to measure evolutionary "distances" was pioneered by [[Carl Woese]] when formulating the first modern 'tree of life', and his results led him to propose the [[Archaea]] (single celled organisms superficially similar to bacteria) as a third domain (sub-kingdom) of life.  


===Which metaphor: tree, a net or cobweb?===
[[Image:Tree_phylogeny_3_domain.gif|thumb|300px|left|A three domain representation of the [[phylogenetic tree|tree]] of life based on SSU rRNA sequences, showing the separation of Bacteria, Archaea, and Eukaryote domains. See [[Microorganisms]] article for further explanation]]
In his article ''Uprooting the Tree of Life'', W. [[Ford Doolittle]] discusses the [[Last universal ancestor|Last Universal Common Ancestor]] - the root of the Tree of Life - and the problems with that concept posed by HGT<ref>W. Ford Doolitte (2000) ''Uprooting the Tree of Life'' ''Scientific American'' February 2000, pp 72-7</ref>. He describes the microorganism ''Archaeoglobus fulgidus'' as an anomaly with respect to a [[phylogenetic]] tree based upon the code for the [[enzyme]] [[HMGCoA reductase]] - the organism is definitely an archaean, with all the cell lipids and transcription machinery  expected of an archaean, but its HMGCoA genes are of bacterial origin. In the article, Doolittle says that while it is now widely accepted from the wight of evidence that [[mitochondria]] in [[eukaryote]]s derived from alpha-proteobacterial cells and that [[chloroplast]]s came from ingested [[cyanobacteria]],  
Microbiologists introduced the term ''domain'' for the three main early branches of the tree of life, where ''domain'' is  a [[phylogenetic]] term very similar in meaning to biological kingdom. These represent the three main lineages in evolution of early cellular life, and are currently represented by the ''Bacteria'', the ''Archaea'' and ''Eukarya (eukaryote)'' domains. Eukaryotes are all organisms with a well defined nucleus, and this domain comprises protists, fungi, and all organisms in the animal and plant kingdoms, including humans. As seen in the figure (left), studies of SSU rRNA genes (and some other genes) might suggest that ''Archaea'' and ''Eukarya'' have a ''sister'' relationship in evolution, and it has often been assumed that eukaryotes evolved from archaeal cells. However, the fact that genes can move between distant branches of the tree of life even at low probabilities poses problems for scientists trying to reconstruct evolution from studying genes and gene sequences in different organisms due to the scrambling effect of HGT. The challenges are most awkward for the ambitious reconstruction of the earliest branches of the tree of life - because over a long enough time and with large numbers of organisms, many HGT events are certain to have occurred even though each particular transfer event has a low probability.


<blockquote>".. it is no longer safe to assume that those were the only lateral gene transfers that occurred after the first eukaryotes arose. Only in later, multicellular eukaryotes do we know of definite restrictions on horizontal gene exchange, such as the advent of separated (and protected) [[germ cell]]s...
Thus recent discoveries of 'rampant' HGT in microorganisms, and the detection of horizontal movement of genes for SSU rRNA have forced biologists to question the accuracy of at least the early branches in the tree of life, and even to question the validity of trees as useful models of microbial evolution.<ref>Simonson AB ''et al.'' (2005) Decoding the genomic tree of life. Proc Natl Acad Sci USA[http://www.pnas.org/cgi/content/full/102/suppl_1/6608 102 Suppl 1:6608-13] PMID 15851667 (Open access)
<br/>
*Yap WH ''et al.'' (1999) Distinct types of rRNA operons exist in the genome of the actinomycete ''Thermomonspora chromogena'' and evidence for horizontal gene transfer of an entire rRNA operon. J Bacteriol [http://jb.asm.org/cgi/content/full/181/17/5201?view=long&pmid=10464188 181:5201-9]  PMID 10464188 (Open access)
* Gogarten JP Townsend JP (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 9:679-87  PMID 16138096</ref>  


If there had never been any lateral gene transfer, all these individual gene trees would have the same topology (the same branching order), and the ancestral genes at the root of each tree would have all been present in the last universal common ancestor, a single ancient cell. But extensive transfer means that neither is the case: gene trees will differ (although many will have regions of similar topology) ''and'' there would never have been a single cell that could be called the last universal common ancestor..."</blockquote>
===Recent efforts to infer evolutionary trees while recognizing HGT===
: ''For more information, see Citizendium's article on [[Evolution of cells]]''


