No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.

Fungal Genomes and Insights into the Evolution of the Kingdom

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
  • PDF
    1.34 MB
  • HTML
    131.79 Kb
  • XML
    135.77 Kb
  • Author: Jason E. Stajich1
  • Editors: Joseph Heitman2, Eva Holtgrewe Stukenbrock3
    Affiliations: 1: Department of Plant Pathology and Microbiology and Institute of Integrative Genome Biology, University of California, Riverside, CA 92521; 2: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710; 3: Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany, and Max Planck Institute for Evolutionary Biology, Plön, Germany
  • Source: microbiolspec August 2017 vol. 5 no. 4 doi:10.1128/microbiolspec.FUNK-0055-2016
  • Received 19 May 2017 Accepted 19 June 2017 Published 18 August 2017
  • Jason E Stajich, [email protected]
image of Fungal Genomes and Insights into the Evolution of the Kingdom
    Preview this microbiology spectrum article:
    Zoom in

    Fungal Genomes and Insights into the Evolution of the Kingdom, Page 1 of 2

    | /docserver/preview/fulltext/microbiolspec/5/4/FUNK-0055-2016-1.gif /docserver/preview/fulltext/microbiolspec/5/4/FUNK-0055-2016-2.gif
  • Abstract:

    The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute’s Fungal Genome Initiative, and the 1000 Fungal Genomes Project (http://1000.fungalgenomes.org). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.

  • Citation: Stajich J. 2017. Fungal Genomes and Insights into the Evolution of the Kingdom. Microbiol Spectrum 5(4):FUNK-0055-2016. doi:10.1128/microbiolspec.FUNK-0055-2016.


