Fungal genomes tell a story of ecological adaptations

Open access


One genome enables a fungus to have various lifestyles and strategies depending on environmental conditions and in the presence of specific counterparts. The nature of their interactions with other living and abiotic elements is a consequence of their osmotrophism. The ability to degrade complex compounds and especially plant biomass makes them a key component of the global carbon circulation cycle. Since the first fungal genomic sequence was published in 1996 mycology has benefited from the technolgical progress. The available data create an unprecedented opportunity to perform massive comparative studies with complex study design variants targeted at all cellular processes.

Abe, A., Asano, K. & Sone, T. 2009. Identification and characterization of rhizot, a novel LTR Retrotransposon of Rhizopus oryzae and R. delemar. Bioscience, Biotechnology, and Biochemistry, 73(8), 1860-1862. doi:10.1271/bbb.90017

Aramayo, R. & Selker, E.U. 2013. Neurospora crassa, a model system for epigenetics research. Cold Spring Harbor Perspectives in Biology, 5(10), a017921. doi:10.1101/cshperspect.a017921

Byrne, K.P. & Wolfe, K.H. 2007. Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication. Genetics, 175(3), 1341-1350. doi:10.1534/genetics.106.066951

Capy, P., Gasperi, G., Biémont, C. & Bazin, C. 2000. Stress and transposable elements: coevolution or useful parasites? Heredity, 85 ( Pt 2), 101-106. Retrieved from

Cissé, O.H., Almeida, J.M.G.C.F., Fonseca, A., Kumar, A.A., Salojärvi, J., Overmyer, K. & Pagni, M. 2013. Genome sequencing of the plant pathogen Taphrina deformans, the causal agent of peach leaf curl. mBio, 4(3), e00055-13. doi:10.1128/mBio.00055-13

Coleman, J.J., Rounsley, S.D., Rodriguez-Carres, M., Kuo, A., Wasmann, C.C., Grimwood, J. & Vanetten, H. D. 2009. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genetics, 5(8), e1000618. doi:10.1371/journal.pgen.1000618

Cuomo, C.A., Desjardins, C.A., Bakowski, M.A., Goldberg, J., Ma, A.T., Becnel, J.J. & Troemel, E.R. 2012. Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth. Genome Research, 22(12), 2478-2488. doi:10.1101/gr.142802.112

De Jonge, R., Bolton, M.D. & Thomma, B.P.H.J. 2011. How filamentous pathogens co-opt plants: the ins and outs of fungal effectors. Current Opinion in Plant Biology, 14(4), 400-406. doi:10.1016/j.pbi.2011.03.005

Desjardins, C.A., Champion, M.D., Holder, J. W., Muszewska, A., Goldberg, J., Bailão, A.M. & Cuomo, C.A. 2011. Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis. PLoS Genetics, 7(10), e1002345. doi:10.1371/journal.pgen.1002345

Engel, S.R., Dietrich, F.S., Fisk, D.G., Binkley, G., Balakrishnan, R., Costanzo, M.C., Dwight, S.S., Hitz, B.C., Karra, K., Nash, R.S., et al. 2014. The reference genome sequence of Saccharomyces cerevisiae: then and now. G3 (Bethesda) [Internet]. [cited 2014 Jul 12]; 4:389-398. Available from: type=abstract

Fernandez-Fueyo, E., Ruiz-Dueñas, F.J., Ferreira, P., Floudas, D., Hibbett, D.S., Canessa, P. & Cullen, D. 2012. Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proceedings of the National Academy of Sciences of the United States of America, 109(14), 5458-5463. doi:10.1073/pnas.1119912109

Fisher, M.C., Henk, D.A., Briggs, C.J., Brownstein, J.S., Madoff, L.C., McCraw, S.L. & Gurr, S.J. 2012. Emerging fungal threats to animal, plant and ecosystem health. Nature, 484(7393), 186-194. doi:10.1038/nature10947

Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J.D., Jacq, C., Johnston, M., et al. 1996. Life with 6000 genes. Science [Internet]. [cited 2014 Jul 12]; 274:546, 563-567. Available from:

Halary, S., Malik, S.-B., Lildhar, L., Slamovits, C.H., Hijri, M. & Corradi, N. 2011. Conserved meiotic machinery in Glomus spp., a putatively ancient asexual fungal lineage. Genome Biology and Evolution, 3, 950-958. doi:10.1093/gbe/evr089

Heitman, J., Sun, S. & James, T.Y. 2013. Evolution of fungal sexual reproduction. Mycologia, 105(1), 1-27. doi:10.3852/12-253

Hess, J., Skrede, I., Wolfe, B., LaButti, K., Ohm, R.A., Grigoriev, I.V. & Pringle, A. 2014. Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi. Genome Biology and Evolution, 1-45. doi:10.1093/gbe/evu121

Hua-Van, A., Le Rouzic, A., Boutin, T.S., Filée, J. & Capy, P. 2011. The struggle for life of the genome’s selfish architects. Biology Direct, 6, 19. doi:10.1186/1745-6150-6-19

James, T.Y., Pelin, A., Bonen, L., Ahrendt, S., Sain, D., Corradi, N. & Stajich, J.E. 2013. Shared signatures of parasitism and phylogenomics unite Cryptomycota and microsporidia. Current Biology [Internet]. [cited 2014 Jul 16]; 23:1548-1553. Available from:

Kang, S., Lebrun, M.H., Farrall, L. & Valent, B. 2001. Gain of virulence caused by insertion of a Pot3 transposon in a Magnaporthe grisea avirulence gene. Molecular Plant-Microbe Interactions : MPMI, 14(5), 671-674. doi:10.1094/MPMI.2001.14.5.671

Lynch, M. & Conery, J. S. 2003. The origins of genome complexity. Science (New York, N.Y.), 302(5649), 1401-1404. doi:10.1126/science.1089370