Doolittle suggested that the universal common ancestor cannot have been one particular organism, but was a loosely knit, diverse conglomeration of primitive cells that evolved together. These early cells, each with relatively few genes, differed in many ways, and swapped their [[gene]]s freely. Eventually, from these eclectic cells came the three domains of life as we know them today: [[bacteria]], [[archaea]] and [[eukaryote]]. These domains are now recognizably distinct because much of the gene transfer that still occurs is within these domains, rather than between them. Biologist Peter Gogarten reinforced these arguments, and suggested that the metaphor of a tree does not fit the data from recent genome research, and that biologists should instead use "the metaphor of a mosaic to describe the different histories combined in individual genomes and use [the] metaphor of a net to visualize the rich exchange and cooperative effects of HGT among microbes." <ref>Gogarten JP 'Horizontal Gene Transfer - A New Paradigm for Biology' [http://www.esalenctr.org/display/confpage.cfm?confid=10&pageid=105&pgtype=1 PhD thesis]
The challenges of ascertaining an accurate branching structure for evolutionary trees of microbes, especially the earliest branches in the tree of life, have been a great spur for current biological research. Clear answers to important questions about these trees are not yet available, but many interesting discoveries and ideas are emerging.
*Zhaxybayeva O, Gogarten JP (2004) Cladogenesis, coalescence and the evolution of the three domains of life ''Trends in Genetics'' [http://web.uconn.edu/gogarten/articles/TIG2004_cladogenesis_paper.pdf '''20''':]</ref>


===Resolution of uncertainty with Phylogenomics===
Instead of relying primarily on a single gene such as the SSU rRNA gene to reconstruct evolution, scientific effort has now shifted to exploiting the comprehensive information from the many complete genome sequences of organisms that are now available.<ref>Eisen JA, Fraser CM (2003) Viewpoint phylogenomics: intersection of evolution and genomics. Science 300:1706-7  PMID 12805538
[[Image:Tree_microbialgenomes_nocobwebs.jpg|right|frame|Tree Based on the Median Tree Algorithm.  Ge F ''et al'' The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer ''PLoS Biol'' '''3'''(10), [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030316 e316]. Branches with bootstrap (statistical) scores less than 50% were collapsed. Three domains of life are shown as (A) archaea, (B–J) bacteria, and (K) eukaryote. Species are labeled with different colors based on their inferred HGT rates: red, >4%; yellow, 3%–4%; pink, 2%–3%; blue, 1%–2%; green, <1%. Taxonomy labels are (A) Euryarchaea, (B) Proteobacteria, (C) Chlamydiae, (D) Spirochaetes, (E) Thermotogae, (F) Aquificae, (G) Actinobacteria, (H) Deinococcus, (I) Cyanobacteria, (J) Firmicutes, and (K) Fungi.]]
* Fitzpatrick DA ''et al.'' (2006) A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol[http://www.biomedcentral.com/1471-2148/6/99 6:99] PMID 17121679 (Open access)
* Ge F ''et al.'' (2005) The Cobweb of Life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol[http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030316 3:e316] PMID 16122348 (Open access)
* Henz SR ''et al.'' (2005) Whole-genome prokaryotic phylogeny.Bioinformatics [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/10/2329 21:2329-35] PMID 15166018 (Open access)
* Urwin R, Maiden MC (2003) Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol 11:479-87  PMID 14557031</ref> So far, this comparative [[genomics]] approach, made possible by specially developed computer programs and mathematical algorithms, suggests that most of the core genes of bacteria that are useful for deducing evolutionary histories are unaffected by HGT. This confirms the practical experience of microbiologists that consistent and reliable trees can still be deduced for the more recent stages in microbial evolution, such as evolutionary relationships within particular bacterial phyla. This does require, however, using multiple, well chosen genes to investigate how lineages are related to one another. Thus the 'tree' is still a valid metaphor for microbial evolution - but a tree adorned with 'cobwebs' of horizontally transferred genes.  


But it is also clear that trees based only on SSU rRNA alone do not capture the events of early eukaryote evolution accurately, and the origins of the first nucleated cells are still uncertain. For instance, careful analysis of the complete genome of the eukaryote yeast shows that many of its genes are more closely related to bacterial genes than they are to archaea, and it is now clear that archaea were not the simple progenitors of the eukaryotes. This discovery is a stark contradiction to earlier findings based on SSU rRNA and limited samples of other genes.<ref>Esser C ''et al.'' (2004) A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol [http://mbe.oxfordjournals.org/cgi/content/full/21/9/1643 21:1643-50] PMID 15155797 (Open access)</ref> (See [[Evolution of cells]] for further discussion.)