1. Stajich JE, Berbee ML, Blackwell M, Hibbett DS, James TY, Spatafora JW, Taylor JW. 2009. The fungi. Curr Biol 19:R840–R845 http://dx.doi.org/10.1016/j.cub.2009.07.004. [PubMed]
2. James TY, Letcher PM, Longcore JE, Mozley-Standridge SE, Porter D, Powell MJ, Griffith GW, Vilgalys R. 2006. A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota). Mycologia 98:860–871 http://dx.doi.org/10.1080/15572536.2006.11832616.
3. Sanger F, Nicklen S, Coulson AR. 1977. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467 http://dx.doi.org/10.1073/pnas.74.12.5463. [PubMed]
4. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491 http://dx.doi.org/10.1126/science.2448875.
5. White TJ, Bruns TD, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, p 315–322. In Innis MA, Gelfand DH, Sninsky JJ, White TJ (ed), PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA.
6. Bruns TD, Vilgalys R, Barns SM, Gonzalez D, Hibbett DS, Lane DJ, Simon L, Stickel S, Szaro TM, Weisburg WG, Sogin ML. 1992. Evolutionary relationships within the fungi: analyses of nuclear small subunit rRNA sequences. Mol Phylogenet Evol 1:231–241 http://dx.doi.org/10.1016/1055-7903(92)90020-H.
7. Kurtzman CP. 1994. Molecular taxonomy of the yeasts. Yeast 10:1727–1740 http://dx.doi.org/10.1002/yea.320101306.
8. Spatafora JW, Mitchell TG, Vilgalys R. 1995. Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens. J Clin Microbiol 33:1322–1326. [PubMed]
9. Moncalvo JM, Lutzoni FM, Rehner SA, Johnson J, Vilgalys R. 2000. Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. Syst Biol 49:278–305 http://dx.doi.org/10.1093/sysbio/49.2.278.
10. Moncalvo JM, Vilgalys R, Redhead SA, Johnson JE, James TY, Catherine Aime M, Hofstetter V, Verduin SJ, Larsson E, Baroni TJ, Greg Thorn R, Jacobsson S, Clémençon H, Miller OK Jr. 2002. One hundred and seventeen clades of euagarics. Mol Phylogenet Evol 23:357–400 http://dx.doi.org/10.1016/S1055-7903(02)00027-1.
11. O’Donnell K, Lutzoni FM, Ward TJ, Benny GL. 2001. Evolutionary relationships among mucoralean fungi (Zygomycota): evidence for family polyphyly on a large scale. Mycologia 93:286–297 http://dx.doi.org/10.2307/3761650.
12. Redecker D, Raab P. 2006. Phylogeny of the glomeromycota (arbuscular mycorrhizal fungi): recent developments and new gene markers. Mycologia 98:885–895 http://dx.doi.org/10.1080/15572536.2006.11832618.
13. Spatafora JW, Sung G-H, Johnson D, Hesse C, O’Rourke B, Serdani M, Spotts R, Lutzoni F, Hofstetter V, Miadlikowska J, Reeb V, Gueidan C, Fraker E, Lumbsch T, Lücking R, Schmitt I, Hosaka K, Aptroot A, Roux C, Miller AN, Geiser DM, Hafellner J, Hestmark G, Arnold AE, Büdel B, Rauhut A, Hewitt D, Untereiner WA, Cole MS, Scheidegger C, Schultz M, Sipman H, Schoch CL. 2006. A five-gene phylogeny of Pezizomycotina. Mycologia 98:1018–1028 http://dx.doi.org/10.1080/15572536.2006.11832630.
14. James TY, et al. 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818–822 http://dx.doi.org/10.1038/nature05110. [PubMed]
15. Suh S-O, Blackwell M, Kurtzman CP, Lachance M-A. 2006. Phylogenetics of Saccharomycetales, the ascomycete yeasts. Mycologia 98:1006–1017 http://dx.doi.org/10.1080/15572536.2006.11832629. [PubMed]
16. White MM, James TY, O’Donnell K, Cafaro MJ, Tanabe Y, Sugiyama J. 2006. Phylogeny of the Zygomycota based on nuclear ribosomal sequence data. Mycologia 98:872–884 http://dx.doi.org/10.1080/15572536.2006.11832617. [PubMed]
17. McLaughlin DJ, Hibbett DS, Lutzoni F, Spatafora JW, Vilgalys R. 2009. The search for the fungal tree of life. Trends Microbiol 17:488–497 http://dx.doi.org/10.1016/j.tim.2009.08.001.
18. Schoch CL, et al. 2009. The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Syst Biol 58:224–239 http://dx.doi.org/10.1093/sysbio/syp020. [PubMed]
19. Wang Y, Tretter ED, Johnson EM, Kandel P, Lichtwardt RW, Novak SJ, Smith JF, White MM. 2014. Using a five-gene phylogeny to test morphology-based hypotheses of Smittium and allies, endosymbiotic gut fungi (Harpellales) associated with arthropods. Mol Phylogenet Evol 79:23–41 http://dx.doi.org/10.1016/j.ympev.2014.05.008.
20. Porter TM, Martin W, James TY, Longcore JE, Gleason FH, Adler PH, Letcher PM, Vilgalys R. 2011. Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA. Fungal Biol 115:381–392 http://dx.doi.org/10.1016/j.funbio.2011.02.004.
21. Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett DS, Fisher MC. 2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol 31:21–32 http://dx.doi.org/10.1006/fgbi.2000.1228.
22. Taylor JW, Turner E, Townsend JP, Dettman JR, Jacobson D. 2006. Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi. Philos Trans R Soc Lond B Biol Sci 361:1947–1963 http://dx.doi.org/10.1098/rstb.2006.1923.
23. Dettman JR, Jacobson DJ, Taylor JW. 2006. Multilocus sequence data reveal extensive phylogenetic species diversity within the Neurospora discreta complex. Mycologia 98:436–446 http://dx.doi.org/10.1080/15572536.2006.11832678.
24. Vialle A, Feau N, Frey P, Bernier L, Hamelin RC. 2013. Phylogenetic species recognition reveals host-specific lineages among poplar rust fungi. Mol Phylogenet Evol 66:628–644. [PubMed]
25. Hibbett DS, et al. 2007. A higher-level phylogenetic classification of the Fungi. Mycol Res 111:509–547 http://dx.doi.org/10.1016/j.mycres.2007.03.004.
26. O’Malley MA, Wideman JG, Ruiz-Trillo I. 2016. Losing complexity: the role of simplification in macroevolution. Trends Ecol Evol 31:608–621 http://dx.doi.org/10.1016/j.tree.2016.04.004. [PubMed]
27. Celio GJ, Padamsee M, Dentinger BTM, Bauer R, McLaughlin DJ. 2006. Assembling the fungal tree of life: constructing the structural and biochemical database. Mycologia 98:850–859 http://dx.doi.org/10.1080/15572536.2006.11832615.
28. Kumar TKA, Crow JA, Wennblom TJ, Abril M, Letcher PM, Blackwell M, Roberson RW, McLaughlin DJ. 2011. An ontology of fungal subcellular traits. Am J Bot 98:1504–1510 http://dx.doi.org/10.3732/ajb.1100047.
29. Hibbett DS, Stajich JE, Spatafora JW. 2013. Toward genome-enabled mycology. Mycologia 105:1339–1349 http://dx.doi.org/10.3852/13-196. [PubMed]
30. Hall C, Dietrich FS. 2007. The reacquisition of biotin prototrophy in Saccharomyces cerevisiae involved horizontal gene transfer, gene duplication and gene clustering. Genetics 177:2293–2307 http://dx.doi.org/10.1534/genetics.107.074963.
31. Gojković Z, Knecht W, Zameitat E, Warneboldt J, Coutelis JB, Pynyaha Y, Neuveglise C, Møller K, Löffler M, Piskur J. 2004. Horizontal gene transfer promoted evolution of the ability to propagate under anaerobic conditions in yeasts. Mol Genet Genomics 271:387–393 http://dx.doi.org/10.1007/s00438-004-0995-7.
32. Piskur J, Rozpedowska E, Polakova S, Merico A, Compagno C. 2006. How did Saccharomyces evolve to become a good brewer? Trends Genet 22:183–186 http://dx.doi.org/10.1016/j.tig.2006.02.002.
33. Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R, Kodira CD, Neafsey DE, Zeng Q, Hung C-Y, McMahan C, Muszewska A, Grynberg M, Mandel MA, Kellner EM, Barker BM, Galgiani JN, Orbach MJ, Kirkland TN, Cole GT, Henn MR, Birren BW, Taylor JW. 2009. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Res 19:1722–1731 http://dx.doi.org/10.1101/gr.087551.108.
34. Whiston E, Taylor JW. 2016. Comparative phylogenomics of pathogenic and nonpathogenic species. G3 (Bethesda) 6:235–244 http://dx.doi.org/10.1534/g3.115.022806.
