Editing Polyploidy (section)

=== Fungi ===

Besides plants and animals, the evolutionary history of various [[Fungus|fungal species]] is dotted by past and recent whole-genome duplication events (see Albertin and Marullo 2012<ref name=Albertin12>{{cite journal | vauthors = Albertin W, Marullo P | title = Polyploidy in fungi: evolution after whole-genome duplication | journal = Proceedings. Biological Sciences | volume = 279 | issue = 1738 | pages = 2497–2509 | date = July 2012 | pmid = 22492065 | pmc = 3350714 | doi = 10.1098/rspb.2012.0434 }}</ref> for review). Several examples of polyploids are known:
*autopolyploid: the aquatic fungi of genus ''Allomyces'',<ref>{{cite journal | vauthors = Emerson R, Wilson CM |year=1954 |title=Interspecific Hybrids and the Cytogenetics and Cytotaxonomy of Euallomyces |journal=Mycologia |volume=46 |issue=4 |pages=393–434 |jstor=4547843|doi=10.1080/00275514.1954.12024382 }}</ref> some ''[[Saccharomyces cerevisiae]]'' strains used in [[baker]]y,<ref>{{cite journal | vauthors = Albertin W, Marullo P, Aigle M, Bourgais A, Bely M, Dillmann C, DE Vienne D, Sicard D | display-authors = 6 | title = Evidence for autotetraploidy associated with reproductive isolation in Saccharomyces cerevisiae: towards a new domesticated species | journal = Journal of Evolutionary Biology | volume = 22 | issue = 11 | pages = 2157–2170 | date = November 2009 | pmid = 19765175 | doi = 10.1111/j.1420-9101.2009.01828.x | doi-access = free }}</ref> etc.
*allopolyploid: the widespread ''[[Cyathus stercoreus]]'',<ref>{{cite journal | vauthors = Lu BC |year=1964 |title=Polyploidy in the Basidiomycete ''Cyathus stercoreus'' |journal=American Journal of Botany |volume=51 |issue=3 |pages=343–347 |jstor=2440307 |doi=10.2307/2440307}}</ref> the allotetraploid lager yeast ''[[Saccharomyces pastorianus]]'',<ref>{{cite journal | vauthors = Libkind D, Hittinger CT, Valério E, Gonçalves C, Dover J, Johnston M, Gonçalves P, Sampaio JP | display-authors = 6 | title = Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 35 | pages = 14539–14544 | date = August 2011 | pmid = 21873232 | pmc = 3167505 | doi = 10.1073/pnas.1105430108 | doi-access = free | bibcode = 2011PNAS..10814539L }}</ref> the allotriploid wine spoilage yeast ''[[Dekkera bruxellensis]]'',<ref>{{cite journal | vauthors = Borneman AR, Zeppel R, Chambers PJ, Curtin CD | title = Insights into the Dekkera bruxellensis genomic landscape: comparative genomics reveals variations in ploidy and nutrient utilisation potential amongst wine isolates | journal = PLOS Genetics | volume = 10 | issue = 2 | pages = e1004161 | date = February 2014 | pmid = 24550744 | pmc = 3923673 | doi = 10.1371/journal.pgen.1004161 | doi-access = free }}</ref> etc.
*paleopolyploid: the human pathogen ''[[Rhizopus oryzae]]'',<ref>{{cite journal | vauthors = Ma LJ, Ibrahim AS, Skory C, Grabherr MG, Burger G, Butler M, Elias M, Idnurm A, Lang BF, Sone T, Abe A, Calvo SE, Corrochano LM, Engels R, Fu J, Hansberg W, Kim JM, Kodira CD, Koehrsen MJ, Liu B, Miranda-Saavedra D, O'Leary S, Ortiz-Castellanos L, Poulter R, Rodriguez-Romero J, Ruiz-Herrera J, Shen YQ, Zeng Q, Galagan J, Birren BW, Cuomo CA, Wickes BL | display-authors = 6 | title = Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication | journal = PLOS Genetics | volume = 5 | issue = 7 | pages = e1000549 | date = July 2009 | pmid = 19578406 | pmc = 2699053 | doi = 10.1371/journal.pgen.1000549 | veditors = Madhani HD | doi-access = free }}</ref> the genus ''[[Saccharomyces]]'',<ref>{{cite journal | vauthors = Wong S, Butler G, Wolfe KH | title = Gene order evolution and paleopolyploidy in hemiascomycete yeasts | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 99 | issue = 14 | pages = 9272–9277 | date = July 2002 | pmid = 12093907 | pmc = 123130 | doi = 10.1073/pnas.142101099 | doi-access = free | bibcode = 2002PNAS...99.9272W | jstor = 3059188 }}</ref> etc.

