Supplementary table 1: Examples of polyploid fungal species described in the literature

Дата канвертавання18.04.2016
Памер79.6 Kb.
Supplementary table 1: Examples of polyploid fungal species described in the literature




Rhizopus oryzae



Phycomyces blakesleeanus



Allomyces macrogynus


Haploid, diploid, tetraploid

Allomyces arbuscula

[4, 5]

Haploid, diploid, triploid, tetraploid

Allomyces javanicus


Putative allopolyploid whose progenitors may be A. arbuscula & A. macrogynus

Glomus etunicatum


Cyathus stercoreus

[7, 8]

Tetraploid, possibly allotetraploid

Agaricus campestris


Coprinellus micaceus


Coprinopsis atramentaria


Botrytis alli


Allotetraploid whose progenitors may be B. byssoidea and B. aclada

Phyllactinia sp.


Autopolyploid and allopolyploid

Xylaria curta


Multivalent at meiosis

Stephensia shanori


Zygosaccharomyces rouxii


Allopolyploid whose progenitors may be Z. rouxii and Z. pseudorouxii

Saccharomyces genus



Saccharomyces cerevisiae


Autotetraploid, allotetraploid

Saccharomyces pastorianus

[25, 26]

Allotetraploid (in the curse of diploidization) whose progenitors may be S. cerevisiae and S. eubayanus

Candida utilis


Ploidy status unclear, possibly tetraploid

Supplementary table 2: Examples of natural intra- and inter-specific fungal hybrids




Melampsora medusa-populina


Interspecific hybrids whose progenitors are M. medusa and M. larici-populina

Melampsora x columbiana


Interspecific hybrids whose progenitors are M. medusa and M.occidentalis

Epichloe sp.


Verticillium dahliae


Interspecific hybrid

Agaricus bisporus


Interspecific hybrid

Flammulina genus


Interspecific hybrid whose progenitors are F.velutipes and F. rossica

Dekkera bruxellensis


Interspecific origin or/and duplications

Supplementary table 3: Factors affecting genome size in Fungi.





Candida albicans



Chromosome loss associated with heat shock

Candida glabrata



Chromosome duplications and rearrangements associated with antifungal drug resistance

Dictyostelium discoideum



Ploidy increase associated with fungicides

Saccharomyces cerevisiae



Ploidy increase associated with saline stress during lab evolution

Saccharomyces cerevisiae



Ploidy increase associated with , esp1, spa1, cdc31, kar1, ndc1, chc1, mps1, mps2 mutants

Saccharomyces cerevisiae



Aneuploidy associated with Hsp90 stress.

Schizosaccharomyces pombe



Ploidy increase associated with bub1 mutant

Armillaria mellea



Ploidy associated with cellular differentiation

Aspergillus nidulans



Frequent aneuploidy that increases with tissue age

Didymium iridis



Polyploidy, chromosome loss and aneuploidy

Helicobasidium mompa



Haploid, diploid and tetraploid cells

Macrophomina phaseoli



Ploidy variation associated with development

Mucor hiemalis



Ploidy variations associated with life cycle, including haploid, diploid, and aneuploid cells

Neurospora crassa



Unreduced gametes, frequent aneuploidy

Phymatotrichum omnivorum



Ploidy variations associated with life cycle, including haploids, diploids, and aneuploids

Pleurotus ostreatus



Variation of genome size and chromosome number

Ajellomyces capsulatus


Formerly Histoplasma capsulatem, possible aneuploidy

Septoria tritici


Chromosome polymorphism

Nectrla haematococca



Chromosome polymorphism associated with pathogenicity

Fusarium oxysporum



Chromosome polymorphism associated with pathogenicity

Supplementary table 4: Examples of polyploid species belonging to the Chromalveolata eukaryotic supergroup




Phytophthora infestans


Triploid & tetraploid

Phytophthora megasperma


Phytophthora alni


Autotetraploid, allotriploid

Phytophthora meadii



Phytophthora genus



Achlya racemosa


Saprolegnia multispora


Ascophyllum nodosum


Cystoseira nodicaulis


Macrocystis angustifolia


Dickieia ulvacea


Seminavis sp.


Paramecium tetraurelia




1. Ma L., Ibrahim A., Skory C., Grabherr M., Burger G., Butler M., Elias M., Idnurm A., Lang B., Sone T. 2009 Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genet 5(7), e1000549.

