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'''Plant–fungus horizontal gene transfer''' is the movement of [[genetic material]] between individuals in the [[plant]] and [[fungus]] [[kingdom (biology)|kingdoms]]. [[Horizontal gene transfer]] is universal in [[fungi]], [[virus]]es, [[bacteria]], and other [[eukaryote]]s.<ref>{{cite journal | vauthors = Bansal AK, Meyer TE | title = Evolutionary analysis by whole-genome comparisons | journal = Journal of Bacteriology | volume = 184 | issue = 8 | pages = 2260–72 | date = April 2002 | pmid = 11914358 | doi = 10.1128/JB.184.8.2260-2272.2002 | pmc = 134949 }}</ref> Horizontal gene transfer research often focuses on [[prokaryote]]s because of the abundant sequence data from diverse lineages, and because it is assumed not to play a significant role in eukaryotes.<ref name="Andersson 1182–1197">{{cite journal | vauthors = Andersson JO | title = Lateral gene transfer in eukaryotes | journal = Cellular and Molecular Life Sciences | volume = 62 | issue = 11 | pages = 1182–97 | date = June 2005 | pmid = 15761667 | doi = 10.1007/s00018-005-4539-z | s2cid = 32205767 | pmc = 11138376 }}</ref>

Most plant–fungus horizontal gene transfer events are ancient and rare, but they may have provided important gene functions leading to wider substrate use and habitat spread for plants and fungi.<ref name="Richards 1897–1911">{{cite journal | vauthors = Richards TA, Soanes DM, Foster PG, Leonard G, Thornton CR, Talbot NJ | title = Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi | journal = The Plant Cell | volume = 21 | issue = 7 | pages = 1897–911 | date = July 2009 | pmid = 19584142 | pmc = 2729602 | doi = 10.1105/tpc.109.065805 }}</ref> Since these events are rare and ancient, they have been difficult to detect and remain relatively unknown.<ref name="Rosewich 2000 325–363">{{cite journal | vauthors = Rosewich UL, Kistler HC | title = Role of Horizontal Gene Transfer in the Evolution of Fungi | journal = Annual Review of Phytopathology | volume = 38 | pages = 325–363 | date = 2000 | pmid = 11701846 | doi = 10.1146/annurev.phyto.38.1.325  }}</ref> Plant–fungus interactions could play a part in a multi-horizontal gene transfer pathway among many other organisms.<ref name=GaoRen2014 />

== Mechanisms ==
Fungus–plant-mediated horizontal gene transfer can occur via [[phagotrophic]] mechanisms (mediated by phagotrophic eukaryotes) and nonphagotropic mechanisms. Nonphagotrophic mechanisms have been seen in the transmission of [[transposable element]]s, [[plastid]]-derived [[endosymbiotic]] gene transfer, prokaryote-derived gene transfer, ''[[Agrobacterium tumefaciens]]''-mediated [[DNA]] transfer, cross-species [[Hybrid (biology)|hybridization]] events, and gene transfer between [[Mitochondrion|mitochondrial]] genes.<ref name="Richards 1897–1911" /> Horizontal gene transfer could bypass eukaryotic barrier features like linear [[chromatin]]-based [[chromosome]]s, [[intron]]–[[exon]] gene structures, and the [[nuclear envelope]].<ref>{{cite journal | vauthors = Richards TA, Soanes DM, Foster PG, Leonard G, Thornton CR, Talbot NJ | title = Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi | journal = The Plant Cell | volume = 21 | issue = 7 | pages = 1897–911 | date = July 2009 | pmid = 19584142 | doi = 10.1105/tpc.109.065805 | pmc = 2729602 }}</ref>

Horizontal gene transfer occurs between microorganisms sharing overlapping ecological niches and associations like [[parasitism]] or [[symbiosis]]. Ecological association can facilitate horizontal gene transfer in plants and fungi and is an unstudied factor in shared evolutionary histories.