In addition, polyploidy is frequently associated with [[Hybrid (biology)|hybridization]] and reticulate evolution that appear to be highly prevalent in several fungal taxa. Indeed, [[Hybrid speciation|homoploid speciation]] (hybrid speciation without a change in [[chromosome]] number) has been evidenced for some fungal species (such as the [[basidiomycota]] ''[[Microbotryum violaceum]]''<ref>{{cite journal | vauthors = Devier B, Aguileta G, Hood ME, Giraud T | title = Using phylogenies of pheromone receptor genes in the Microbotryum violaceum species complex to investigate possible speciation by hybridization | journal = Mycologia | volume = 102 | issue = 3 | pages = 689–696 | year = 2009 | pmid = 20524600 | doi = 10.3852/09-192 }}</ref>).

[[File:Polyploidy in fungi.png|thumb|left|upright=1.2|Schematic phylogeny of the Chromalveolata. Red circles indicate polyploidy, blue squares indicate hybridization. From Albertin and Marullo, 2012<ref name=Albertin12 />]]
As for plants and animals, fungal hybrids and polyploids display structural and functional modifications compared to their progenitors and diploid counterparts. In particular, the structural and functional outcomes of polyploid ''Saccharomyces'' genomes strikingly reflect the evolutionary fate of plant polyploid ones. Large chromosomal rearrangements<ref>{{cite journal | vauthors = Dunn B, Sherlock G | title = Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus | journal = Genome Research | volume = 18 | issue = 10 | pages = 1610–1623 | date = October 2008 | pmid = 18787083 | pmc = 2556262 | doi = 10.1101/gr.076075.108 }}</ref> leading to [[Chimera (genetics)|chimeric]] chromosomes<ref>{{cite journal | vauthors = Nakao Y, Kanamori T, Itoh T, Kodama Y, Rainieri S, Nakamura N, Shimonaga T, Hattori M, Ashikari T | display-authors = 6 | title = Genome sequence of the lager brewing yeast, an interspecies hybrid | journal = DNA Research | volume = 16 | issue = 2 | pages = 115–129 | date = April 2009 | pmid = 19261625 | pmc = 2673734 | doi = 10.1093/dnares/dsp003 }}</ref> have been described, as well as more punctual genetic modifications such as gene loss.<ref>{{cite journal | vauthors = Scannell DR, Byrne KP, Gordon JL, Wong S, Wolfe KH | title = Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts | journal = Nature | volume = 440 | issue = 7082 | pages = 341–345 | date = March 2006 | pmid = 16541074 | doi = 10.1038/nature04562 | hdl-access = free | bibcode = 2006Natur.440..341S | hdl = 2262/22660 }}</ref> The homoealleles of the allotetraploid yeast ''S. pastorianus'' show unequal contribution to the [[transcriptome]].<ref>{{cite journal | vauthors = Minato T, Yoshida S, Ishiguro T, Shimada E, Mizutani S, Kobayashi O, Yoshimoto H | title = Expression profiling of the bottom fermenting yeast Saccharomyces pastorianus orthologous genes using oligonucleotide microarrays | journal = Yeast | volume = 26 | issue = 3 | pages = 147–165 | date = March 2009 | pmid = 19243081 | doi = 10.1002/yea.1654 }}</ref> [[Phenotypic]] diversification is also observed following polyploidization and/or hybridization in fungi,<ref>{{cite journal | vauthors = Lidzbarsky GA, Shkolnik T, Nevo E | title = Adaptive response to DNA-damaging agents in natural Saccharomyces cerevisiae populations from "Evolution Canyon", Mt. Carmel, Israel | journal = PLOS ONE | volume = 4 | issue = 6 | pages = e5914 | date = June 2009 | pmid = 19526052 | pmc = 2690839 | doi = 10.1371/journal.pone.0005914 | veditors = Idnurm A | doi-access = free | bibcode = 2009PLoSO...4.5914L }}</ref> producing the fuel for [[natural selection]] and subsequent [[adaptation]] and speciation.