Publications

2024

Transcriptomics reveals the regulation of the immune system of the mushroom-forming fungus Schizophyllum commune during interaction with four competitors.
Beijen EPW, van Maanen MH, Marian IM, Klusener JX, van Roosmalen E, Herman KC, Koster MC, Ohm RA
Microbiol Res. 2024 Oct; 289: 127929. doi: 10.1016/j.micres.2024.127929

High phenotypic and genotypic plasticity among strains of the mushroom-forming fungus Schizophyllum commune.
Marian IM, Valdes ID, Hayes RD, LaButti K, Duffy K, Chovatia M, Johnson J, Ng V, Lugones LG, Wosten HAB, Grigoriev IV, Ohm RA
Fungal Genet Biol. 2024 Aug; 173: 103913. doi: 10.1016/j.fgb.2024.103913

The regulatory network of the White Collar complex during early mushroom development in Schizophyllum commune.
Vonk PJ, van der Poel MJP, Niemeijer ZE, Ohm RA
Microbiol Res. 2024 Jul; 284: 127736. doi: 10.1016/j.micres.2024.127736

Genome annotations for the ascomycete fungi Trichoderma harzianum, Trichoderma aggressivum, and Purpureocillium lilacinum.
Beijen EPW, Ohm RA
Microbiol Resour Announc. 2024 Mar; 13(3): e0115323. doi: 10.1128/mra.01153-23

2023

Genome-scale phylogeny and comparative genomics of the fungal order Sordariales.
Hensen N, Bonometti L, Westerberg I, Brannstrom IO, Guillou S, Cros-Aarteil S, Calhoun S, Haridas S, Kuo A, Mondo S, Pangilinan J, Riley R, LaButti K, Andreopoulos B, Lipzen A, Chen C, Yan M, Daum C, Ng V, Clum A, Steindorff A, Ohm RA, Martin F, Silar P, Natvig DO, Lalanne C, Gautier V, Ament-Velasquez SL, Kruys A, Hutchinson MI, Powell AJ, Barry K, Miller AN, Grigoriev IV, Debuchy R, Gladieux P, Hiltunen Thoren M, Johannesson H
Mol Phylogenet Evol. 2023 Dec; 189: 107938. doi: 10.1016/j.ympev.2023.107938

Compatible solutes determine the heat resistance of conidia.
Seekles SJ, van den Brule T, Punt M, Dijksterhuis J, Arentshorst M, Ijadpanahsaravi M, Roseboom W, Meuken G, Ongenae V, Zwerus J, Ohm RA, Kramer G, Wosten HAB, de Winde JH, Ram AFJ
Fungal Biol Biotechnol. 2023 Nov; 10(1): 21. doi: 10.1186/s40694-023-00168-9

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes.
Nagy LG, Vonk PJ, Kunzler M, Foldi C, Viragh M, Ohm RA, Hennicke F, Balint B, Csernetics A, Hegedus B, Hou Z, Liu XB, Nan S, Pareek M, Sahu N, Szathmari B, Varga T, Wu H, Yang X, Merenyi Z
Stud Mycol. 2023 Jul; 104: 1-85. doi: 10.3114/sim.2022.104.01

2022

Masters of the manipulator: two new hypocrealean genera, Niveomyces (Cordycipitaceae) and Torrubiellomyces (Ophiocordycipitaceae), parasitic on the zombie ant fungus Ophiocordyceps camponoti-floridani
Araújo JPM, Lebert BM, Vermeulen S, Brachmann A, Ohm RA, Evans HC, De Bekker C
Persoonia: Molecular Phylogeny and Evolution of Fungi. 2022 Dec; 49: 171-194. doi: 10.3767/persoonia.2022.49.05

Genome sequences of 24 Aspergillus niger sensu stricto strains to study strain diversity, heterokaryon compatibility, and sexual reproduction.
Seekles SJ, Punt M, Savelkoel N, Houbraken J, Wosten HAB, Ohm RA, Ram AFJ
G3 (Bethesda). 2022 Jul; 12(7). doi: 10.1093/g3journal/jkac124

The Transcription Factor Roc1 Is a Key Regulator of Cellulose Degradation in the Wood-Decaying Mushroom Schizophyllum commune.
Marian IM, Vonk PJ, Valdes ID, Barry K, Bostock B, Carver A, Daum C, Lerner H, Lipzen A, Park H, Schuller MBP, Tegelaar M, Tritt A, Schmutz J, Grimwood J, Lugones LG, Choi IG, Wosten HAB, Grigoriev IV, Ohm RA
mBio. 2022 Jun; 13(3): e0062822. doi: 10.1128/mbio.00628-22