Despite the uncertainties in reconstructing phylogenies back to the beginings of life, progress is being made in reconstructing the tree of life in the face of uncertainties raised by HGT. The uncertainty of any inferred phylogenetic tree based on a single gene can be resolved by using several common genes or even evidence from whole genomes <ref> Henz SR ''et al'' (2005) Whole-genome prokaryotic phylogeny ''Bioinformatics'' [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/10/2329 '''21''':2329-35] PMID 15166018
On the other hand, the concept that rampant HGT took place in 'gene-swapping collectives' involved in metabolism and replication at the [[Origin of life|earliest stages of life's origins]], before a postulated transition to Darwinian evolution of the cellular lineages known today, has been used by Carl Woese and colleagues to develop fresh insight into the origins of the universal [[genetic code]].<ref>Goldenfeld N, Woese C (2007) Essays: Connections. Biology's next revolution The emerging picture of microbes as gene–swapping collectives demands a revision of such concepts as organism, species and evolution itself. Nature 445:369 [http://nature.com/nature/focus/arts/connections/index.html doi:10.1038/445369a]  
*Fitzpatrick DA ''et al'' (2006) A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. ''BMC Evol Biol'' [http://www.biomedcentral.com/1471-2148/6/99 '''6''':99]</ref>. One such approach, sometimes called 'multi-locus typing', has been used to deduce phylogenic trees for organisms that exchange genes, such as meningitis bacteria<ref>Urwin R, Maiden MC (2003) Multi-locus sequence typing: a tool for global epidemiology ''Trends Microbiol'' '''11''':479-87
* Vetsigian K ''et al.'' (2006) Collective evolution and the genetic code. Proc Natl Acad Sci USA [http://www.pnas.org/cgi/content/full/103/28/10696 103:10696–700] PMID 1681888</ref>
*Yang Z (2002) Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci ''Genetics'' [http://www.genetics.org/cgi/content/full/162/4/1811 '''162''':1811-23]
*Jennings WB, Edwards SV (2005) Speciational history of Australian grass finches (''Poephila'') inferred from thirty gene trees ''Evolution Int J Org Evolution'' '''59''':2033-47 PMID 16261740</ref>.
 
Jonathan Eisen and Claire Fraser have pointed out that:
 
<blockquote>"In building the tree of life, analysis of whole genomes has begun to supplement, and in some cases to improve upon, studies previously done with one or a few genes. For example, recent studies of complete bacterial genomes have suggested that the hyperthermophilic species are not deeply branching; if this is true, it casts doubt on the idea that the first forms of life were thermophiles. Analysis of the genome of the eukaryotic parasite ''Encephalitozoon cuniculi'' supports suggestions that the group ''Microsporidia'' are not deep branching protists but are in fact members of the fungal kingdom. Genome analysis can even help resolve relationships within species, such as by providing new genetic markers for population genetics studies in the bacteria causing anthrax or tuberculosis. In all these studies, it is the additional data provided by a complete genome sequence that allows one to separate the phylogenetic signal from the noise. This is not to say the tree of life is now resolved— we only have sampled a smattering of genomes, and many groups are not yet touched"<ref>Eisen JA, Fraser CM (2003) Viewpoint phylogenomics: intersection of evolution and genomics ''Science'' '''300''':1706-7 DOI: 10.1126/science.1086292</ref></blockquote>
 
These whole genome approaches are enabling estimates of the relative frequency of HGT and the relative low values being observed suggests that the tree model is still a valid metaphor for evolution - but adorned with cobwebs of horizontally transferred genes. This is the main conclusion of a 2005 study of more than 40 complete microbial genomic sequences by Fan Ge, Li-San Wang, and Junhyong Kim. They estimate the frequency of HGT events at about 2% of core genes per genome by using a novel statistical method to compare the gene trees and whole-genome trees of these 40 microbes.<ref>Ge F ''et al''(2005) The Cobweb of Life revealed by genome-scale estimates of horizontal gene transfer ''PLoS Biol'' [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030316 '''3'''(10):e316]</ref>.


==See also==
==See also==
*[[Gene flow]]
*[[Gene flow]]
*[[Species]]
*[[Phylogenetic tree]]
*[[Phylogenetic tree]]
*[[Endogenous retrovirus]]
*[[Evolution of cells]]
*[[Germline]]
*[[Germline]]
*[[Systems biology]]
*[[Origin of life]]
*[[Mitochondrion]]
*[[Mitochondrion]]
*[[Endosymbiont]]
*[[Endosymbiotic theory]]
*[[Integron]]
*[[Integron]]
*[[Virus]]
*[[Provirus]]
*[[Provirus]]
*[[Retrotransposon]]
*[[Retrotransposon]]
*[[Endogenous retrovirus]]
*[[Plasmid]]
*[[Mobile DNA]]
*[[Mobile DNA]]
*[[Pilus]]
*[[Pilus]]
*[[Transgenic plant]]


==References==
==References==
===Citations===
====Citations====
<references/>
<div class="references-small" style="-moz-column-count:2; column-count:2;">
<references />
</div>