2. Marcet-Houben M., Marceddu G., Gabaldon T. 2009 Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence. BMC Evolutionary Biology 9(1), 295.

3. Olson L.W., Borkhardt B. 1978 Polyploidy and its control in Allomyces macrogynus. Transactions of the British Mycological Society 71(1), 65-76.

4. Wilson C.M. 1952 Meiosis in Allomyces. Bulletin of the Torrey Botanical Club 79(2), 139-160.

5. Emerson R., Wilson C.M. 1954 Interspecific Hybrids and the Cytogenetics and Cytotaxonomy of Euallomyces. Mycologia 46(4), 393-434.

6. Pawlowska T.E., Taylor J.W. 2004 Organization of genetic variation in individuals of arbuscular mycorrhizal fungi. Nature 427, 733-737.

7. Lu B. 1964 Polyploidy in the Basidiomycete Cyathus stercoreus. Am J Bot 51(3), 343-347.

8. Lu B.C. 1964 Chromosome cycles of the basidiomycete Cyathus stercoreus (Schw.) De Toni. Chromosoma 15(2), 170-184. (doi:10.1007/bf00285728).

9. Hughes D.T. 1961 Chromosomes of the Wild Mushroom. Nature 190(4772), 285-286.

10. Lu B.C., Raju N.B. 1970 Meiosis in Coprinus. Chromosoma 29(3), 305-316. (doi:10.1007/bf00325945).

11. Nielsen K., Yohalem D.Y. 2001 Origin of a Polyploid Botrytis Pathogen through Interspecific Hybridization between Botrytis aclada and B. byssoidea. Mycologia 93(6), 1064-1071.

12. Sharma A.K., Koul A.K. 1984 Chromosomal variability in Phyllactinia (Erysiphaceae). Transactions of the British Mycological Society 82(2), 355-359.

13. Rogers J.D. 1968 Xylaria curta: cytology of the ascus. Can J Bot 46(11), 1337-1340.

14. Uecker F.A. 1967 Stephensia shanori. I. Cytology of the Ascus and Other Observations. Mycologia 59(5), 819-832.

15. Gordon J.L., Wolfe K.H. 2008 Recent allopolyploid origin of Zygosaccharomyces rouxii strain ATCC 42981. Yeast 25(6), 449-456. (doi:10.1002/yea.1598).

16. Kellis M., Birren B.W., Lander E.S. 2004 Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428(6983), 617-624.

17. Wolfe K.H., Shields D.C. 1997 Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387(6634), 708-713.

18. Wong S., Butler G., Wolfe K.H. 2002 Gene order evolution and paleopolyploidy in hemiascomycete yeasts. Proc Natl Acad Sci U S A 99(14), 9272-9277. (doi:10.1073/pnas.142101099

142101099 [pii]).

19. Naumov G.I., Naumova E.S., Masneuf I., Aigle M., Kondratieva V.I., Dubourdieu D. 2000 Natural polyploidization of some cultured yeast Saccharomyces sensu stricto: auto- and allotetraploidy. Syst Appl Microbiol 23(3), 442-449.

20. Albertin W., Marullo P., Aigle M., Bourgais A., Bely M., Dillmann C., D D.E.V., Sicard D. 2009 Evidence for autotetraploidy associated with reproductive isolation in Saccharomyces cerevisiae: towards a new domesticated species. J Evol Biol 22(11), 2157-2170. (doi:JEB1828 [pii]


21. Stift M., Reeve R., van Tienderen P.H. 2010 Inheritance in tetraploid yeast revisited: segregation patterns and statistical power under different inheritance models. J Evol Biol 23(7), 1570-1578. (doi:JEB2012 [pii]


22. Al Safadi R., Weiss-Gayet M., Briolay J., Aigle M. 2010 A polyploid population of Saccharomyces cerevisiae with separate sexes (dioecy). FEMS Yeast Res 10(6), 757-768. (doi:FYR660 [pii]


23. Guijo S., Mauricio J.C., Salmon J.M., Ortega J.M. 1997 Determination of the relative ploidy in different Saccharomyces cerevisiae strains used for fermentation and 'flor' film ageing of dry sherry-type wines. Yeast 13(2), 101-117. (doi:10.1002/(SICI)1097-0061(199702)13:2<101::AID-YEA66>3.0.CO;2-H [pii]


24. Naumov G.I., Naumova E.S., Antunovics Z., Sipiczki M. 2002 Saccharomyces bayanus var. uvarum in Tokaj wine-making of Slovakia and Hungary. Appl Microbiol Biotechnol 59(6), 727-730. (doi:10.1007/s00253-002-1077-6).