High sorbic acid resistance of Penicillium roqueforti is mediated by the SORBUS gene cluster.
Punt M, Seekles SJ, van Dam JL, de Adelhart Toorop C, Martina RR, Houbraken J, Ram AFJ, Wosten HAB, Ohm RA
PLoS Genet. 2022 Jun; 18(6): e1010086. doi: 10.1371/journal.pgen.1010086

2021

H3K4me2 ChIP-Seq reveals the epigenetic landscape during mushroom formation and novel developmental regulators of Schizophyllum commune.
Vonk PJ, Ohm RA
Sci Rep. 2021 Apr; 11(1): 8178. doi: 10.1038/s41598-021-87635-8

Cycling in degradation of organic polymers and uptake of nutrients by a litter-degrading fungus.
Vos AM, Bleichrodt RJ, Herman KC, Ohm RA, Scholtmeijer K, Schmitt H, Lugones LG, Wosten HAB
Environ Microbiol. 2021 Jan; 23(1): 224-238. doi: 10.1111/1462-2920.15297

2020

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits.
Miyauchi S, Kiss E, Kuo A, Drula E, Kohler A, Sanchez-Garcia M, Morin E, Andreopoulos B, Barry KW, Bonito G, Buee M, Carver A, Chen C, Cichocki N, Clum A, Culley D, Crous PW, Fauchery L, Girlanda M, Hayes RD, Keri Z, LaButti K, Lipzen A, Lombard V, Magnuson J, Maillard F, Murat C, Nolan M, Ohm RA, Pangilinan J, Pereira MF, Perotto S, Peter M, Pfister S, Riley R, Sitrit Y, Stielow JB, Szollosi G, Zifcakova L, Stursova M, Spatafora JW, Tedersoo L, Vaario LM, Yamada A, Yan M, Wang P, Xu J, Bruns T, Baldrian P, Vilgalys R, Dunand C, Henrissat B, Grigoriev IV, Hibbett D, Nagy LG, Martin FM
Nat Commun. 2020 Oct; 11(1): 5125. doi: 10.1038/s41467-020-18795-w

Impact of maturation and growth temperature on cell-size distribution, heat-resistance, compatible solute composition and transcription profiles of Penicillium roqueforti conidia.
Punt M, van den Brule T, Teertstra WR, Dijksterhuis J, den Besten HMW, Ohm RA, Wosten HAB
Food Res Int. 2020 Oct; 136: 109287. doi: 10.1016/j.foodres.2020.109287

Telomere-to-telomere assembled and centromere annotated genomes of the two main subspecies of the button mushroom Agaricus bisporus reveal especially polymorphic chromosome ends.
Sonnenberg ASM, Sedaghat-Telgerd N, Lavrijssen B, Ohm RA, Hendrickx PM, Scholtmeijer K, Baars JJP, van Peer A
Sci Rep. 2020 Sep; 10(1): 14653. doi: 10.1038/s41598-020-71043-5

Degradative Capacity of Two Strains of Rhodonia placenta: From Phenotype to Genotype.
Kolle M, Horta MAC, Nowrousian M, Ohm RA, Benz JP, Pilgard A
Front Microbiol. 2020 Jul; 11: 1338. doi: 10.3389/fmicb.2020.01338

Genetic Underpinnings of Host Manipulation by Ophiocordyceps as Revealed by Comparative Transcriptomics.
Will I, Das B, Trinh T, Brachmann A, Ohm RA, de Bekker C
G3 (Bethesda). 2020 Jul; 10(7): 2275-2296. doi: 10.1534/g3.120.401290

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

2019

First evidence of cholinesterase-like activity in Basidiomycota.
Sepcic K, Sabotic J, A Ohm R, Drobne D, Jemec Kokalj A
PLoS One. 2019 Jul; 14(4): e0216077. doi: 10.1371/journal.pone.0216077

High-throughput targeted gene deletion in the model mushroom Schizophyllum commune using pre-assembled Cas9 ribonucleoproteins.
Vonk PJ, Escobar N, Wosten HAB, Lugones LG, Ohm RA
Sci Rep. 2019 May; 9(1): 7632. doi: 10.1038/s41598-019-44133-2