35. Muszewska A, Taylor JW, Szczesny P, Grynberg M. 2011. Independent subtilases expansions in fungi associated with animals. Mol Biol Evol 28:3395–3404 http://dx.doi.org/10.1093/molbev/msr176.
36. Nagy LG, Ohm RA, Kovács GM, Floudas D, Riley R, Gácser A, Sipiczki M, Davis JM, Doty SL, de Hoog GS, Lang BF, Spatafora JW, Martin FM, Grigoriev IV, Hibbett DS. 2014. Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts. Nat Commun 5:4471 http://dx.doi.org/10.1038/ncomms5471.
37. Nguyen TA, Cissé OH, Yun Wong J, Zheng P, Hewitt D, Nowrousian M, Stajich JE, Jedd G. 2017. Innovation and constraint leading to complex multicellularity in the Ascomycota. Nat Commun 8:14444 http://dx.doi.org/10.1038/ncomms14444.
38. Carvalho-Santos Z, Machado P, Branco P, Tavares-Cadete F, Rodrigues-Martins A, Pereira-Leal JB, Bettencourt-Dias M. 2010. Stepwise evolution of the centriole-assembly pathway. J Cell Sci 123:1414–1426 http://dx.doi.org/10.1242/jcs.064931.
39. Wapinski I, Pfeffer A, Friedman N, Regev A. 2007. Natural history and evolutionary principles of gene duplication in fungi. Nature 449:54–61 http://dx.doi.org/10.1038/nature06107.
40. Fitzpatrick DA, Logue ME, Stajich JE, Butler G. 2006. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol 6:99 http://dx.doi.org/10.1186/1471-2148-6-99. [PubMed]
41. Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P, Rokas A. 2009. Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Mol Biol Evol 26:2731–2744 http://dx.doi.org/10.1093/molbev/msp188.
42. Floudas D, et al. 2012. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336:1715–1719 http://dx.doi.org/10.1126/science.1221748.
43. Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, Berbee ML, Bonito G, Corradi N, Grigoriev I, Gryganskyi A, James TY, O’Donnell K, Roberson RW, Taylor TN, Uehling J, Vilgalys R, White MM, Stajich JE. 2016. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108:1028–1046 http://dx.doi.org/10.3852/16-042.
44. Reeb V, Lutzoni F, Roux C. 2004. Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory. Mol Phylogenet Evol 32:1036–1060. [PubMed]
45. Moncalvo J-M, Nilsson RH, Koster B, Dunham SM, Bernauer T, Matheny PB, Porter TM, Margaritescu S, Weiss M, Garnica S, Danell E, Langer G, Langer E, Larsson E, Larsson K-H, Vilgalys R. 2006. The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods. Mycologia 98:937–948 http://dx.doi.org/10.1080/15572536.2006.11832623.
46. Strandberg R, Nygren K, Menkis A, James TY, Wik L, Stajich JE, Johannesson H. 2010. Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora. Fungal Genet Biol 47:869–878 http://dx.doi.org/10.1016/j.fgb.2010.06.008.
47. Salichos L, Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497:327–331 http://dx.doi.org/10.1038/nature12130.
48. Salichos L, Stamatakis A, Rokas A. 2014. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol Biol Evol 31:1261–1271 http://dx.doi.org/10.1093/molbev/msu061.
49. Bradley DJ, Kjellbom P, Lamb CJ. 1992. Elicitor- and wound-induced oxidative cross-linking of a proline-rich plant cell wall protein: a novel, rapid defense response. Cell 70:21–30 http://dx.doi.org/10.1016/0092-8674(92)90530-P.
50. Lamb CJ, Lawton MA, Dron M, Dixon RA. 1989. Signals and transduction mechanisms for activation of plant defenses against microbial attack. Cell 56:215–224 http://dx.doi.org/10.1016/0092-8674(89)90894-5.
51. Kohler A, et al., Mycorrhizal Genomics Initiative Consortium. 2015. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat Genet 47:410–415 http://dx.doi.org/10.1038/ng.3223.
52. Martin F, et al. 2008. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452:88–92 http://dx.doi.org/10.1038/nature06556.
53. Plett JM, Kemppainen M, Kale SD, Kohler A, Legué V, Brun A, Tyler BM, Pardo AG, Martin F. 2011. A secreted effector protein of Laccaria bicolor is required for symbiosis development. Curr Biol 21:1197–1203 http://dx.doi.org/10.1016/j.cub.2011.05.033.
54. Kloppholz S, Kuhn H, Requena N. 2011. A secreted fungal effector of Glomus intraradices promotes symbiotic biotrophy. Curr Biol 21:1204–1209 http://dx.doi.org/10.1016/j.cub.2011.06.044.
55. Sędzielewska Toro K, Brachmann A. 2016. The effector candidate repertoire of the arbuscular mycorrhizal fungus Rhizophagus clarus. BMC Genomics 17:101 http://dx.doi.org/10.1186/s12864-016-2422-y.
56. Dashtban M, Schraft H, Syed TA, Qin W. 2010. Fungal biodegradation and enzymatic modification of lignin. Int J Biochem Mol Biol 1:36–50. [PubMed]
57. Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, Asiegbu FO, Baker SE, Barry K, Bendiksby M, Blumentritt M, Coutinho PM, Cullen D, de Vries RP, Gathman A, Goodell B, Henrissat B, Ihrmark K, Kauserud H, Kohler A, LaButti K, Lapidus A, Lavin JL, Lee YH, Lindquist E, Lilly W, Lucas S, Morin E, Murat C, Oguiza JA, Park J, Pisabarro AG, Riley R, Rosling A, Salamov A, Schmidt O, Schmutz J, Skrede I, Stenlid J, Wiebenga A, Xie X, Kües U, Hibbett DS, Hoffmeister D, Högberg N, Martin F, Grigoriev IV, Watkinson SC. 2011. The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science 333:762–765 http://dx.doi.org/10.1126/science.1205411.
58. Ohm RA, Riley R, Salamov A, Min B, Choi I-G, Grigoriev IV. 2014. Genomics of wood-degrading fungi. Fungal Genet Biol 72:82–90 http://dx.doi.org/10.1016/j.fgb.2014.05.001.
59. Nagy LG, Riley R, Tritt A, Adam C, Daum C, Floudas D, Sun H, Yadav JS, Pangilinan J, Larsson K-H, Matsuura K, Barry K, Labutti K, Kuo R, Ohm RA, Bhattacharya SS, Shirouzu T, Yoshinaga Y, Martin FM, Grigoriev IV, Hibbett DS. 2016. Comparative genomics of early-diverging mushroom-forming fungi provides insights into the origins of lignocellulose decay capabilities. Mol Biol Evol 33:959–970 http://dx.doi.org/10.1093/molbev/msv337.
60. Floudas D, Held BW, Riley R, Nagy LG, Koehler G, Ransdell AS, Younus H, Chow J, Chiniquy J, Lipzen A, Tritt A, Sun H, Haridas S, LaButti K, Ohm RA, Kües U, Blanchette RA, Grigoriev IV, Minto RE, Hibbett DS. 2015. Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii. Fungal Genet Biol 76:78–92 http://dx.doi.org/10.1016/j.fgb.2015.02.002.
61. Riley R, Salamov AA, Brown DW, Nagy LG, Floudas D, Held BW, Levasseur A, Lombard V, Morin E, Otillar R, Lindquist EA, Sun H, LaButti KM, Schmutz J, Jabbour D, Luo H, Baker SE, Pisabarro AG, Walton JD, Blanchette RA, Henrissat B, Martin F, Cullen D, Hibbett DS, Grigoriev IV. 2014. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci USA 111:9923–9928 http://dx.doi.org/10.1073/pnas.1400592111. (Erratum, 111:14959. doi:10.1073/pnas.1400592111.)
62. Fernandez-Fueyo E, et al. 2012. Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proc Natl Acad Sci USA 109:5458–5463 http://dx.doi.org/10.1073/pnas.1119912109.
63. Orpin CG, Joblin KN. 1997. The rumen anaerobic fungi, p 140–195. In Hobson PN, Stewart CS (ed), The Rumen Microbial Ecosystem. Springer Netherlands, Dordrecht, The Netherlands. http://dx.doi.org/10.1007/978-94-009-1453-7_4
64. Orpin CG. 1994. Anaerobic fungi: taxonomy, biology and distribution in nature, p 1–46. In Mountfort DO, Orpin CG (ed), Anaerobic Fungi: Biology, Ecology, and Function. Marcel Dekker, New York, NY.
65. Conley CA, Ishkhanova G, McKay CP, Cullings K. 2006. A preliminary survey of non-lichenized fungi cultured from the hyperarid Atacama Desert of Chile. Astrobiology 6:521–526 http://dx.doi.org/10.1089/ast.2006.6.521.