===Further Reading===
====Further reading====
* One dramatic claim of HGT - in which a distinguished group of scientists claimed that bacteria transferred their DNA directly into the human lineage - was simply wrong: Salzberg SL ''et al'' (2001) Microbial genes in the human genome: lateral transfer or gene loss?" ''Science'' '''292''':1903-6 [http://www.cbcb.umd.edu/~salzberg/docs/ScienceLateralTransfer.pdf]  
*[http://www.nature.com/nrmicro/focus/genetransfer/index.html Focus on horizontal gene transfer] Webfocus in ''Nature'' with free access review articles.
* Discussion of both the evolutionary and ecological activities of viruses in the ocean, a major source of HGT in nature: Weinbauer MG, Rassoulzadegan F (2004) Are viruses driving microbial diversification and diversity? ''Envir Microbiol'' [http://www.blackwell-synergy.com/links/doi/10.1046/j.1462-2920.2003.00539.x/full/ '''6''':1-11] doi: 10.1046/j.1462-2920.2003.00539.x
*[http://cryptome.org/smallpox-wmd.htm Smallpox knows how to make a mouse protein. How did smallpox learn that?] ''The New Yorker'' July 12, 1999, p44-61. 'The poxviruses are promiscuous at capturing genes from their hosts,' Esposito said. 'It tells you that smallpox was once inside a mouse or some other small rodent'. (Open access)
* This article shifts the emphasis in early [[Phylogenetics|phylogenic adaptation]] from vertical to horizontal gene transfer. Woese C (2002) On the evolution of cells ''PNAS USA'' [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12077305 '''99''':8742-7]  
* ''[http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030169  Where Do All Those Genes Come From?]'' This study resolves a long-standing paradox: how is it possible to deduce reliable evolutionary histories from gene sequences in bacteria despite extensive HGT? (Open access)
* Convincing evidence of horizontal transfer of bacterial DNA: Hall C ''et al'' (2005) Contribution of horizontal gene transfer to the evolution of "Saccharomyces cerevisiae" ''Eukaryot Cell'' [http://ec.asm.org/cgi/content/full/4/6/1102 '''4''':1102-15]
* Woese C (2002) [http://www.pnas.org/cgi/content/full/99/13/8742 On the evolution of cells.]Proc Natl Acad Sci USA 99:8742-7  PMID 12077305. This article shifts the emphasis in early phylogenic adaptation from vertical to horizontal gene transfer. (Open access)
* Book with a comprehensive discussion of mobile DNA, jumping genes, transposons etc in many organisms, not only bacteria. Berg DE, Howe MM (Eds.)(1989) "Mobile DNA". American Society for Microbiology. Washington D.C.
* Salzberg SL ''et al.'' (2001) [http://www.cbcb.umd.edu/~salzberg/docs/ScienceLateralTransfer.pdf Microbial genes in the human genome: lateral transfer or gene loss?] Science 292:1903-6 PMID 11358996. This reports that one dramatic claim of HGT - in which a distinguished group of scientists claimed that bacteria transferred their DNA directly into the human lineage - was simply wrong. (Open access)
* Proposal for using the presence or absence of a set of genes to infer phylogenies, in order to avoid confounding factors such as HGT. Snel B ''et al'' (1999) Genome phylogeny based on gene content ''Nature Genetics'' '''21''':66-7 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9916801&dopt=Abstract]
* Jain R ''et al.'' Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA [http://www.pnas.org/cgi/content/abstract/96/7/3801 96:3801-6] PMID 10097118 (Open access)
* A comprehensive treatise: Syvanen M, Kado CI (2002) ''Horizontal Gene Transfer'' 2nd edition, Academic Press ISBN 0-12-680126-6
* Hall C ''et al.'' (2005) Contribution of horizontal gene transfer to the evolution of ''Saccharomyces cerevisiae''. Eukaryot Cell [http://ec.asm.org/cgi/content/full/4/6/1102 4:1102-15] PMID 15947202 Convincing evidence of horizontal transfer of bacterial DNA into yeast. (Open access.)
* Zhu J ''et al.'' (2000) The bases of crown gall tumorigenesis.J Bacteriol [http://jb.asm.org/cgi/content/full/182/14/3885?view=long&pmid=10869063  182:3885-95]  PMID 10869063  This article describes the biology of crown-gall bacterium, and the mechanism of DNA injection by this bacterium, and explains how genes can move between bacterial species and from bacteria to eukaryotic organisms, and illustrates the extent to which different species can co-evolve. (Open access)
* ''Horizontal Gene Transfer'' Syvanen M, Kado CI (2002) 2nd edition, Academic Press ISBN 0-12-680126-6  A comprehensive treatise. [http://www.nature.com/hdy/journal/v90/n1/full/6800196a.html Reviewed here by M-W Ho]
* ''Acquiring genomes: a theory of the origin of species.'' Margulis L and Sagan D (2002) Basic Books ISBN 0-465-04392-5. A book that looks at gene transfer from a different perspective to many conventional interpretations, but with an emphasis on microbial diversity. [http://home.planet.nl/~gkorthof/korthof72.htm Reviewed here.]
* Richardson AO, Palmer, JD (2007) Horizontal gene transfer in plants. J Exp Bot 58:1–9 doi:10.1093/jxb/erl148  PMID 17030541
* Gogarten JP Townsend JP (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 9:679-87 PMID 16138096. One article in a whole issue of the journal ''Nature Reviews Microbiology'' largely devoted to HGT.
* Weinbauer MG, Rassoulzadegan F (2004) Are viruses driving microbial diversification and diversity? Envir Microbiol [http://www.blackwell-synergy.com/links/doi/10.1046/j.1462-2920.2003.00539.x/full/ 6:1-11 ]  PMID 14686936 Discussion of both the evolutionary and ecological activities of viruses in the ocean, a major source of HGT in nature.