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

FlbA-Regulated Gene rpnR Is Involved in Stress Resistance and Impacts Protein Secretion when Aspergillus niger Is Grown on Xylose.
Aerts D, van den Bergh SG, Post H, Altelaar MAF, Arentshorst M, Ram AFJ, Ohm RA, Wosten HAB
Appl Environ Microbiol. 2019 Jan; 85(2). doi: 10.1128/AEM.02282-18

2018

Genomics and Development of Lentinus tigrinus: A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies.
Wu B, Xu Z, Knudson A, Carlson A, Chen N, Kovaka S, LaButti K, Lipzen A, Pennachio C, Riley R, Schakwitz W, Umezawa K, Ohm RA, Grigoriev IV, Nagy LG, Gibbons J, Hibbett D
Genome Biol Evol. 2018 Dec; 10(12): 3250-3261. doi: 10.1093/gbe/evy246

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

Expression profile analysis reveals that Aspergillus fumigatus but not Aspergillus niger makes type II epithelial lung cells less immunological alert.
Escobar N, Valdes ID, Keizer EM, Ordonez SR, Ohm RA, Wosten HAB, de Cock H
BMC Genomics. 2018 Jul; 19(1): 534. doi: 10.1186/s12864-018-4895-3

Production of alpha-1,3-L-arabinofuranosidase active on substituted xylan does not improve compost degradation by Agaricus bisporus.
Vos AM, Jurak E, de Gijsel P, Ohm RA, Henrissat B, Lugones LG, Kabel MA, Wosten HAB
PLoS One. 2018 Jun; 13(7): e0201090. doi: 10.1371/journal.pone.0201090

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

Nucleus-specific expression in the multinuclear mushroom-forming fungus Agaricus bisporus reveals different nuclear regulatory programs.
Gehrmann T, Pelkmans JF, Ohm RA, Vos AM, Sonnenberg ASM, Baars JJP, Wosten HAB, Reinders MJT, Abeel T
Proc Natl Acad Sci U S A. 2018 Apr; 115(17): 4429-4434. doi: 10.1073/pnas.1721381115

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

The FlbA-regulated predicted transcription factor Fum21 of Aspergillus niger is involved in fumonisin production.
Aerts D, Hauer EE, Ohm RA, Arentshorst M, Teertstra WR, Phippen C, Ram AFJ, Frisvad JC, Wosten HAB
Antonie Van Leeuwenhoek. 2018 Mar; 111(3): 311-322. doi: 10.1007/s10482-017-0952-1

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

2017

Ant-infecting Ophiocordyceps genomes reveal a high diversity of potential behavioral manipulation genes and a possible major role for enterotoxins.
de Bekker C, Ohm RA, Evans HC, Brachmann A, Hughes DP
Sci Rep. 2017 Oct; 7(1): 12508. doi: 10.1038/s41598-017-12863-w

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

Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling.
Triana S, de Cock H, Ohm RA, Danies G, Wosten HAB, Restrepo S, Gonzalez Barrios AF, Celis A
Front Microbiol. 2017 Jun; 8: 1772. doi: 10.3389/fmicb.2017.01772

Coprinopsis cinerea intracellular lactonases hydrolyze quorum sensing molecules of Gram-negative bacteria.
Stockli M, Lin CW, Sieber R, Plaza DF, Ohm RA, Kunzler M
Fungal Genet Biol. 2017 May; 102: 49-62. doi: 10.1016/j.fgb.2016.07.009

Maturation of conidia on conidiophores of Aspergillus niger.
Teertstra WR, Tegelaar M, Dijksterhuis J, Golovina EA, Ohm RA, Wosten HAB
Fungal Genet Biol. 2017 Jan; 98: 61-70. doi: 10.1016/j.fgb.2016.12.005

2016

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

Comparative genomics of biotechnologically important yeasts.
Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Goker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW
Proc Natl Acad Sci U S A. 2016 Aug; 113(35): 9882-7. doi: 10.1073/pnas.1603941113

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

Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage.
Mosier AC, Miller CS, Frischkorn KR, Ohm RA, Li Z, LaButti K, Lapidus A, Lipzen A, Chen C, Johnson J, Lindquist EA, Pan C, Hettich RL, Grigoriev IV, Singer SW, Banfield JF
Front Microbiol. 2016 Jun; 7: 238. doi: 10.3389/fmicb.2016.00238