25. Libkind D., Hittinger C.T., Valerio E., Goncalves C., Dover J., Johnston M., Goncalves P., Sampaio J.P. 2011 Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Proc Natl Acad Sci U S A 108(35), 14539-14544. (doi:1105430108 [pii]


26. Nguyen H.V., Legras J.L., Neuveglise C., Gaillardin C. 2011 Deciphering the Hybridisation History Leading to the Lager Lineage Based on the Mosaic Genomes of Saccharomyces bayanus Strains NBRC1948 and CBS380. PLoS One 6(10), e25821. (doi:10.1371/journal.pone.0025821

PONE-D-11-07052 [pii]).

27. Ikushima S., Fujii T., Kobayashi O. 2009 Efficient gene disruption in the high-ploidy yeast Candida utilis using the Cre-loxP system. Biosci Biotechnol Biochem 73(4), 879-884. (doi:JST.JSTAGE/bbb/80799 [pii]).

28. Spiers A.G., Hopcroft D.H. 1994 Comparative studies of the poplar rusts Melampsora medusae, M. larici-populina and their interspecific hybrid M.medusae-populina. Mycological Research 98(8), 889-903.

29. Newcombe G., Stirling B., McDonald S., Bradshaw Jr H.D. 2000 Melampsora × columbiana, a natural hybrid of M. medusae and M. occidentalis. Mycological Research 104(3), 261-274.

30. Tsai H.F., Liu J.S., Staben C., Christensen M.J., Latch G.C., Siegel M.R., Schardl C.L. 1994 Evolutionary diversification of fungal endophytes of tall fescue grass by hybridization with Epichloe species. Proc Natl Acad Sci U S A 91(7), 2542-2546.

31. Collins A., Mercado-Blanco J., Jiménez-Diaz R.M., Olivares C., Clewes E., Barbara D.J. 2005 Correlation of molecular markers and biological properties in Verticillium dahliae and the possible origins of some isolates. Plant Pathology 54, 549-557.

32. Callac P., Jacobe de Haut I., Imbernon M., Guinberteau J., Desmerger C., Theochari I. 2003 A novel homothallic variety of Agaricus bisporus comprises rare tetrasporic isolates from Europe. Mycologia 95(2), 222-231. (doi:95/2/222 [pii]).

33. Hughes K.W., Petersen R.H. 2001 Apparent recombination or gene conversion in the ribosomal ITS region of a Flammulina (Fungi, Agaricales) hybrid. Mol Biol Evol 18(1), 94-96.

34. Hellborg L., Piskur J. 2009 Complex nature of the genome in a wine spoilage yeast, Dekkera bruxellensis. Eukaryot Cell 8(11), 1739-1749. (doi:EC.00115-09 [pii]


35. Hilton C., Markie D., Corner B., Rikkerink E., Poulter R. 1985 Heat shock induces chromosome loss in the yeast Candida albicans. Mol Gen Genet 200(1), 162-168.

36. Polakova S., Blume C., Zarate J.a., Mentel M., Jorck-Ramberg D., Stenderup J., Piskur J. 2009 Formation of new chromosomes as a virulence mechanism in yeast Candida glabrata. Proceedings of the National Academy of Sciences 106(8), 2688-2693. (doi:10.1073/pnas.0809793106).

37. Welker D.L., Williams K.L. 1980 Mitotic Arrest and Chromosome Doubling Using Thiabendazole, Cambendazole, Nocodazole and Ben Late in the Slime Mould Dictyostelium discoideum. Journal of General Microbiology 116(2), 397-407. (doi:10.1099/00221287-116-2-397).

38. Dhar R., Sagesser R., Weikert C., Yuan J., Wagner A. 2011 Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution. J Evol Biol. (doi:10.1111/j.1420-9101.2011.02249.x).

39. Baum P., Yip C., Goetsch L., Byers B. 1988 A yeast gene essential for regulation of spindle pole duplication. Molecular and Cellular Biology 8(12), 5386-5397. (doi:10.1128/mcb.8.12.5386).