===External links===
====External links====
*Webfocus in ''Nature'' with free access review articles [http://www.nature.com/nrmicro/focus/genetransfer/index.html Focus on horizontal gene transfer]
* [http://opbs.okstate.edu/~melcher/MG/MGW3/MG334.html Horizontal gene transfer] (p334 of Molecular Genetics by Ulrich Melcher).
*[http://www.pnas.org/cgi/content/abstract/96/7/3801 (1999) Horizontal gene transfer among genomes: The complexity hypothesis ''PNAS USA'' '''96''':3801-6 ]
*[http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/genetic-exchange/exchange/exchange.html  Horizontal gene transfer at sciences.sdsu.edu]
*[http://www.stat.rice.edu/~mathbio/Ochman2000.pdf Ochman H ''et al'' (2000) Lateral gene transfer and the nature of bacterial innovation (pdf)]
*[http://www.stat.rice.edu/~mathbio/Ochman2000.pdf Lateral gene transfer and the nature of bacterial innovation (pdf), Ochman ''et al.'' (2000)]
*[http://cryptome.org/smallpox-wmd.htm ''The New Yorker'' July 12, 1999, p44-61] "Smallpox knows how to make a mouse protein. How did smallpox learn that? 'The poxviruses are promiscuous at capturing genes from their hosts,' Esposito said. 'It tells you that smallpox was once inside a mouse or some other small rodent'"
* [http://gogarten.uconn.edu/ Gogarten Laboratory Webpages.]
*[http://mic.sgmjournals.org/cgi/content/full/145/12/3321 Retrotransfer or gene capture: a feature of conjugative plasmids, with ecological and evolutionary significance]
*[http://www.esalenctr.org/display/confpage.cfm?confid=10&pageid=105&pgtype=1  Horizontal gene transfer - A new paradigm for biology]
*[http://www.esalenctr.org/display/confpage.cfm?confid=10&pageid=105&pgtype=1  Horizontal Gene Transfer - A New Paradigm for Biology]
*Horizontal Gene Transfer [http://opbs.okstate.edu/~melcher/MG/MGW3/MG334.html (p334 of Molecular Genetics by Ulrich Melcher)]
*[http://www.i-sis.org.uk/ireaff99.php Report on horizontal gene transfer] by Mae-Wan Ho, 1999
*[http://www.i-sis.org.uk/ireaff99.php Report on horizontal gene transfer] by Mae-Wan Ho, 1999
*[http://www.i-sis.org.uk/FSAopenmeeting.php Recent Evidence Confirms Risks of Horizontal Gene Transfer]
*[http://www.i-sis.org.uk/FSAopenmeeting.php Recent evidence confirms risks of horizontal gene transfer]
*[http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/genetic-exchange/exchange/exchange.html  Horizontal Gene Transfer at sciences.sdsu.edu]
<br/>
<br/>
[[Category:Genetics]]
[[Category:CZ Live]]
[[Category:Biology]]
[[Category:Microbiology]]

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Legionella pneumophila are prokaryotic bacteria that can survive and reproduce inside phagocytic cells such as protists that have eaten them. They are competent in DNA transformation and occasionally capture genes from their eukaryotic host cells.

Horizontal gene transfer occurs when an organism transfers its genetic material to a being other than one of its own offspring. The actual process of this transfer can be by any mechanism, but because genes are not passing by descent, horizontal gene transfer (abbreviated as HGT) is always very different from vertical gene transfer. In vertical descent, parental traits are inherited by progeny by one of two general methods: either (1) sexual reproduction in which gametes form zygotes, a common method in higher animals and plants, or (2) by asexual reproduction, where splitting of cells or an entire organism grows from a fragment, as is usual in bacteria and fungi, but which also happens in some animals and plants. HGT is a much more recently discovered route of passage for genetic material; it is relatively common in microorganisms, and to a lesser extent in plants. By HGT, genetic material can be shared between organisms without the immediate relatedness of mother cell to daughter cells, or parent organisms to offspring; indeed, by HGT material can pass between organismsthat are not even be of the same species, genus, sub-kingdom or kingdom of life form. HGT (sometimes called lateral gene transfer) is very much less common than vertical gene transfer, so its detection requires special techniques.

Introduction

Evidence from genome science and bioinformatics shows that HGT has occurred between diverse biological taxa that are widely separated in the phylogenetic tree of life. Known HGTs include movement of genetic material between different species of microbes and other microbial taxa such as protists, gene movement between different plant families, between different animals, and between bacteria and plants.

HGT — gene exchange between non-related organisms —appears commonplace among bacteria, but contributes just small fragments of genetic information, leaving the traditional tree of life intact. From: Comparing Gene Trees and Genome Trees: A Cobweb of Life? PLoS Biol 3:e347

Microorganisms appear to be most affected by HGT, but even in microbes only about 2% of core genes are transferred laterally. Because this percentage is so low, the main lineages of microbial evolution can still be treated as 'trees' branched by vertical descent, with HGT included in the scheme only as 'cobwebs' (see figure at right).