66. Gonçalves VN, Cantrell CL, Wedge DE, Ferreira MC, Soares MA, Jacob MR, Oliveira FS, Galante D, Rodrigues F, Alves TMA, Zani CL, Junior PAS, Murta S, Romanha AJ, Barbosa EC, Kroon EG, Oliveira JG, Gomez-Silva B, Galetovic A, Rosa CA, Rosa LH. 2016. Fungi associated with rocks of the Atacama Desert: taxonomy, distribution, diversity, ecology and bioprospection for bioactive compounds. Environ Microbiol 18:232–245 http://dx.doi.org/10.1111/1462-2920.13005.
67. Kogej T, Ramos J, Plemenitaš A, Gunde-Cimerman N. 2005. The halophilic fungus Hortaea werneckii and the halotolerant fungus Aureobasidium pullulans maintain low intracellular cation concentrations in hypersaline environments. Appl Environ Microbiol 71:6600–6605 http://dx.doi.org/10.1128/AEM.71.11.6600-6605.2005.
68. Selbmann L, de Hoog GS, Mazzaglia A, Friedmann EI, Onofri S. 2005. Fungi at the edge of life: cryptendolithic black fungi from Antarctic desert. Stud Mycol 51:1–32.
69. Zucconi L, Onofri S, Cecchini C, Isola D, Ripa C, Fenice M, Madonna S, Reboleiro-Rivas P, Selbmann L. 2016. Mapping the lithic colonization at the boundaries of life in Northern Victoria Land, Antarctica. Polar Biol 39:91–102 http://dx.doi.org/10.1007/s00300-014-1624-5.
70. Powell AJ, Parchert KJ, Bustamante JM, Ricken JB, Hutchinson MI, Natvig DO. 2012. Thermophilic fungi in an aridland ecosystem. Mycologia 104:813–825 http://dx.doi.org/10.3852/11-298.
71. Morgenstern I, Powlowski J, Ishmael N, Darmond C, Marqueteau S, Moisan M-C, Quenneville G, Tsang A. 2012. A molecular phylogeny of thermophilic fungi. Fungal Biol 116:489–502 http://dx.doi.org/10.1016/j.funbio.2012.01.010.
72. Romanelli RA, Houston CW, Barnett SM. 1975. Studies on thermophilic cellulolytic fungi. Appl Microbiol 30:276–281. [PubMed]
73. Berka RM, Grigoriev IV, Otillar R, Salamov A, Grimwood J, Reid I, Ishmael N, John T, Darmond C, Moisan M-C, Henrissat B, Coutinho PM, Lombard V, Natvig DO, Lindquist E, Schmutz J, Lucas S, Harris P, Powlowski J, Bellemare A, Taylor D, Butler G, de Vries RP, Allijn IE, van den Brink J, Ushinsky S, Storms R, Powell AJ, Paulsen IT, Elbourne LDH, Baker SE, Magnuson J, Laboissiere S, Clutterbuck AJ, Martinez D, Wogulis M, de Leon AL, Rey MW, Tsang A. 2011. Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. Nat Biotechnol 29:922–927 http://dx.doi.org/10.1038/nbt.1976.
74. Amlacher S, Sarges P, Flemming D, van Noort V, Kunze R, Devos DP, Arumugam M, Bork P, Hurt E. 2011. Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile. Cell 146:277–289 http://dx.doi.org/10.1016/j.cell.2011.06.039. [PubMed]
75. Keeling PJ, Slamovits CH. 2004. Simplicity and complexity of microsporidian genomes. Eukaryot Cell 3:1363–1369 http://dx.doi.org/10.1128/EC.3.6.1363-1369.2004.
76. Akiyoshi DE, Morrison HG, Lei S, Feng X, Zhang Q, Corradi N, Mayanja H, Tumwine JK, Keeling PJ, Weiss LM, Tzipori S. 2009. Genomic survey of the non-cultivatable opportunistic human pathogen, Enterocytozoon bieneusi. PLoS Pathog 5:e1000261 http://dx.doi.org/10.1371/journal.ppat.1000261.
77. Corradi N, Haag KL, Pombert J-F, Ebert D, Keeling PJ. 2009. Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions. Genome Biol 10:R106 http://dx.doi.org/10.1186/gb-2009-10-10-r106.
78. Pombert J-F, Xu J, Smith DR, Heiman D, Young S, Cuomo CA, Weiss LM, Keeling PJ. 2013. Complete genome sequences from three genetically distinct strains reveal high intraspecies genetic diversity in the microsporidian Encephalitozoon cuniculi. Eukaryot Cell 12:503–511 http://dx.doi.org/10.1128/EC.00312-12.
79. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG. 1996. Life with 6000 genes. Science 274:546–567, 563–567 http://dx.doi.org/10.1126/science.274.5287.546.
80. Wood V, et al. 2002. The genome sequence of Schizosaccharomyces pombe. Nature 415:871–880 http://dx.doi.org/10.1038/nature724.
81. James TY, Pelin A, Bonen L, Ahrendt S, Sain D, Corradi N, Stajich JE. 2013. Shared signatures of parasitism and phylogenomics unite Cryptomycota and microsporidia. Curr Biol 23:1548–1553 http://dx.doi.org/10.1016/j.cub.2013.06.057.
82. Toome M, Ohm RA, Riley RW, James TY, Lazarus KL, Henrissat B, Albu S, Boyd A, Chow J, Clum A, Heller G, Lipzen A, Nolan M, Sandor L, Zvenigorodsky N, Grigoriev IV, Spatafora JW, Aime MC. 2014. Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae. New Phytol 202:554–564 http://dx.doi.org/10.1111/nph.12653.
83. Janbon G, et al. 2014. Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PLoS Genet 10:e1004261 http://dx.doi.org/10.1371/journal.pgen.1004261.
84. Loftus BJ, et al. 2005. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 307:1321–1324 http://dx.doi.org/10.1126/science.1103773.
85. D’Souza CA, Kronstad JW, Taylor G, Warren R, Yuen M, Hu G, Jung WH, Sham A, Kidd SE, Tangen K, Lee N, Zeilmaker T, Sawkins J, McVicker G, Shah S, Gnerre S, Griggs A, Zeng Q, Bartlett K, Li W, Wang X, Heitman J, Stajich JE, Fraser JA, Meyer W, Carter D, Schein J, Krzywinski M, Kwon-Chung KJ, Varma A, Wang J, Brunham R, Fyfe M, Ouellette BFF, Siddiqui A, Marra M, Jones S, Holt R, Birren BW, Galagan JE, Cuomo CA. 2011. Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. MBio 2:e00342-10 http://dx.doi.org/10.1128/mBio.00342-10.
86. Dujon B, et al. 2004. Genome evolution in yeasts. Nature 430:35–44 http://dx.doi.org/10.1038/nature02579.
87. Peter M, Kohler A, Ohm RA, Kuo A, Krützmann J, Morin E, Arend M, Barry KW, Binder M, Choi C, Clum A, Copeland A, Grisel N, Haridas S, Kipfer T, LaButti K, Lindquist E, Lipzen A, Maire R, Meier B, Mihaltcheva S, Molinier V, Murat C, Pöggeler S, Quandt CA, Sperisen C, Tritt A, Tisserant E, Crous PW, Henrissat B, Nehls U, Egli S, Spatafora JW, Grigoriev IV, Martin FM. 2016. Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum. Nat Commun 7:12662 http://dx.doi.org/10.1038/ncomms12662.
88. Martin F, et al. 2010. Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature 464:1033–1038 http://dx.doi.org/10.1038/nature08867.
89. Spanu PD, et al. 2010. Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science 330:1543–1546 http://dx.doi.org/10.1126/science.1194573.
90. Murrin F, Holtby J, Noland RA, Davidson WS. 1986. The genome of Entomophaga aulicae (Entomophthorales, Zygomycetes): base composition and size. Exp Mycol 10:67–75 http://dx.doi.org/10.1016/0147-5975(86)90032-0.
91. De Fine Licht HH, Jensen AB, Eilenberg J. 2017. Comparative transcriptomics reveal host-specific nucleotide variation in entomophthoralean fungi. Mol Ecol 26:2092–2110 http://dx.doi.org/10.1111/mec.13863.
92. Małagocka J, Grell MN, Lange L, Eilenberg J, Jensen AB. 2015. Transcriptome of an entomophthoralean fungus ( Pandora formicae) shows molecular machinery adjusted for successful host exploitation andtransmission. J Invertebr Pathol 128:47–56 http://dx.doi.org/10.1016/j.jip.2015.05.001.
93. Tavares S, Ramos AP, Pires AS, Azinheira HG, Caldeirinha P, Link T, Abranches R, Silva MC, Voegele RT, Loureiro J, Talhinhas P. 2014. Genome size analyses of Pucciniales reveal the largest fungal genomes. Front Plant Sci 5:422 http://dx.doi.org/10.3389/fpls.2014.00422.
94. Williams BAP, Lee RCH, Becnel JJ, Weiss LM, Fast NM, Keeling PJ. 2008. Genome sequence surveys of Brachiola algerae and Edhazardia aedis reveal microsporidia with low gene densities. BMC Genomics 9:200 http://dx.doi.org/10.1186/1471-2164-9-200.