40. Snyder M., Davis R.W. 1988 SPA1: A gene important for chromosome segregation and other mitotic functions in S. cerevisiae. Cell 54(6), 743-754.

41. Schild D., Ananthaswamy H.N., Mortimer R.K. 1981 An endomitotic effect of a cell cycle mutation of Saccharomyces cerevisiae. Genetics 97(3-4), 551-562.

42. Rose M.D., Fink G.R. 1987 KAR1, a gene required for function of both intranuclear and extranuclear microtubules in yeast. Cell 48(6), 1047-1060.

43. Thomas J.H., Botstein D. 1986 A gene required for the separation of chromosomes on the spindle apparatus in yeast. Cell 44(1), 65-76.

44. Lemmon S., Jones E. 1987 Clathrin requirement for normal growth of yeast. Science 238(4826), 504-509. (doi:10.1126/science.3116672).

45. Winey M., Goetsch L., Baum P., Byers B. 1991 MPS1 and MPS2: novel yeast genes defining distinct steps of spindle pole body duplication. The Journal of Cell Biology 114(4), 745-754. (doi:10.1083/jcb.114.4.745).

46. Chen G., Bradford W.D., Seidel C.W., Li R. 2012 Hsp90 stress potentiates rapid cellular adaptation through induction of aneuploidy. Nature 482(7384), 246-250. (doi:nature10795 [pii]


47. Bernard P., Hardwick K., Javerzat J.-P. 1998 Fission Yeast Bub1 Is a Mitotic Centromere Protein Essential for the Spindle Checkpoint and the Preservation of Correct Ploidy through Mitosis. The Journal of Cell Biology 143(7), 1775-1787.

48. Peabody D.C., Motta J.J., Therrien C.D. 1978 Cytophotometric Evidence for Heteroploidy in the Life Cycle of Armillaria mellea. Mycologia 70(3), 487-498.

49. Gabrielli A.C., Azevedo J.L. 1980 A strain of Aspergillus nidulans producing a high frequency of disomics. Transactions of the British Mycological Society 75(1), 15-20.

50. Kafer E., Upshall A. 1973 The Phenotypes of the Eight Disomics and Trisomics of Aspergillus nidulans. Journal of Heredity 64(1), 35-38.

51. Upshall A. 1981 Naturally Occurring Diploid Isolates of Aspergillus nidulans. Journal of General Microbiology 122(1), 7-10. (doi:10.1099/00221287-122-1-7).

52. Collins O.R., Therrien C.D., Betterley D.A. 1978 Genetical and cytological evidence for chromosomal elimination in a true slime mold, Didymium iridis. Am J Bot 65(6), 660-670.

53. Aimi T., Yotsutani Y., Morinaga T. 2001 Alternation of nuclear phase in the filamentous basidiomycete Helicobasidium mompa. Mycoscience 42(3), 247-254. (doi:10.1007/bf02463915).

54. Knox-Davies P.S. 1966 Nuclear Division in the Developing Pycnospores of Macrophomina phaseoli. Am J Bot 53(3), 220-224.

55. James F.R. 1982 Studies on the Genetics of Mucor hiemalis. Mycologia 74(5), 744-751.

56. Threlkeld S.F.H., Stephens V. 1966 Ascospore isolates of Neurospora crassa giving rise to cultures containing two or more genetically different nuclei. Canadian Journal of Genetics and Cytology 8(3), 414-421. (doi:doi:10.1139/g66-052).

57. Hosford R.M., Griees G.A. 1966 The Nuclei and Parasexuality in Phymatotrichum omnivorum. Am J Bot 53(6), 570-579.

58. Kullman B., Greve B. 2007 Diversity of DNA and protein contents of spores of the closely related oyster fungi Pleurotus pulmonarius and P. ostreatus as studied by flow cytometry. Folia Cryptog Estonica 43, 17-21.

59. Carr J., Shearer G. 1998 Genome Size, Complexity, and Ploidy of the Pathogenic Fungus Histoplasma capsulatum. Journal of Bacteriology 180(24), 6697-6703.

60. McDonald B.A., Martinez J.P. 1991 Chromosome length polymorphisms in a Septoria tritici population. Current Genetics 19(4), 265-271. (doi:10.1007/bf00355053).