Gene transfers between different biological sub-kingdoms (domains), such as between eukaryotic protists and bacteria, or between bacteria and insects are the most phylogenetically extreme cases of HGT. An example is bacterial 'rol' genes from Agrobacterium species which have been found in tobacco plants (Nicotiniana).[1]

HGT is just one of several processes that can cause rearrangement of genomes during evolution. The possibility of intracellular movement of genes between different parts of an organism's genome (that is, between the chromosomes of the nucleus, the circular mitochondrion chromosome, or the circular plastid (chloroplast) chromosome) needs to be considered when evaluating HGT between different species.[2]

Main features of HGT in nature

  • A hallmark of HGT is the presence of the same gene in organisms that are only very distantly related to each other. The frequent discovery of shared DNA sequences such as the mariner class of transposons, insertion sequence DNA, retrovirus genes in diverse species and shared mitochondrial genes in diverse flowering plants indicate that mobile DNA has natural pathways for movement between species. (The name mariner for a class of related transposons is an allusion to The Rime of the Ancient Mariner, meaning a traveller to distant lands.) Close relatives of mariner mobile DNA have been identified in organisms as diverse as mites, flatworms, hydras, insects, nematodes, mammals and humans.[3]
Millet. From: Jumping Genes Cross Plant Species Boundaries.Analysis of the genomes of millet and rice revealed evidence for HGT between chromosomes in the nucleus of one plant to chromosomes in the nucleus of a reproductively isolated species
  • Horizontal movement of genes is common among bacteria, and is a major factor in accelerating the rate of their evolution. HGT is involved in multiple-antibiotic resistance in pathogenic bacteria, and this is a major factor that is limiting the effectiveness of antibiotics. Inter-domain (sub-kingdom) transfer of several genes from eukaryotes to bacteria for instance, has occurred in the 'accidentally pathogenic' bacterium (Legionella pneumophila, see illustration) that lives within vacuoles of protist and mammalian macrophage cells.[4]
  • HGT is documented in diverse unicellular protists, which can contain several genes transferred from both prokaryotes and other protists.[5]
  • HGT occurs globally on a massive scale among marine microorganisms. Viruses, which, at total numbers near 1029 are the most common biological entities in the sea, are a major pathway for gene movement between different species. It has been estimated that, on average, 1013 virus-mediated gene transfer events occur in the Mediterranean sea each year. Endosymbiosis with an alga is identified as a route for HGT in marine dinoflagellates, the organisms that cause 'red tides'.[6]
  • Interspecies gene movement by cross-hybridization is common in flowering plants. Mechanisms for HGT in flowering plants between more distant taxa involving parasitic plants such as dodder and endophytes (such as mosses, which are in intimate cell-to-cell contact with their host plants) are also well established (see Horizontal gene transfer in plants). Plant mitochondria can be unusually active in HGT.
  • Not all of the ways in which HGT occurs are fully characterized, but some have been identified. HGT is hard to detect directly, as it is relatively rare within a species, but can be detected by modern DNA analysis which can enable detailed comparison of genomes. In insects, mites and viruses are probably vectors for HGT. In certain bacteria, surface appendages called pili have various roles in DNA uptake, DNA secretion and DNA transfer which have been extensively analyzed; HGT in bacteria includes plasmid-mediated promiscuous mating by bacteria (for instance by the crown-gall bacterium Agrobacterium tumefaciens) and carriage of genes between species by viruses. Direct DNA uptake is another transfer mechanism, as illustrated by Legionella bacteria, which are naturally competent for DNA uptake.

Prokaryotes

See main article HGT in prokaryotes
The three main mechanisms of HGT in bacteria and archaea discussed here are:

Eukaryotes

See also Endosymbiotic theory

Protists

Analysis of the complete genome sequence of the protist Entamoeba histolytica indicates 96 cases of relatively recent HGT from prokaryotes. There is also convincing evidence that a bacterial gene for a biosynthetic enzyme has been recruited by the protist Trichomonas vaginalis from bacteria related to the ancestors of Pasteurella bacteria. Similar analysis of the protist Cryptosporidium parvum reveals 24 candidates of HGT from bacteria. These results fit the idea that 'you are what you eat'. That is, in unicellular grazing organisms, foreign genetic material is constantly entering the cell from food organisms, and occasionally some of this material enters the genome.[7]

Fungi

Comparison of the genome sequences of two fungi, baker's yeast (Saccharomyces cerevisiae) and Ashbya gossypii, has shown that Saccharomyces has received two genes from bacteria by HGT. One of these genes codes for an enzyme that allows baker's yeast to make pyrimidine nucleotide bases anaerobically, and the other allows usage of sulfur from several organic sulfur sources. Other work with yeasts suggests that eight genes from Yarrowia lipolytica, five from Kluyveromyces lactis, and one from Debaryomyces hansenii are horizontally transferred.[8]

Other eukaryotes

Analysis of DNA sequences suggests that HGT has also occurred within multicellular eukaryotes, by a route that involves transfer of genes from chloroplast and mitochondrial genomes to the nuclear genomes.[9] According to the endosymbiotic theory, chloroplasts and mitochondria originated as the bacterial endosymbionts of a progenitor to the eukaryotic cell, and endosymbiosis can be considered to be a special case of HGT.