Most horizontal gene transfers from fungi into plants predate the rise of land plants. A greater genomic inventory of gene family and taxon sampling has been identified as a desirable prerequisite for identifying further plant–fungus events.<ref name="Rosewich 2000 325–363"/>

== Indicators of past horizontal gene transfer ==

Evidence for gene transfer between fungi and eukaryotes is discovered indirectly. Evidence is found in the unusual features of genetic elements. These features include: inconsistency between [[phylogeny]] across genetic elements, high [[DNA]] or [[amino acid]] similarity from phylogenetically distant organisms, irregular distribution of genetic elements in a variety of species, similar genes shared among species within a specific habitat or geography independent of their phylogenetic relationship, and gene characteristics inconsistent with the resident genome such as high [[guanine]] and [[cytosine]] content, [[codon]] usage, and introns.<ref name="Rosewich 2000 325–363"/>

Alternative hypotheses and explanations for such findings include erroneous species phylogenies, inappropriate comparison of [[paralogous]] sequences, sporadic retention of shared ancestral characteristics, uneven rates of character change in other lineages, and [[introgressive hybridization]].<ref name="Rosewich 2000 325–363"/>

The "complexity hypothesis" is a different approach to understanding why informational genes have less success in being transferred than operational genes. It has been proposed that informational genes are part of larger, more conglomerate systems, while operational genes are less complex, allowing them to be horizontally transferred at higher frequencies. The hypothesis incorporates the "continual hypothesis", which states that horizontal gene transfer is constantly occurring in operational genes.<ref>{{cite journal | vauthors = Jain R, Rivera MC, Lake JA | title = Horizontal gene transfer among genomes: the complexity hypothesis | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 96 | issue = 7 | pages = 3801–6 | date = March 1999 | pmid = 10097118 | doi = 10.1073/pnas.96.7.3801 | pmc = 22375 | bibcode = 1999PNAS...96.3801J | doi-access = free }}</ref>

== Examples ==<!--not a great way to group anything, what about 'Taxonomic range' or 'Pathways' or whatever-->

=== Horizontal gene transfer as a multi-vector pathway ===
Plant–fungus horizontal gene transfer could take place during plant infection. There are many possible vectors, such as plant–fungus–insect interactions. The ability for fungi to infect other organisms provides this possible pathway.<ref name=GaoRen2014>{{cite journal | vauthors = Gao C, Ren X, Mason AS, Liu H, Xiao M, Li J, Fu D | title = Horizontal gene transfer in plants | journal = Functional & Integrative Genomics | volume = 14 | issue = 1 | pages = 23–9 | date = March 2014 | pmid = 24132513 | doi = 10.1007/s10142-013-0345-0  | s2cid = 16670298 | url = https://espace.library.uq.edu.au/view/UQ:328531/UQ328531OA.pdf }}</ref>

=== In rice ===
A fungus–plant pathway has been demonstrated in rice (''[[Oryza sativa]]'') through ancestral lineages. A phylogeny was constructed from 1689 identified genes and all [[Homology (biology)|homologs]] available from the rice genome (3177 gene families). Fourteen candidate plant–fungus horizontal gene transfer events were identified, nine of which showed infrequent patterns of transfer between plants and fungi. From the phylogenetic analysis, horizontal gene transfer events could have contributed to the L-fucose permease sugar transporter, zinc binding [[alcohol dehydrogenase]], [[membrane transporter]], [[phospholipase]]/[[carboxylesterase]], [[iucA]]/[[iucC]] family protein in [[siderophore]] biosynthesis, [[DUF239]] domain protein, phosphate-response 1 family protein, a hypothetical protein similar to [[zinc finger]] (C2H2-type) protein, and another conserver hypothetical protein.<ref name="Richards 1897–1911"/>