Ma, L.-J., Ibrahim, A.S., Skory, C., Grabherr, M.G., Burger, G., Butler, M. & Wickes, B.L. 2009. Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genetics, 5(7), e1000549. doi:10.1371/journal.pgen.1000549

Ma, L.-J., van der Does, H.C., Borkovich, K. a, Coleman, J.J., Daboussi, M.-J., Di Pietro, A. & Rep, M. 2010. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature, 464(7287), 367-373. doi:10.1038/nature08850

Manning, V.A., Pandelova, I., Dhillon, B., Wilhelm, L.J., Goodwin, S.B., Berlin, A.M. & Ciuffetti, L.M. 2013. Comparative genomics of a plant-pathogenic fungus, Pyrenophora triticirepentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3 (Bethesda, Md.), 3(1), 41-63. doi:10.1534/g3.112.004044

Marcet-Houben, M. & Gabaldón, T. 2010. Acquisition of prokaryotic genes by fungal genomes. Trends in Genetics: TIG, 26(1), 5-8. doi:10.1016/j.tig.2009.11.007

Martin, F., Kohler, A., Murat, C., Balestrini, R., Coutinho, P.M., Jaillon, O. & Wincker, P. 2010. Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature, 464(7291), 1033-1038. doi:10.1038/nature08867

McGary, K.L., Slot, J.C. & Rokas, A. 2013. Physical linkage of metabolic genes in fungi is an adaptation against the accumulation of toxic intermediate compounds. Proceedings of the National Academy of Sciences of the United States of America, 110(28), 11481-11486. doi:10.1073/pnas.1304461110

Muszewska, A., Hoffman-Sommer, M. & Grynberg, M. 2011. LTR Retrotransposons in Fungi. PLoS ONE, 6(12), e29425. Retrieved from

Muszewska, A., Steczkiewicz, K. & Ginalski, K. 2013. DIRS and Ngaro Retrotransposons in Fungi. PloS One, 8(9), e76319. doi:10.1371/journal.pone.0076319

Novikova, O., Fet, V. & Blinov, A. 2009. Non-LTR retrotransposons in fungi. Functional & Integrative Genomics, 9(1), 27-42. doi:10.1007/s10142-008-0093-8

Plett, J.M., Kemppainen, M., Kale, S.D., Kohler, A., Legué, V., Brun, A. & Martin, F. 2011. A secreted effector protein of Laccaria bicolor is required for symbiosis development. Current Biology : CB, 21(14), 1197-1203. doi:10.1016/j.cub.2011.05.033

Proctor, R.H., Van Hove, F., Susca, A., Stea, G., Busman, M., van der Lee, T. & Ward, T.J. 2013. Birth, death and horizontal transfer of the fumonisin biosynthetic gene cluster during the evolutionary diversification of Fusarium. Molecular Microbiology, 90(2), 290-306. doi:10.1111/mmi.12362

Raffaele, S. & Kamoun, S. 2012. Genome evolution in filamentous plant pathogens: why bigger can be better. Nature Reviews. Microbiology, 10(6), 417-430. doi:10.1038/nrmicro2790

Richards, T.A. 2011. Genome evolution: horizontal movements in the fungi. Current Biology: CB, 21(4), R166-168. doi:10.1016/j.cub.2011.01.028

Richards, T.A. & Talbot, N.J. 2013. Horizontal gene transfer in osmotrophs: playing with public goods. Nature Reviews. Microbiology, 11(10), 720-727. doi:10.1038/nrmicro3108

Riley, R., Charron, P., Idnurm, A., Farinelli, L., Dalpé, Y., Martin, F. & Corradi, N. 2014. Extreme diversification of the mating typehigh- mobility group (MATA-HMG) gene family in a plant-associated arbuscular mycorrhizal fungus. The New Phytologist, 201(1), 254-268. doi:10.1111/nph.12462

Schmidt, S.M. & Panstruga, R. 2011. Pathogenomics of fungal plant parasites: what have we learnt about pathogenesis? Current Opinion in Plant Biology, 14(4), 392-399. doi:10.1016/j.pbi.2011.03.006

Spatafora, J. W., Sung, G.-H., Sung, J.-M., Hywel- Jones, N.L. & White, J.F. 2007. Phylogenetic evidence for an animal pathogen origin of ergot and the grass endophytes. Molecular Ecology, 16(8), 1701-1711. doi:10.1111/j.1365-294X.2007.03225.x Taylor, J.W., Jacobson, D.J., Kroken, S., Kasuga, T., Geiser, D.M., Hibbett, D.S. & Fisher, M.C. 2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology : FG & B, 31(1), 21-32. doi:10.1006/fgbi.2000.1228

Teixeira, M.M., Theodoro, R.C., de Carvalho, M.J.A., Fernandes, L., Paes, H.C., Hahn, R.C. & Felipe, M.S.S. 2009. Phylogenetic analysis reveals a high level of speciation in the Paracoccidioides genus. Molecular Phylogenetics and Evolution, 52(2), 273-283. doi:10.1016/j.ympev.2009.04.005

Van de Wouw, A.P., Cozijnsen, A.J., Hane, J.K., Brunner, P.C., McDonald, B.A., Oliver, R.P. & Howlett, B.J. 2010. Evolution of linked avirulence effectors in Leptosphaeria maculans is affected by genomic environment and exposure to resistance genes in host plants. PLoS Pathogens, 6(11), e1001180. doi:10.1371/journal.ppat.1001180

Folia Biologica et Oecologica

The Journal of University of Lodz

Journal Information


All Time Past Year Past 30 Days
Abstract Views 0 0 0
Full Text Views 237 237 18
PDF Downloads 57 57 15