95. Katinka MD, Duprat S, Cornillot E, Méténier G, Thomarat F, Prensier G, Barbe V, Peyretaillade E, Brottier P, Wincker P, Delbac F, El Alaoui H, Peyret P, Saurin W, Gouy M, Weissenbach J, Vivarès CP. 2001. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414:450–453 http://dx.doi.org/10.1038/35106579.
96. Cuomo CA, Desjardins CA, Bakowski MA, Goldberg J, Ma AT, Becnel JJ, Didier ES, Fan L, Heiman DI, Levin JZ, Young S, Zeng Q, Troemel ER. 2012. Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth. Genome Res 22:2478–2488 http://dx.doi.org/10.1101/gr.142802.112.
97. Troemel ER, Becnel JJ. 2015. Genome analysis and polar tube firing dynamics of mosquito-infecting microsporidia. Fungal Genet Biol 83:41–44 http://dx.doi.org/10.1016/j.fgb.2015.08.007.
98. Corradi N, Akiyoshi DE, Morrison HG, Feng X, Weiss LM, Tzipori S, Keeling PJ. 2007. Patterns of genome evolution among the microsporidian parasites Encephalitozoon cuniculi, Antonospora locustae and Enterocytozoon bieneusi. PLoS One 2:e1277 http://dx.doi.org/10.1371/journal.pone.0001277.
99. Corradi N, Gangaeva A, Keeling PJ. 2008. Comparative profiling of overlapping transcription in the compacted genomes of microsporidia Antonospora locustae and Encephalitozoon cuniculi. Genomics 91:388–393 http://dx.doi.org/10.1016/j.ygeno.2007.12.006.
100. Hauser PM, Burdet FX, Cissé OH, Keller L, Taffé P, Sanglard D, Pagni M. 2010. Comparative genomics suggests that the fungal pathogen pneumocystis is an obligate parasite scavenging amino acids from its host’s lungs. PLoS One 5:e15152. [PubMed]
101. Cissé OH, Pagni M, Hauser PM. 2012. De novo assembly of the Pneumocystis jirovecii genome from a single bronchoalveolar lavage fluid specimen from a patient. MBio 4:e00428-12 http://dx.doi.org/10.1128/mBio.00428-12.
102. Almeida JMGCF, Cissé OH, Fonseca Á, Pagni M, Hauser PM. 2015. Comparative genomics suggests primary homothallism of Pneumocystis species. MBio 6:e02250-14 http://dx.doi.org/10.1128/mBio.02250-14.
103. Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, Steiner S, Mohr C, Pöhlmann R, Luedi P, Choi S, Wing RA, Flavier A, Gaffney TD, Philippsen P. 2004. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304:304–307 http://dx.doi.org/10.1126/science.1095781.
104. Raffaele S, Kamoun S. 2012. Genome evolution in filamentous plant pathogens: why bigger can be better. Nat Rev Microbiol 10:417–430.
105. Dong S, Raffaele S, Kamoun S. 2015. The two-speed genomes of filamentous pathogens: waltz with plants. Curr Opin Genet Dev 35:57–65 http://dx.doi.org/10.1016/j.gde.2015.09.001. (Erratum, www.ncbi.nlm.nih.gov/pubmed/26451981?dopt=Abstract#comments.)
106. Rouxel T, Grandaubert J, Hane JK, Hoede C, van de Wouw AP, Couloux A, Dominguez V, Anthouard V, Bally P, Bourras S, Cozijnsen AJ, Ciuffetti LM, Degrave A, Dilmaghani A, Duret L, Fudal I, Goodwin SB, Gout L, Glaser N, Linglin J, Kema GH, Lapalu N, Lawrence CB, May K, Meyer M, Ollivier B, Poulain J, Schoch CL, Simon A, Spatafora JW, Stachowiak A, Turgeon BG, Tyler BM, Vincent D, Weissenbach J, Amselem J, Quesneville H, Oliver RP, Wincker P, Balesdent MH, Howlett BJ. 2011. Effector diversification within compartments of the Leptosphaeria maculans genome affected by repeat-induced point mutations. Nat Commun 2:202 http://dx.doi.org/10.1038/ncomms1189.
107. Raffaele S, Farrer RA, Cano LM, Studholme DJ, MacLean D, Thines M, Jiang RHY, Zody MC, Kunjeti SG, Donofrio NM, Meyers BC, Nusbaum C, Kamoun S. 2010. Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science 330:1540–1543 http://dx.doi.org/10.1126/science.1193070.
108. Sperschneider J, Gardiner DM, Thatcher LF, Lyons R, Singh KB, Manners JM, Taylor JM. 2015. Genome-wide analysis in three Fusarium pathogens identifies rapidly evolving chromosomes and genes associated with pathogenicity. Genome Biol Evol 7:1613–1627 http://dx.doi.org/10.1093/gbe/evv092.
109. Croll D, McDonald BA. 2012. The accessory genome as a cradle for adaptive evolution in pathogens. PLoS Pathog 8:e1002608 http://dx.doi.org/10.1371/journal.ppat.1002608.
110. Grandaubert J, Lowe RG, Soyer JL, Schoch CL, Van de Wouw AP, Fudal I, Robbertse B, Lapalu N, Links MG, Ollivier B, Linglin J, Barbe V, Mangenot S, Cruaud C, Borhan H, Howlett BJ, Balesdent M-H, Rouxel T. 2014. Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans- Leptosphaeria biglobosa species complex of fungal pathogens. BMC Genomics 15:891 http://dx.doi.org/10.1186/1471-2164-15-891.
111. Faino L, Seidl MF, Shi-Kunne X, Pauper M, van den Berg GCM, Wittenberg AHJ, Thomma BPHJ. 2016. Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen. Genome Res 26:1091–1100 http://dx.doi.org/10.1101/gr.204974.116.
112. Burke DT, Carle GF, Olson MV. 1987. Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 236:806–812 http://dx.doi.org/10.1126/science.3033825.
113. Galitski T, Saldanha AJ, Styles CA, Lander ES, Fink GR. 1999. Ploidy regulation of gene expression. Science 285:251–254 http://dx.doi.org/10.1126/science.285.5425.251.
114. Mable BK, Otto SP. 2001. Masking and purging mutations following EMS treatment in haploid, diploid and tetraploid yeast ( Saccharomyces cerevisiae). Genet Res 77:9–26 http://dx.doi.org/10.1017/S0016672300004821.
115. Torres EM, Sokolsky T, Tucker CM, Chan LY, Boselli M, Dunham MJ, Amon A. 2007. Effects of aneuploidy on cellular physiology and cell division in haploid yeast. Science 317:916–924 http://dx.doi.org/10.1126/science.1142210.
116. Lynch M, Conery JS. 2003. The origins of genome complexity. Science 302:1401–1404 http://dx.doi.org/10.1126/science.1089370.
117. Lynch M. 2007. The Origins of Genome Architecture. Sinauer Associates, Sunderland, MA.
118. Huerta-Cepas J, Capella-Gutiérrez S, Pryszcz LP, Marcet-Houben M, Gabaldón T. 2014. PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. Nucleic Acids Res 42(D1) :D897–D902 http://dx.doi.org/10.1093/nar/gkt1177.
119. Kersey PJ, Allen JE, Christensen M, Davis P, Falin LJ, Grabmueller C, Hughes DST, Humphrey J, Kerhornou A, Khobova J, Langridge N, McDowall MD, Maheswari U, Maslen G, Nuhn M, Ong CK, Paulini M, Pedro H, Toneva I, Tuli MA, Walts B, Williams G, Wilson D, Youens-Clark K, Monaco MK, Stein J, Wei X, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Staines DM. 2014. Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res 42(D1) :D546–D552 http://dx.doi.org/10.1093/nar/gkt979.
120. Akcapinar GB, Kappel L, Sezerman OU, Seidl-Seiboth V. 2015. Molecular diversity of LysM carbohydrate-binding motifs in fungi. Curr Genet 61:103–113 http://dx.doi.org/10.1007/s00294-014-0471-9.
121. Kombrink A, Thomma BPHJ. 2013. LysM effectors: secreted proteins supporting fungal life. PLoS Pathog 9:e1003769 http://dx.doi.org/10.1371/journal.ppat.1003769.
122. Teixeira MM, de Almeida LGP, Kubitschek-Barreira P, Alves FL, Kioshima ES, Abadio AKR, Fernandes L, Derengowski LS, Ferreira KS, Souza RC, Ruiz JC, de Andrade NC, Paes HC, Nicola AM, Albuquerque P, Gerber AL, Martins VP, Peconick LDF, Neto AV, Chaucanez CB, Silva PA, Cunha OL, de Oliveira FFM, dos Santos TC, Barros ALN, Soares MA, de Oliveira LM, Marini MM, Villalobos-Duno H, Cunha MML, de Hoog S, da Silveira JF, Henrissat B, Niño-Vega GA, Cisalpino PS, Mora-Montes HM, Almeida SR, Stajich JE, Lopes-Bezerra LM, Vasconcelos ATR, Felipe MSS. 2014. Comparative genomics of the major fungal agents of human and animal sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis. BMC Genomics 15:943 http://dx.doi.org/10.1186/1471-2164-15-943.