=== Ancestral shikimate pathway ===
Some plants may have obtained the [[shikimate pathway]] from symbiotic fungi. Plant shikimate pathway enzymes share similarities to prokaryote homologs and could have ancestry from a [[plastid]] progenitor genome. It is possible that the shikimate pathway and the pentafunctional ''arom'' have their ancient origins in eukaryotes or were conveyed by eukaryote–eukaryote horizontal gene transfer. The evolutionary history of the pathway could have been influenced by a prokaryote-to-eukaryote gene transfer event. [[Ascomycete]] fungi along with [[zygomycete]]s, [[basidiomycete]]s, [[apicomplexa]], [[ciliate]]s, and [[oomycete]]s retained elements of an ancestral pathway given through the bikont/unikont eukaryote root.<ref>{{cite journal | vauthors = Richards TA, Dacks JB, Campbell SA, Blanchard JL, Foster PG, McLeod R, Roberts CW | title = Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements | journal = Eukaryotic Cell | volume = 5 | issue = 9 | pages = 1517–31 | date = September 2006 | pmid = 16963634 | pmc = 1563581 | doi = 10.1128/EC.00106-06  }}</ref>

=== Ancestral land plants ===
Fungi and bacteria could have contributed to the phenylpropanoid pathway in ancestral land plants for the synthesis of [[flavonoid]]s and [[lignin]] through horizontal gene transfer. [[Phenylalanine ammonia lyase]] (PAL) is known to be present in fungi, such as [[Basidiomycota]] yeast like ''[[Rhodotorula]]'' and [[Ascomycota]] such as ''[[Aspergillus]]'' and ''[[Neurospora]]''. These fungi participate in the [[catabolism]] of [[phenylalanine]] for carbon and nitrogen. PAL in some plants and fungi also has a [[tyrosine ammonia lyase]] (TAL) for the synthesis of [[p-coumaric acid]] into [[p-coumaroyl-CoA]]. PAL likely emerged from bacteria in an antimicrobial role. Horizontal gene transfer took place through a pre-[[Dikarya]] divergent fungal lineage and a ''[[Nostocales|Nostocale]]'' or soil-sediment bacterium through symbiosis. The fungal PAL was then transferred to an ancestor of a land plant by an ancient [[arbuscular mycorrhizal]] symbiosis that later developed in the phenylpropanoid pathway and land plant colonization. PAL enzymes in early bacteria and fungi could have contributed to protection against [[Ultraviolet|ultraviolet radiation]], acted as a light capturing pigment, or assisted in antimicrobial defense.<ref>{{cite journal | vauthors = Emiliani G, Fondi M, Fani R, Gribaldo S | title = A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land | journal = Biology Direct | volume = 4 | pages = 7 | date = February 2009 | pmid = 19220881 | pmc = 2657906 | doi = 10.1186/1745-6150-4-7 | doi-access = free }}</ref>

=== Gene transfer for enhanced intermediate and secondary metabolism ===
''[[Sterigmatocystin]]'' gene transfer has been observed with ''[[Podospora anserina]]'' and ''[[Aspergillus]]''. Horizontal gene transfer in ''Aspergillus'' and ''Podospora'' contributed to fungal metabolic diversity in secondary metabolism. ''[[Aspergillus nidulans]]'' produces [[sterigmatocystin]] – a precursor to [[aflatoxin]]s. ''Aspergillus'' was found to have horizontally transferred genes to ''Podospora anserina''. ''Podospora'' and ''Aspergillus'' show high conservation and microsynteny sterigmatocystin/aflatoxin clusters along with intergenic regions containing 14 binding sites for [[AfIR]], a transcription factor for the activation of sterigmatocystin/aflatoxin biosynthetic genes. ''Aspergillus'' to ''Podospora'' represents a large metabolic gene transfer which could have contributed to fungal metabolic diversity. Transposable elements and other mobile genetic elements like plasmids and viruses could allow for chromosomal rearrangement and integration of foreign genetic material. Horizontal gene transfer could have significantly contributed to fungal genome remodeling and metabolic diversity.<ref>{{cite journal | vauthors = Slot JC, Rokas A | title = Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi | journal = Current Biology | volume = 21 | issue = 2 | pages = 134–9 | date = January 2011 | pmid = 21194949 | doi = 10.1016/j.cub.2010.12.020 | doi-access = free }}</ref>