Plants

See Horizontal gene transfer in plants for
  • Natural gene transfer between plants that do not cross-pollinate
  • Jumping genes cross naturally between rice and millet
  • Epiphytes and parasites as a bridge for gene flow between diverse plant species
See Transgenic plant for hybridization by cross-pollination and artificial horizontal gene transfer in biotechnology.

It has also been discovered that plant genes can move to endophyte fungi that grow on them. Several plant endophyte fungi that grow on taxol-producing yew trees have gained the ability to make taxol themselves.[10] (Taxol, also called paclitaxel, is an anti-cancer drug found in yew trees.)

Animals

Junk DNA is the most obvious general evidence of HGT in eukaryotes. Junk DNA is the name given to the seemingly non-functional repetitive DNA sequences that are a major portion of the genomes of many plants and animals. This DNA usually includes multiple copies of various 'Jumping genes' which can proliferate within a genome after they have been transferred from another species. Examples in the human of such mobile elements are 'Hsmar1' and 'Hsmar2' which are related to the widely studied 'mariner' transposon. Close relatives of mariner mobile DNA have been discovered in organisms as diverse as mites, flatworms, hydras, insects, nematodes, mammals and humans.[11] Retroviruses and retrotransposons are other examples of mobile horizontally transferred DNA found in animals.

The adzuki bean beetle Callosobruchus chinensis is infected with several strains of bacterial Wolbachia endosymbionts. A genome fragment of one of these endosymbionts has been found transferred to the X chromosome of the host insect.[12]

History of discovery of HGT

See main article Horizontal gene transfer (History)
  • Bacterial genetics starts in 1946
see main article Horizontal gene transfer in prokaryotes
  • First glimpses of horizontal transfer of traits in plant evolution
see also main article Barbara McClintock
  • Discovery of mobile genes in flies, and mariner
  • HGT and genetic engineering

Decoding the tree of life from genomes scrambled by HGT

For more information, see Citizendium's article on Prokaryote phylogeny and evolution

Because each organism carries a record of its ancestry in its DNA, methods for rapid gene isolation and analysis of DNA encoded sequences - which can extract the information from this ancestral archive - have been important for answering questions about evolution, and they have enabled rapid expansion of the field of biological systematics known as phylogenetic inference. Comparison of related (homologous) gene sequences from different organisms has made it possible to reconstruct the history of many evolutionary lineages.[13] Many issues about evolution have been clarifed by comparing homologous genes from different species, genera, families, and phyla. Unfortunately, HGT complicates the picture, because HGT 'scrambles' the evidence needed to deduce the branching patterns of evolutionary trees. One area of current research in phylogenetic inference, and arguably one of the most challenging problems in evolutionary theory, is the early stages in the evolution of life. This quandary about the origins of different cell types provides a good illustration of the complications introduced by HGT into the reconstruction of evolutionary history.

The main early branches of the tree of life have been intensively studied by microbiologists because the first organisms were microrganisms. A gene very often used for constructing phylogenetic relationships in microorganisms is the small ribosomal subunit ribosomal RNA (SSU rRNA) gene, as its sequences tend to be conserved among members with close phylogenetic distances, yet it is variable enough that differences can be measured.[14] The use of SSU rRNA to measure evolutionary "distances" was pioneered by Carl Woese when formulating the first modern 'tree of life', and his results led him to propose the Archaea (single celled organisms superficially similar to bacteria) as a third domain (sub-kingdom) of life.

A three domain representation of the tree of life based on SSU rRNA sequences, showing the separation of Bacteria, Archaea, and Eukaryote domains. See Microorganisms article for further explanation

Microbiologists introduced the term domain for the three main early branches of the tree of life, where domain is a phylogenetic term very similar in meaning to biological kingdom. These represent the three main lineages in evolution of early cellular life, and are currently represented by the Bacteria, the Archaea and Eukarya (eukaryote) domains. Eukaryotes are all organisms with a well defined nucleus, and this domain comprises protists, fungi, and all organisms in the animal and plant kingdoms, including humans. As seen in the figure (left), studies of SSU rRNA genes (and some other genes) might suggest that Archaea and Eukarya have a sister relationship in evolution, and it has often been assumed that eukaryotes evolved from archaeal cells. However, the fact that genes can move between distant branches of the tree of life even at low probabilities poses problems for scientists trying to reconstruct evolution from studying genes and gene sequences in different organisms due to the scrambling effect of HGT. The challenges are most awkward for the ambitious reconstruction of the earliest branches of the tree of life - because over a long enough time and with large numbers of organisms, many HGT events are certain to have occurred even though each particular transfer event has a low probability.