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

Entomotoxic and nematotoxic lectins and protease inhibitors from fungal fruiting bodies.
Sabotic J, Ohm RA, Kunzler M
Appl Microbiol Biotechnol. 2016 Jan; 100(1): 91-111. doi: 10.1007/s00253-015-7075-2

2015

Draft Genome Sequence of the Animal and Human Pathogen Malassezia pachydermatis Strain CBS 1879.
Triana S, Gonzalez A, Ohm RA, Wosten HA, de Cock H, Restrepo S, Celis A
Genome Announc. 2015 Oct; 3(5). doi: 10.1128/genomeA.01197-15

Gene expression during zombie ant biting behavior reflects the complexity underlying fungal parasitic behavioral manipulation.
de Bekker C, Ohm RA, Loreto RG, Sebastian A, Albert I, Merrow M, Brachmann A, Hughes DP
BMC Genomics. 2015 Aug; 16: 620. doi: 10.1186/s12864-015-1812-x

Genomics and Transcriptomics Analyses of the Oil-Accumulating Basidiomycete Yeast Trichosporon oleaginosus: Insights into Substrate Utilization and Alternative Evolutionary Trajectories of Fungal Mating Systems.
Kourist R, Bracharz F, Lorenzen J, Kracht ON, Chovatia M, Daum C, Deshpande S, Lipzen A, Nolan M, Ohm RA, Grigoriev IV, Sun S, Heitman J, Bruck T, Nowrousian M
mBio. 2015 Jul; 6(4): e00918. doi: 10.1128/mBio.00918-15

Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants.
Chang Y, Wang S, Sekimoto S, Aerts AL, Choi C, Clum A, LaButti KM, Lindquist EA, Yee Ngan C, Ohm RA, Salamov AA, Grigoriev IV, Spatafora JW, Berbee ML
Genome Biol Evol. 2015 May; 7(6): 1590-601. doi: 10.1093/gbe/evv090

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.
Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, Canback B, Choi C, Cichocki N, Clum A, Colpaert J, Copeland A, Costa MD, Dore J, Floudas D, Gay G, Girlanda M, Henrissat B, Herrmann S, Hess J, Hogberg N, Johansson T, Khouja HR, LaButti K, Lahrmann U, Levasseur A, Lindquist EA, Lipzen A, Marmeisse R, Martino E, Murat C, Ngan CY, Nehls U, Plett JM, Pringle A, Ohm RA, Perotto S, Peter M, Riley R, Rineau F, Ruytinx J, Salamov A, Shah F, Sun H, Tarkka M, Tritt A, Veneault-Fourrey C, Zuccaro A, Tunlid A, Grigoriev IV, Hibbett DS, Martin F
Nat Genet. 2015 Apr; 47(4): 410-5. doi: 10.1038/ng.3223

Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen.
Dhillon B, Feau N, Aerts AL, Beauseigle S, Bernier L, Copeland A, Foster A, Gill N, Henrissat B, Herath P, LaButti KM, Levasseur A, Lindquist EA, Majoor E, Ohm RA, Pangilinan JL, Pribowo A, Saddler JN, Sakalidis ML, de Vries RP, Grigoriev IV, Goodwin SB, Tanguay P, Hamelin RC
Proc Natl Acad Sci U S A. 2015 Mar; 112(11): 3451-6. doi: 10.1073/pnas.1424293112

Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii.
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, Kues U, Blanchette RA, Grigoriev IV, Minto RE, Hibbett DS
Fungal Genet Biol. 2015 Mar; 76: 78-92. doi: 10.1016/j.fgb.2015.02.002

2014

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

Transcriptional responses of the Bdtf1-deletion mutant to the phytoalexin brassinin in the necrotrophic fungus Alternaria brassicicola.
Cho Y, Ohm RA, Devappa R, Lee HB, Grigoriev IV, Kim BY, Ahn JS
Molecules. 2014 Jul; 19(8): 10717-32. doi: 10.3390/molecules190810717

Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts.
Nagy LG, Ohm RA, Kovacs GM, Floudas D, Riley R, Gacser A, Sipiczki M, Davis JM, Doty SL, de Hoog GS, Lang BF, Spatafora JW, Martin FM, Grigoriev IV, Hibbett DS
Nat Commun. 2014 Jul; 5: 4471. doi: 10.1038/ncomms5471

Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species.
Gostincar C, Ohm RA, Kogej T, Sonjak S, Turk M, Zajc J, Zalar P, Grube M, Sun H, Han J, Sharma A, Chiniquy J, Ngan CY, Lipzen A, Barry K, Grigoriev IV, Gunde-Cimerman N
BMC Genomics. 2014 Jul; 15: 549. doi: 10.1186/1471-2164-15-549

Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi.
Hess J, Skrede I, Wolfe BE, LaButti K, Ohm RA, Grigoriev IV, Pringle A
Genome Biol Evol. 2014 Jun; 6(7): 1564-78. doi: 10.1093/gbe/evu121

Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae.
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
New Phytol. 2014 Apr; 202(2): 554-64. doi: 10.1111/nph.12653

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

MycoCosm portal: gearing up for 1000 fungal genomes.
Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R, Riley R, Salamov A, Zhao X, Korzeniewski F, Smirnova T, Nordberg H, Dubchak I, Shabalov I
Nucleic Acids Res. 2014 Jan; 42(Database issue): D699-704. doi: 10.1093/nar/gkt1183

2013

Fungal-specific transcription factor AbPf2 activates pathogenicity in Alternaria brassicicola.
Cho Y, Ohm RA, Grigoriev IV, Srivastava A
Plant J. 2013 Aug; 75(3): 498-514. doi: 10.1111/tpj.12217

Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens.
Condon BJ, Leng Y, Wu D, Bushley KE, Ohm RA, Otillar R, Martin J, Schackwitz W, Grimwood J, MohdZainudin N, Xue C, Wang R, Manning VA, Dhillon B, Tu ZJ, Steffenson BJ, Salamov A, Sun H, Lowry S, LaButti K, Han J, Copeland A, Lindquist E, Barry K, Schmutz J, Baker SE, Ciuffetti LM, Grigoriev IV, Zhong S, Turgeon BG
PLoS Genet. 2013 Jun; 9(1): e1003233. doi: 10.1371/journal.pgen.1003233

The blue light receptor complex WC-1/2 of Schizophyllum commune is involved in mushroom formation and protection against phototoxicity.
Ohm RA, Aerts D, Wosten HA, Lugones LG
Environ Microbiol. 2013 Mar; 15(3): 943-55. doi: 10.1111/j.1462-2920.2012.02878.x

2012

Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche.
Morin E, Kohler A, Baker AR, Foulongne-Oriol M, Lombard V, Nagy LG, Ohm RA, Patyshakuliyeva A, Brun A, Aerts AL, Bailey AM, Billette C, Coutinho PM, Deakin G, Doddapaneni H, Floudas D, Grimwood J, Hilden K, Kues U, Labutti KM, Lapidus A, Lindquist EA, Lucas SM, Murat C, Riley RW, Salamov AA, Schmutz J, Subramanian V, Wosten HA, Xu J, Eastwood DC, Foster GD, Sonnenberg AS, Cullen D, de Vries RP, Lundell T, Hibbett DS, Henrissat B, Burton KS, Kerrigan RW, Challen MP, Grigoriev IV, Martin F
Proc Natl Acad Sci U S A. 2012 Oct; 109(43): 17501-6. doi: 10.1073/pnas.1206847109

The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes.
Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martinez AT, Otillar R, Spatafora JW, Yadav JS, Aerts A, Benoit I, Boyd A, Carlson A, Copeland A, Coutinho PM, de Vries RP, Ferreira P, Findley K, Foster B, Gaskell J, Glotzer D, Gorecki P, Heitman J, Hesse C, Hori C, Igarashi K, Jurgens JA, Kallen N, Kersten P, Kohler A, Kues U, Kumar TK, Kuo A, LaButti K, Larrondo LF, Lindquist E, Ling A, Lombard V, Lucas S, Lundell T, Martin R, McLaughlin DJ, Morgenstern I, Morin E, Murat C, Nagy LG, Nolan M, Ohm RA, Patyshakuliyeva A, Rokas A, Ruiz-Duenas FJ, Sabat G, Salamov A, Samejima M, Schmutz J, Slot JC, St John F, Stenlid J, Sun H, Sun S, Syed K, Tsang A, Wiebenga A, Young D, Pisabarro A, Eastwood DC, Martin F, Cullen D, Grigoriev IV, Hibbett DS
Science. 2012 Jun; 336(6089): 1715-9. doi: 10.1126/science.1221748

Transcription factor Amr1 induces melanin biosynthesis and suppresses virulence in Alternaria brassicicola.
Cho Y, Srivastava A, Ohm RA, Lawrence CB, Wang KH, Grigoriev IV, Marahatta SP
PLoS Pathog. 2012 Jun; 8(10): e1002974. doi: 10.1371/journal.ppat.1002974