123. Martinez DA, Oliver BG, Gräser Y, Goldberg JM, Li W, Martinez-Rossi NM, Monod M, Shelest E, Barton RC, Birch E, Brakhage AA, Chen Z, Gurr SJ, Heiman D, Heitman J, Kosti I, Rossi A, Saif S, Samalova M, Saunders CW, Shea T, Summerbell RC, Xu J, Young S, Zeng Q, Birren BW, Cuomo CA, White TC. 2012. Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection. MBio 3:e00259-12 http://dx.doi.org/10.1128/mBio.00259-12.
124. Buist G, Steen A, Kok J, Kuipers OP. 2008. LysM, a widely distributed protein motif for binding to (peptido)glycans. Mol Microbiol 68:838–847 http://dx.doi.org/10.1111/j.1365-2958.2008.06211.x.
125. de Jonge R, van Esse HP, Kombrink A, Shinya T, Desaki Y, Bours R, van der Krol S, Shibuya N, Joosten MH, Thomma BP. 2010. Conserved fungal LysM effector Ecp6 prevents chitin-triggered immunity in plants. Science 329:953–955 http://dx.doi.org/10.1126/science.1190859.
126. Xue C, Liu T, Chen L, Li W, Liu I, Kronstad JW, Seyfang A, Heitman J. 2010. Role of an expanded inositol transporter repertoire in Cryptococcus neoformans sexual reproduction and virulence. MBio 1:e00084-10 http://dx.doi.org/10.1128/mBio.00084-10.
127. Zaragoza O, Rodrigues ML, De Jesus M, Frases S, Dadachova E, Casadevall A. 2009. The capsule of the fungal pathogen Cryptococcus neoformans. Adv Appl Microbiol 68:133–216.
128. Perfect JR. 2005. Cryptococcus neoformans: a sugar-coated killer with designer genes. FEMS Immunol Med Microbiol 45:395–404 http://dx.doi.org/10.1016/j.femsim.2005.06.005. [PubMed]
129. O’Meara TR, Alspaugh JA. 2012. The Cryptococcus neoformans capsule: a sword and a shield. Clin Microbiol Rev 25:387–408 http://dx.doi.org/10.1128/CMR.00001-12.
130. Li J, Zhang K-Q. 2014. Independent expansion of zincin metalloproteinases in Onygenales fungi may be associated with their pathogenicity. PLoS One 9:e90225 http://dx.doi.org/10.1371/journal.pone.0090225.
131. Whiston E, Taylor JW. 2014. Genomics in Coccidioides: insights into evolution, ecology, and pathogenesis. Med Mycol 52:149–155 http://dx.doi.org/10.1093/mmy/myt001. [PubMed]
132. Muñoz JF, Gauthier GM, Desjardins CA, Gallo JE, Holder J, Sullivan TD, Marty AJ, Carmen JC, Chen Z, Ding L, Gujja S, Magrini V, Misas E, Mitreva M, Priest M, Saif S, Whiston EA, Young S, Zeng Q, Goldman WE, Mardis ER, Taylor JW, McEwen JG, Clay OK, Klein BS, Cuomo CA. 2015. The dynamic genome and transcriptome of the human fungal pathogen Blastomyces and close relative Emmonsia. PLoS Genet 11:e1005493 http://dx.doi.org/10.1371/journal.pgen.1005493.
133. Joneson S, Stajich JE, Shiu S-H, Rosenblum EB. 2011. Genomic transition to pathogenicity in chytrid fungi. PLoS Pathog 7:e1002338 http://dx.doi.org/10.1371/journal.ppat.1002338.
134. Thekkiniath JC, Zabet-Moghaddam M, San Francisco SK, San Francisco MJ. 2013. A novel subtilisin-like serine protease of Batrachochytrium dendrobatidis is induced by thyroid hormone and degrades antimicrobial peptides. Fungal Biol 117:451–461 http://dx.doi.org/10.1016/j.funbio.2013.05.002.
135. Abramyan J, Stajich JE. 2012. Species-specific chitin-binding module 18 expansion in the amphibian pathogen Batrachochytrium dendrobatidis. MBio 3:e00150-12 http://dx.doi.org/10.1128/mBio.00150-12.
136. Farrer RA, Martel A, Verbrugghe E, Abouelleil A, Ducatelle R, Longcore JE, James TY, Pasmans F, Fisher MC, Cuomo CA. 2017. Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi. Nat Commun 8:14742 http://dx.doi.org/10.1038/ncomms14742.
137. Liu P, Stajich JE. 2015. Characterization of the Carbohydrate Binding Module 18 gene family in the amphibian pathogen Batrachochytrium dendrobatidis. Fungal Genet Biol 77:31–39 http://dx.doi.org/10.1016/j.fgb.2015.03.003.
138. Pendleton AL, Smith KE, Feau N, Martin FM, Grigoriev IV, Hamelin R, Nelson CD, Burleigh JG, Davis JM. 2014. Duplications and losses in gene families of rust pathogens highlight putative effectors. Front Plant Sci 5:299 http://dx.doi.org/10.3389/fpls.2014.00299.
139. Goodwin SB, et al. 2011. Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis. PLoS Genet 7:e1002070 http://dx.doi.org/10.1371/journal.pgen.1002070.
140. Hu X, Xiao G, Zheng P, Shang Y, Su Y, Zhang X, Liu X, Zhan S, St Leger RJ, Wang C. 2014. Trajectory and genomic determinants of fungal-pathogen speciation and host adaptation. Proc Natl Acad Sci USA 111:16796–16801 http://dx.doi.org/10.1073/pnas.1412662111.
141. Gao Q, Jin K, Ying S-H, Zhang Y, Xiao G, Shang Y, Duan Z, Hu X, Xie X-Q, Zhou G, Peng G, Luo Z, Huang W, Wang B, Fang W, Wang S, Zhong Y, Ma L-J, St Leger RJ, Zhao G-P, Pei Y, Feng M-G, Xia Y, Wang C. 2011. Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum. PLoS Genet 7:e1001264 http://dx.doi.org/10.1371/journal.pgen.1001264.
142. Schiøtt M, De Fine Licht HH, Lange L, Boomsma JJ. 2008. Towards a molecular understanding of symbiont function: identification of a fungal gene for the degradation of xylan in the fungus gardens of leaf-cutting ants. BMC Microbiol 8:40 http://dx.doi.org/10.1186/1471-2180-8-40.
143. De Fine Licht HH, Schiøtt M, Mueller UG, Boomsma JJ. 2010. Evolutionary transitions in enzyme activity of ant fungus gardens. Evolution 64:2055–2069.
144. Nygaard S, Zhang G, Schiøtt M, Li C, Wurm Y, Hu H, Zhou J, Ji L, Qiu F, Rasmussen M, Pan H, Hauser F, Krogh A, Grimmelikhuijzen CJP, Wang J, Boomsma JJ. 2011. The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. Genome Res 21:1339–1348 http://dx.doi.org/10.1101/gr.121392.111.
145. De Fine Licht HH, Schiøtt M, Rogowska-Wrzesinska A, Nygaard S, Roepstorff P, Boomsma JJ. 2013. Laccase detoxification mediates the nutritional alliance between leaf-cutting ants and fungus-garden symbionts. Proc Natl Acad Sci USA 110:583–587 http://dx.doi.org/10.1073/pnas.1212709110.
146. De Fine Licht HH, Boomsma JJ, Tunlid A. 2014. Symbiotic adaptations in the fungal cultivar of leaf-cutting ants. Nat Commun 5:5675 http://dx.doi.org/10.1038/ncomms6675.
147. Aylward FO, Khadempour L, Tremmel DM, McDonald BR, Nicora CD, Wu S, Moore RJ, Orton DJ, Monroe ME, Piehowski PD, Purvine SO, Smith RD, Lipton MS, Burnum-Johnson KE, Currie CR. 2015. Enrichment and broad representation of plant biomass-degrading enzymes in the specialized hyphal swellings of Leucoagaricus gongylophorus, the fungal symbiont of leaf-cutter ants. PLoS One 10:e0134752. [PubMed]
148. Khadempour L, Burnum-Johnson KE, Baker ES, Nicora CD, Webb-Robertson BM, White RA III, Monroe ME, Huang EL, Smith RD, Currie CR. 2016. The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates. Mol Ecol 25:5795–5805 http://dx.doi.org/10.1111/mec.13872.
149. Corrochano LM, et al. 2016. Expansion of signal transduction pathways in fungi by extensive genome duplication. Curr Biol 26:1577–1584 http://dx.doi.org/10.1016/j.cub.2016.04.038.
150. 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. 2009. Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genet 5:e1000549 http://dx.doi.org/10.1371/journal.pgen.1000549.