61. Miao V.P.W., Matthews D.E., VanEtten H.D. 1991 Identification and chromosomal locations of a family of cytochrome P-450 genes for pisatin detoxification in the fungus Nectrla haematococca. Molecular and General Genetics MGG 226(1), 214-223. (doi:10.1007/bf00273606).

62. Ma L.-J., van der Does H.C., Borkovich K.A., Coleman J.J., Daboussi M.-J., Di Pietro A., Dufresne M., Freitag M., Grabherr M., Henrissat B., et al. 2010 Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464(7287), 367-373.

63. Tooley P.W., Therrien C.D. 1987 Cytophotometric determination of the nuclear DNA content of 23 Mexican and 18 non-Mexican isolates of Phytophthora infestans. Experimental Mycology 11(1), 19-26.

64. Hansen E.M., Brasier C.M., Shaw D.S., Hamm P.B. 1986 The taxonomic structure of Phytophthora megasperma: Evidence for emerging biological species groups. Transactions of the British Mycological Society 87(4), 557-573.

65. Ioos R., Andrieux A., Marçais B., Frey P. 2006 Genetic characterization of the natural hybrid species Phytophthora alni as inferred from nuclear and mitochondrial DNA analyses. Fungal Genetics and Biology 43(7), 511-529.

66. Sansome E., Brasier C.M., Hamm P.B. 1991 Phytophthora meadii may be a species hybrid. Mycological Research 95(3), 273-277.

67. Martens C., Van de Peer Y. 2010 The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection. BMC Genomics 11, 353. (doi:1471-2164-11-353 [pii]


68. Dick M.W. 1969 Morphology and Taxonomy of the Oomycetes, with Special Reference to Saprolegniaceae, Leptomitaceae and Pythiaceae I. Sexual Reproduction. New Phytologist 68(3), 751-775.

69. Green B.R., Dick M.W. 1972 DNA base composition and the taxonomy of the Oomycetes. Canadian Journal of Microbiology 18(7), 963-968. (doi:doi:10.1139/m72-149).

70. Win T., Dick M.W. 1975 Cytology of oomycetes. Archives of Microbiology 105(1), 283-293. (doi:10.1007/bf00447148).

71. Phillips N., Kapraun D.F., GÃmez Garreta A., Ribera Siguan M.A., Rull J.L., Salvador Soler N., Lewis R., Kawai H. 2011 Estimates of nuclear DNA content in ninety eight species of brown algae (Phaeophyta). AoB Plants. (doi:10.1093/aobpla/plr001).

72. Mann D.G. 1994 Auxospore formation, reproductive plasticity and cell structure in Navicula ulvacea and the resurrection of the genus Dickieia (Bacillariophyta). European Journal of Phycology 29(3), 141 - 157.

73. Chepurnov V.A., Mann D.G., Vyverman W., Sabbe K., Danielidis D.B. 2002 SEXUAL REPRODUCTION, MATING SYSTEM, AND PROTOPLAST DYNAMICS OF SEMINAVIS (BACILLARIOPHYCEAE). J Phycol 38(5), 1004-1019.

74. Aury J.M., Jaillon O., Duret L., Noel B., Jubin C., Porcel B.M., Segurens B., Daubin V., Anthouard V., Aiach N., et al. 2006 Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444(7116), 171-178. (doi:nature05230 [pii]


75. Arnaiz O., Gout J.F., Betermier M., Bouhouche K., Cohen J., Duret L., Kapusta A., Meyer E., Sperling L. 2010 Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia. BMC Genomics 11, 547. (doi:1471-2164-11-547 [pii]


76. Gout J.F., Duret L., Kahn D. 2009 Differential retention of metabolic genes following whole-genome duplication. Mol Biol Evol 26(5), 1067-1072. (doi:msp026 [pii]


77. Gout J.F., Kahn D., Duret L. 2010 The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PLoS Genet 6(5), e1000944. (doi:10.1371/journal.pgen.1000944).

78. Hughes T., Ekman D., Ardawatia H., Elofsson A., Liberles D.A. 2007 Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia. Genome Biol 8(5), 213. (doi:gb-2007-8-5-213 [pii]


База данных защищена авторским правом © 2016
звярнуцца да адміністрацыі

    Галоўная старонка