Fungal Genomics

at Utrecht University

Fungal comparative genomics


Project description

In the past decade, the number of available fungal genome sequences has increased considerably. Moreover, it has become much cheaper to generate high-quality sequences of fungal genomes.

In this on-going project, we analyze fungal genomes (newly sequenced and previously published) to gain more insight into the fungal lifestyle and development. This is done both in collaboration with other labs (including the Joint Genome Institute), and by sequencing new genomes ourselves.

Furthermore, we developed Genome Portals that will facilitate the analysis of the genomes we have sequenced in-house.

Homeodomain transcription factors

Figure. Homeodomain transcription factors in the fungal kingdom. (Vonk et al., Fungal Biology Reviews, 2018)


Lab members currently working on this project


Genome portals


Publications

101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens.
Haridas S, Albert R, Binder M, Bloem J, LaButti K, Salamov A, Andreopoulos B, Baker SE, Barry K, Bills G, Bluhm BH, Cannon C, Castanera R, Culley DE, Daum C, Ezra D, Gonzalez JB, Henrissat B, Kuo A, Liang C, Lipzen A, Lutzoni F, Magnuson J, Mondo SJ, Nolan M, Ohm RA, Pangilinan J, Park HJ, Ramirez L, Alfaro M, Sun H, Tritt A, Yoshinaga Y, Zwiers LH, Turgeon BG, Goodwin SB, Spatafora JW, Crous PW, Grigoriev IV
Stud Mycol. 2020 Jun; 96: 141-153. doi: 10.1016/j.simyco.2020.01.003

Megaphylogeny resolves global patterns of mushroom evolution.
Varga T, Krizsan K, Foldi C, Dima B, Sanchez-Garcia M, Sanchez-Ramirez S, Szollosi GJ, Szarkandi JG, Papp V, Albert L, Andreopoulos W, Angelini C, Antonin V, Barry KW, Bougher NL, Buchanan P, Buyck B, Bense V, Catcheside P, Chovatia M, Cooper J, Damon W, Desjardin D, Finy P, Geml J, Haridas S, Hughes K, Justo A, Karasinski D, Kautmanova I, Kiss B, Kocsube S, Kotiranta H, LaButti KM, Lechner BE, Liimatainen K, Lipzen A, Lukacs Z, Mihaltcheva S, Morgado LN, Niskanen T, Noordeloos ME, Ohm RA, Ortiz-Santana B, Ovrebo C, Racz N, Riley R, Savchenko A, Shiryaev A, Soop K, Spirin V, Szebenyi C, Tomsovsky M, Tulloss RE, Uehling J, Grigoriev IV, Vagvolgyi C, Papp T, Martin FM, Miettinen O, Hibbett DS, Nagy LG
Nat Ecol Evol. 2019 Apr; 3(4): 668-678. doi: 10.1038/s41559-019-0834-1

Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi.
Krizsan K, Almasi E, Merenyi Z, Sahu N, Viragh M, Koszo T, Mondo S, Kiss B, Balint B, Kues U, Barry K, Cseklye J, Hegedus B, Henrissat B, Johnson J, Lipzen A, Ohm RA, Nagy I, Pangilinan J, Yan J, Xiong Y, Grigoriev IV, Hibbett DS, Nagy LG
Proc Natl Acad Sci U S A. 2019 Apr; 116(15): 7409-7418. doi: 10.1073/pnas.1817822116

The role of homeodomain transcription factors in fungal development
Vonk PJ, Ohm RA
Fungal Biol Rev. 2018 Sep; 34(4): 219-230. doi: 10.1016/j.fbr.2018.04.002

Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors.
Lopez D, Ribeiro S, Label P, Fumanal B, Venisse JS, Kohler A, de Oliveira RR, Labutti K, Lipzen A, Lail K, Bauer D, Ohm RA, Barry KW, Spatafora J, Grigoriev IV, Martin FM, Pujade-Renaud V
Front Microbiol. 2018 Jun; 9: 276. doi: 10.3389/fmicb.2018.00276

Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi.
Knapp DG, Nemeth JB, Barry K, Hainaut M, Henrissat B, Johnson J, Kuo A, Lim JHP, Lipzen A, Nolan M, Ohm RA, Tamas L, Grigoriev IV, Spatafora JW, Nagy LG, Kovacs GM
Sci Rep. 2018 Apr; 8(1): 6321. doi: 10.1038/s41598-018-24686-4

Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists.
Martino E, Morin E, Grelet GA, Kuo A, Kohler A, Daghino S, Barry KW, Cichocki N, Clum A, Dockter RB, Hainaut M, Kuo RC, LaButti K, Lindahl BD, Lindquist EA, Lipzen A, Khouja HR, Magnuson J, Murat C, Ohm RA, Singer SW, Spatafora JW, Wang M, Veneault-Fourrey C, Henrissat B, Grigoriev IV, Martin FM, Perotto S
New Phytol. 2018 Feb; 217(3): 1213-1229. doi: 10.1111/nph.14974

Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens.
Uehling J, Gryganskyi A, Hameed K, Tschaplinski T, Misztal PK, Wu S, Desiro A, Vande Pol N, Du Z, Zienkiewicz A, Zienkiewicz K, Morin E, Tisserant E, Splivallo R, Hainaut M, Henrissat B, Ohm R, Kuo A, Yan J, Lipzen A, Nolan M, LaButti K, Barry K, Goldstein AH, Labbe J, Schadt C, Tuskan G, Grigoriev I, Martin F, Vilgalys R, Bonito G
Environ Microbiol. 2017 Aug; 19(8): 2964-2983. doi: 10.1111/1462-2920.13669

Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum.
Peter M, Kohler A, Ohm RA, Kuo A, Krutzmann 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, Poggeler S, Quandt CA, Sperisen C, Tritt A, Tisserant E, Crous PW, Henrissat B, Nehls U, Egli S, Spatafora JW, Grigoriev IV, Martin FM
Nat Commun. 2016 Sep; 7: 12662. doi: 10.1038/ncomms12662

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication.
Corrochano LM, Kuo A, Marcet-Houben M, Polaino S, Salamov A, Villalobos-Escobedo JM, Grimwood J, Alvarez MI, Avalos J, Bauer D, Benito EP, Benoit I, Burger G, Camino LP, Canovas D, Cerda-Olmedo E, Cheng JF, Dominguez A, Elias M, Eslava AP, Glaser F, Gutierrez G, Heitman J, Henrissat B, Iturriaga EA, Lang BF, Lavin JL, Lee SC, Li W, Lindquist E, Lopez-Garcia S, Luque EM, Marcos AT, Martin J, McCluskey K, Medina HR, Miralles-Duran A, Miyazaki A, Munoz-Torres E, Oguiza JA, Ohm RA, Olmedo M, Orejas M, Ortiz-Castellanos L, Pisabarro AG, Rodriguez-Romero J, Ruiz-Herrera J, Ruiz-Vazquez R, Sanz C, Schackwitz W, Shahriari M, Shelest E, Silva-Franco F, Soanes D, Syed K, Tagua VG, Talbot NJ, Thon MR, Tice H, de Vries RP, Wiebenga A, Yadav JS, Braun EL, Baker SE, Garre V, Schmutz J, Horwitz BA, Torres-Martinez S, Idnurm A, Herrera-Estrella A, Gabaldon T, Grigoriev IV
Curr Biol. 2016 Jun; 26(12): 1577-1584. doi: 10.1016/j.cub.2016.04.038

Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities.
Nagy LG, Riley R, Tritt A, Adam C, Daum C, Floudas D, Sun H, Yadav JS, Pangilinan J, Larsson KH, Matsuura K, Barry K, Labutti K, Kuo R, Ohm RA, Bhattacharya SS, Shirouzu T, Yoshinaga Y, Martin FM, Grigoriev IV, Hibbett DS
Mol Biol Evol. 2016 Apr; 33(4): 959-70. doi: 10.1093/molbev/msv337

Genomics of wood-degrading fungi.
Ohm RA, Riley R, Salamov A, Min B, Choi IG, Grigoriev IV
Fungal Genet Biol. 2014 Nov; 72: 82-90. doi: 10.1016/j.fgb.2014.05.001

Prevalence of transcription factors in ascomycete and basidiomycete fungi.
Todd RB, Zhou M, Ohm RA, Leeggangers HA, Visser L, de Vries RP
BMC Genomics. 2014 Mar; 15: 214. doi: 10.1186/1471-2164-15-214

Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi.
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
PLoS Pathog. 2012 Jun; 8(12): e1003037. doi: 10.1371/journal.ppat.1003037

© 2020 - Robin Ohm - Utrecht University - The Netherlands

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