151. Stajich JE, Wilke SK, Ahrén D, Au CH, Birren BW, Borodovsky M, Burns C, Canbäck B, Casselton LA, Cheng CK, Deng J, Dietrich FS, Fargo DC, Farman ML, Gathman AC, Goldberg J, Guigó R, Hoegger PJ, Hooker JB, Huggins A, James TY, Kamada T, Kilaru S, Kodira C, Kües U, Kupfer D, Kwan HS, Lomsadze A, Li W, Lilly WW, Ma L-J, Mackey AJ, Manning G, Martin F, Muraguchi H, Natvig DO, Palmerini H, Ramesh MA, Rehmeyer CJ, Roe BA, Shenoy N, Stanke M, Ter-Hovhannisyan V, Tunlid A, Velagapudi R, Vision TJ, Zeng Q, Zolan ME, Pukkila PJ. 2010. Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea ( Coprinus cinereus). Proc Natl Acad Sci USA 107:11889–11894 http://dx.doi.org/10.1073/pnas.1003391107.
152. Plett JM, Gibon J, Kohler A, Duffy K, Hoegger PJ, Velagapudi R, Han J, Kües U, Grigoriev IV, Martin F. 2012. Phylogenetic, genomic organization and expression analysis of hydrophobin genes in the ectomycorrhizal basidiomycete Laccaria bicolor. Fungal Genet Biol 49:199–209 http://dx.doi.org/10.1016/j.fgb.2012.01.002.
153. Rineau F, Lmalem H, Ahren D, Shah F, Johansson T, Coninx L, Ruytinx J, Nguyen H, Grigoriev I, Kuo A, Kohler A, Morin E, Vangronsveld J, Martin F, Colpaert JV. 2017. Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes. Mycorrhiza 27:383–396 http://dx.doi.org/10.1007/s00572-016-0758-4.
154. Sammer D, Krause K, Gube M, Wagner K, Kothe E. 2016. Hydrophobins in the life cycle of the ectomycorrhizal Basidiomycete Tricholoma vaccinum. PLoS One 11:e0167773 http://dx.doi.org/10.1371/journal.pone.0167773.
155. Martinez D, Larrondo LF, Putnam N, Gelpke MD, Huang K, Chapman J, Helfenbein KG, Ramaiya P, Detter JC, Larimer F, Coutinho PM, Henrissat B, Berka R, Cullen D, Rokhsar D. 2004. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol 22:695–700 http://dx.doi.org/10.1038/nbt967.
156. Doddapaneni H, Chakraborty R, Yadav JS. 2005. Genome-wide structural and evolutionary analysis of the P450 monooxygenase genes (P450ome) in the white rot fungus Phanerochaete chrysosporium: evidence for gene duplications and extensive gene clustering. BMC Genomics 6:92 http://dx.doi.org/10.1186/1471-2164-6-92.
157. Yadav JS, Doddapaneni H, Subramanian V. 2006. P450ome of the white rot fungus Phanerochaete chrysosporium: structure, evolution and regulation of expression of genomic P450 clusters. Biochem Soc Trans 34:1165–1169 http://dx.doi.org/10.1042/BST0341165.
158. Syed K, Yadav JS. 2012. P450 monooxygenases (P450ome) of the model white rot fungus Phanerochaete chrysosporium. Crit Rev Microbiol 38:339–363 http://dx.doi.org/10.3109/1040841X.2012.682050.
159. Syed K, Nelson DR, Riley R, Yadav JS. 2013. Genomewide annotation and comparative genomics of cytochrome P450 monooxygenases (P450s) in the polypore species Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora. Mycologia 105:1445–1455 http://dx.doi.org/10.3852/13-002.
160. Syed K, Shale K, Pagadala NS, Tuszynski J. 2014. Systematic identification and evolutionary analysis of catalytically versatile cytochrome P450 monooxygenase families enriched in model Basidiomycete fungi. PLoS One. 9:e86683. [PubMed]
161. Chen W, Lee M-K, Jefcoate C, Kim S-C, Chen F, Yu J-H. 2014. Fungal cytochrome p450 monooxygenases: their distribution, structure, functions, family expansion, and evolutionary origin. Genome Biol Evol 6:1620–1634 http://dx.doi.org/10.1093/gbe/evu132.
162. Qhanya LB, Matowane G, Chen W, Sun Y, Letsimo EM, Parvez M, Yu J-H, Mashele SS, Syed K. 2015. Genome-wide annotation and comparative analysis of cytochrome P450 monooxygenases in Basidiomycete biotrophic plant pathogens. PLoS One 10:e0142100 http://dx.doi.org/10.1371/journal.pone.0142100.
163. Baroncelli R, Amby DB, Zapparata A, Sarrocco S, Vannacci G, Le Floch G, Harrison RJ, Holub E, Sukno SA, Sreenivasaprasad S, Thon MR. 2016. Gene family expansions and contractions are associated with host range in plant pathogens of the genus Colletotrichum. BMC Genomics 17:555 http://dx.doi.org/10.1186/s12864-016-2917-6.
164. de Man TJB, Stajich JE, Kubicek CP, Teiling C, Chenthamara K, Atanasova L, Druzhinina IS, Levenkova N, Birnbaum SSL, Barribeau SM, Bozick BA, Suen G, Currie CR, Gerardo NM. 2016. Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture. Proc Natl Acad Sci USA 113:3567–3572 http://dx.doi.org/10.1073/pnas.1518501113.
165. Selker EU, Garrett PW. 1988. DNA sequence duplications trigger gene inactivation in Neurospora crassa. Proc Natl Acad Sci USA 85:6870–6874 http://dx.doi.org/10.1073/pnas.85.18.6870.
166. Selker EU. 1990. Premeiotic instability of repeated sequences in Neurospora crassa. Annu Rev Genet 24:579–613 http://dx.doi.org/10.1146/annurev.ge.24.120190.003051.
167. Galagan JE, et al. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859–868 http://dx.doi.org/10.1038/nature01554.
168. Galagan JE, Selker EU. 2004. RIP: the evolutionary cost of genome defense. Trends Genet 20:417–423 http://dx.doi.org/10.1016/j.tig.2004.07.007.
169. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O’Connor KJB, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci USA 102:13950–13955 http://dx.doi.org/10.1073/pnas.0506758102. (Erratum, doi:10.1073/pnas.0506758102.)
170. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R. 2005. The microbial pan-genome. Curr Opin Genet Dev 15:589–594 http://dx.doi.org/10.1016/j.gde.2005.09.006.
171. Strope PK, Skelly DA, Kozmin SG, Mahadevan G, Stone EA, Magwene PM, Dietrich FS, McCusker JH. 2015. The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen. Genome Res 25:762–774 http://dx.doi.org/10.1101/gr.185538.114.
172. Yue J-X, Li J, Aigrain L, Hallin J, Persson K, Oliver K, Bergström A, Coupland P, Warringer J, Lagomarsino MC, Fischer G, Durbin R, Liti G. 2017. Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nat Genet 49:913–924 http://dx.doi.org/10.1038/ng.3847.
173. Rokas A. 2009. The effect of domestication on the fungal proteome. Trends Genet 25:60–63 http://dx.doi.org/10.1016/j.tig.2008.11.003.
174. Gibbons JG, Salichos L, Slot JC, Rinker DC, McGary KL, King JG, Klich MA, Tabb DL, McDonald WH, Rokas A. 2012. The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae. Curr Biol 22:1403–1409 http://dx.doi.org/10.1016/j.cub.2012.05.033.
175. Steenwyk JL, Soghigian JS, Perfect JR, Gibbons JG. 2016. Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest. BMC Genomics 17:700 http://dx.doi.org/10.1186/s12864-016-3044-0.
176. Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, Barry KW, Condon BJ, Copeland AC, Dhillon B, Glaser F, Hesse CN, Kosti I, LaButti K, Lindquist EA, Lucas S, Salamov AA, Bradshaw RE, Ciuffetti L, Hamelin RC, Kema GH, Lawrence C, Scott JA, Spatafora JW, Turgeon BG, de Wit PJ, Zhong S, Goodwin SB, Grigoriev IV. 2012. Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog 8:e1003037 http://dx.doi.org/10.1371/journal.ppat.1003037.
177. Balesdent M-H, Fudal I, Ollivier B, Bally P, Grandaubert J, Eber F, Chèvre A-M, Leflon M, Rouxel T. 2013. The dispensable chromosome of Leptosphaeria maculans shelters an effector gene conferring avirulence towards Brassica rapa. New Phytol 198:887–898 http://dx.doi.org/10.1111/nph.12178.
178. Stukenbrock EH, Jørgensen FG, Zala M, Hansen TT, McDonald BA, Schierup MH. 2010. Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola. PLoS Genet 6:e1001189 http://dx.doi.org/10.1371/journal.pgen.1001189.
179. Galazka JM, Freitag M. 2014. Variability of chromosome structure in pathogenic fungi: of ‘ends and odds’. Curr Opin Microbiol 20:19–26 http://dx.doi.org/10.1016/j.mib.2014.04.002.