The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry.
de Wit PJ, van der Burgt A, Okmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, Bahkali AH, Beenen HG, Chettri P, Cox MP, Datema E, de Vries RP, Dhillon B, Ganley AR, Griffiths SA, Guo Y, Hamelin RC, Henrissat B, Kabir MS, Jashni MK, Kema G, Klaubauf S, Lapidus A, Levasseur A, Lindquist E, Mehrabi R, Ohm RA, Owen TJ, Salamov A, Schwelm A, Schijlen E, Sun H, van den Burg HA, van Ham RC, Zhang S, Goodwin SB, Grigoriev IV, Collemare J, Bradshaw RE
PLoS Genet. 2012 Jun; 8(11): e1003088. doi: 10.1371/journal.pgen.1003088

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

A zinc-finger-family transcription factor, AbVf19, is required for the induction of a gene subset important for virulence in Alternaria brassicicola.
Srivastava A, Ohm RA, Oxiles L, Brooks F, Lawrence CB, Grigoriev IV, Cho Y
Mol Plant Microbe Interact. 2012 Apr; 25(4): 443-52. doi: 10.1094/MPMI-10-11-0275

The genome portal of the Department of Energy Joint Genome Institute.
Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, Kuo A, Minovitsky S, Nikitin R, Ohm RA, Otillar R, Poliakov A, Ratnere I, Riley R, Smirnova T, Rokhsar D, Dubchak I
Nucleic Acids Res. 2012 Jan; 40(Database issue): D26-32. doi: 10.1093/nar/gkr947

2011

Transcription factor genes of Schizophyllum commune involved in regulation of mushroom formation.
Ohm RA, de Jong JF, de Bekker C, Wosten HA, Lugones LG
Mol Microbiol. 2011 Sep; 81(6): 1433-45. doi: 10.1111/j.1365-2958.2011.07776.x

Heterogenic expression of genes encoding secreted proteins at the periphery of Aspergillus niger colonies.
Vinck A, de Bekker C, Ossin A, Ohm RA, de Vries RP, Wosten HAB
Environ Microbiol. 2011 Jan; 13(1): 216-225. doi: 10.1111/j.1462-2920.2010.02322.x

2010

An efficient gene deletion procedure for the mushroom-forming basidiomycete Schizophyllum commune.
Ohm RA, de Jong JF, Berends E, Wang F, Wosten HA, Lugones LG
World J Microbiol Biotechnol. 2010 Oct; 26(10): 1919-1923. doi: 10.1007/s11274-010-0356-0

Genome sequence of the model mushroom Schizophyllum commune.
Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A, Baker SE, Bartholomew KA, Coutinho PM, Erdmann S, Fowler TJ, Gathman AC, Lombard V, Henrissat B, Knabe N, Kues U, Lilly WW, Lindquist E, Lucas S, Magnuson JK, Piumi F, Raudaskoski M, Salamov A, Schmutz J, Schwarze FW, vanKuyk PA, Horton JS, Grigoriev IV, Wosten HA
Nat Biotechnol. 2010 Sep; 28(9): 957-63. doi: 10.1038/nbt.1643

Inactivation of ku80 in the mushroom-forming fungus Schizophyllum commune increases the relative incidence of homologous recombination.
de Jong JF, Ohm RA, de Bekker C, Wosten HA, Lugones LG
FEMS Microbiol Lett. 2010 Sep; 310(1): 91-5. doi: 10.1111/j.1574-6968.2010.02052.x

2009

Genomic and biochemical analysis of N glycosylation in the mushroom-forming basidiomycete Schizophyllum commune.
Berends E, Ohm RA, de Jong JF, Rouwendal G, Wosten HA, Lugones LG, Bosch D
Appl Environ Microbiol. 2009 Jul; 75(13): 4648-52. doi: 10.1128/AEM.00352-09

Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae.
Coutinho PM, Andersen MR, Kolenova K, vanKuyk PA, Benoit I, Gruben BS, Trejo-Aguilar B, Visser H, van Solingen P, Pakula T, Seiboth B, Battaglia E, Aguilar-Osorio G, de Jong JF, Ohm RA, Aguilar M, Henrissat B, Nielsen J, Stalbrand H, de Vries RP
Fungal Genet Biol. 2009 Mar; 46 Suppl 1: S161-S169. doi: 10.1016/j.fgb.2008.07.020

Fungal Genomics