Thus recent discoveries of 'rampant' HGT in microorganisms, and the detection of horizontal movement of genes for SSU rRNA have forced biologists to question the accuracy of at least the early branches in the tree of life, and even to question the validity of trees as useful models of microbial evolution.[15]

Recent efforts to infer evolutionary trees while recognizing HGT

For more information, see Citizendium's article on Evolution of cells

The challenges of ascertaining an accurate branching structure for evolutionary trees of microbes, especially the earliest branches in the tree of life, have been a great spur for current biological research. Clear answers to important questions about these trees are not yet available, but many interesting discoveries and ideas are emerging.

Instead of relying primarily on a single gene such as the SSU rRNA gene to reconstruct evolution, scientific effort has now shifted to exploiting the comprehensive information from the many complete genome sequences of organisms that are now available.[16] So far, this comparative genomics approach, made possible by specially developed computer programs and mathematical algorithms, suggests that most of the core genes of bacteria that are useful for deducing evolutionary histories are unaffected by HGT. This confirms the practical experience of microbiologists that consistent and reliable trees can still be deduced for the more recent stages in microbial evolution, such as evolutionary relationships within particular bacterial phyla. This does require, however, using multiple, well chosen genes to investigate how lineages are related to one another. Thus the 'tree' is still a valid metaphor for microbial evolution - but a tree adorned with 'cobwebs' of horizontally transferred genes.

But it is also clear that trees based only on SSU rRNA alone do not capture the events of early eukaryote evolution accurately, and the origins of the first nucleated cells are still uncertain. For instance, careful analysis of the complete genome of the eukaryote yeast shows that many of its genes are more closely related to bacterial genes than they are to archaea, and it is now clear that archaea were not the simple progenitors of the eukaryotes. This discovery is a stark contradiction to earlier findings based on SSU rRNA and limited samples of other genes.[17] (See Evolution of cells for further discussion.)

On the other hand, the concept that rampant HGT took place in 'gene-swapping collectives' involved in metabolism and replication at the earliest stages of life's origins, before a postulated transition to Darwinian evolution of the cellular lineages known today, has been used by Carl Woese and colleagues to develop fresh insight into the origins of the universal genetic code.[18]

See also

References

Citations

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Further reading

  • Focus on horizontal gene transfer Webfocus in Nature with free access review articles.
  • Smallpox knows how to make a mouse protein. How did smallpox learn that? The New Yorker July 12, 1999, p44-61. 'The poxviruses are promiscuous at capturing genes from their hosts,' Esposito said. 'It tells you that smallpox was once inside a mouse or some other small rodent'. (Open access)
  • Where Do All Those Genes Come From? This study resolves a long-standing paradox: how is it possible to deduce reliable evolutionary histories from gene sequences in bacteria despite extensive HGT? (Open access)
  • Woese C (2002) On the evolution of cells.Proc Natl Acad Sci USA 99:8742-7 PMID 12077305. This article shifts the emphasis in early phylogenic adaptation from vertical to horizontal gene transfer. (Open access)
  • Salzberg SL et al. (2001) Microbial genes in the human genome: lateral transfer or gene loss? Science 292:1903-6 PMID 11358996. This reports that one dramatic claim of HGT - in which a distinguished group of scientists claimed that bacteria transferred their DNA directly into the human lineage - was simply wrong. (Open access)
  • Jain R et al. Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA 96:3801-6 PMID 10097118 (Open access)
  • Hall C et al. (2005) Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. Eukaryot Cell 4:1102-15 PMID 15947202 Convincing evidence of horizontal transfer of bacterial DNA into yeast. (Open access.)
  • Zhu J et al. (2000) The bases of crown gall tumorigenesis.J Bacteriol 182:3885-95 PMID 10869063 This article describes the biology of crown-gall bacterium, and the mechanism of DNA injection by this bacterium, and explains how genes can move between bacterial species and from bacteria to eukaryotic organisms, and illustrates the extent to which different species can co-evolve. (Open access)
  • Horizontal Gene Transfer Syvanen M, Kado CI (2002) 2nd edition, Academic Press ISBN 0-12-680126-6 A comprehensive treatise. Reviewed here by M-W Ho
  • Acquiring genomes: a theory of the origin of species. Margulis L and Sagan D (2002) Basic Books ISBN 0-465-04392-5. A book that looks at gene transfer from a different perspective to many conventional interpretations, but with an emphasis on microbial diversity. Reviewed here.
  • Richardson AO, Palmer, JD (2007) Horizontal gene transfer in plants. J Exp Bot 58:1–9 doi:10.1093/jxb/erl148 PMID 17030541
  • Gogarten JP Townsend JP (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 9:679-87 PMID 16138096. One article in a whole issue of the journal Nature Reviews Microbiology largely devoted to HGT.
  • Weinbauer MG, Rassoulzadegan F (2004) Are viruses driving microbial diversification and diversity? Envir Microbiol 6:1-11 PMID 14686936 Discussion of both the evolutionary and ecological activities of viruses in the ocean, a major source of HGT in nature.

External links