Article metrics loading...



The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute’s Fungal Genome Initiative, and the 1000 Fungal Genomes Project (http://1000.fungalgenomes.org). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.

Highlighted Text: Show | Hide
Loading full text...

Full text loading...



Image of FIGURE 1

Click to view


Phylogenetic relationships of the fungal phyla and subphyla. A phylogenetic tree from 434 conserved protein-coding genes resolves the relationships of most of the known lineages of fungi. This tree is a simplified version of that presented by Spatafora et al. ( 43 ). Phyla are presented in bold and subphyla in regular type. The Chytridiomycetes and Monoblepharidomycetes represent lineages for which a subphylum is not yet named.

Source: microbiolspec August 2017 vol. 5 no. 4 doi:10.1128/microbiolspec.FUNK-0055-2016
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2

Click to view


Scatter plot showing the relationship between genome size and gene count. Genome size varies among subphyla of fungi, with some of the smallest genomes in the Microsporidia and the largest currently sequenced genomes in the Agaricomycotina and Pezizomycotina. Primary data are gathered from genome information available at the National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/) and Joint Genome Institute Mycocosm (https://jgi.doe.gov/fungi) and archived in the 1KFG genome_stats github project (https://github.com/1KFG/genome_stats).

Source: microbiolspec August 2017 vol. 5 no. 4 doi:10.1128/microbiolspec.FUNK-0055-2016
Permissions and Reprints Request Permissions
Download as Powerpoint

Supplemental Material

No supplementary material available for this content.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error