=== Acquired pathogenic capabilities ===
In ''[[Stagonospora]]'' and ''[[Pyrenophora]]'', as well as in ''[[Fusarium]]'' and ''[[Alternaria]]'', horizontal gene transfer provides a powerful mechanism for fungi to acquire [[pathogen]]ic capabilities to infect a new host plant. Horizontal gene transfer and interspecific hybridization between pathogenic species allow for hybrid offspring with an expanded host range. This can cause disease outbreaks on new crops when an encoded protein is able to cause pathogenicity.<ref>{{cite journal | vauthors = Mehrabi R, Bahkali AH, Abd-Elsalam KA, Moslem M, Ben M'barek S, Gohari AM, Jashni MK, Stergiopoulos I, Kema GH, de Wit PJ | title = Horizontal gene and chromosome transfer in plant pathogenic fungi affecting host range | journal = FEMS Microbiology Reviews | volume = 35 | issue = 3 | pages = 542–54 | date = May 2011 | pmid = 21223323 | doi = 10.1111/j.1574-6976.2010.00263.x  | doi-access = free }}</ref>
 
The interspecific transfer of virulence factors in fungal pathogens has been shown between ''[[Stagonospora modorum]]'' and ''[[Pyrenophora tritici-repentis]]'', where a host-selective toxin from ''S. nodorum'' conferred virulence to ''P. tritici-repentis'' on wheat.<ref>{{cite journal | vauthors = Friesen TL, Stukenbrock EH, Liu Z, Meinhardt S, Ling H, Faris JD, Rasmussen JB, Solomon PS, McDonald BA, Oliver RP | title = Emergence of a new disease as a result of interspecific virulence gene transfer | journal = Nature Genetics | volume = 38 | issue = 8 | pages = 953–6 | date = August 2006 | pmid = 16832356 | doi = 10.1038/ng1839  | s2cid = 6349264 }}</ref>

In ''[[Fusarium]]'', a nonpathogenic strain was experimentally converted into a pathogen and could have contributed to pathogen adaption in large genome portions. ''[[Fusarium graminearum]]'', ''[[Fusarium verticilliodes]]'', and ''[[Fusarium oxysprorum]]'' are maize and tomato pathogens that produce [[fumonisin]] [[mycotoxin]]s that contaminate grain. These examples highlight the apparent polyphyletic origins of host specialization and the emergence of new pathogenic lineages distinct from genetic backgrounds.<ref>{{cite journal | vauthors = Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie X, Xu JR, Antoniw J, Baker SE, Bluhm BH, Breakspear A, Brown DW, Butchko RA, Chapman S, Coulson R, Coutinho PM, Danchin EG, Diener A, Gale LR, Gardiner DM, Goff S, Hammond-Kosack KE, Hilburn K, Hua-Van A, Jonkers W, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li L, Manners JM, Miranda-Saavedra D, Mukherjee M, Park G, Park J, Park SY, Proctor RH, Regev A, Ruiz-Roldan MC, Sain D, Sakthikumar S, Sykes S, Schwartz DC, Turgeon BG, Wapinski I, Yoder O, Young S, Zeng Q, Zhou S, Galagan J, Cuomo CA, Kistler HC, Rep M | display-authors = 6 | title = Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium | journal = Nature | volume = 464 | issue = 7287 | pages = 367–73 | date = March 2010 | pmid = 20237561 | doi = 10.1038/nature08850 | pmc = 3048781 | bibcode = 2010Natur.464..367M }}</ref> The ability to transfer genetic material could increase disease in susceptible plant populations.

== References ==
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[[Category:Genetics]]
[[Category:Microbial population biology]]