Genet
52:159–183.
https://doi.org/10.1146/
annurev-genet-120417-031237
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, Ku ¨es U, Lilly WW, Lindquist E, Lucas S, Magnuson JK, Piumi F, Raudaskoski M, Salamov A, Schmutz J, Schwarze FWMR,
vanKuyk PA, Horton JS, Grigoriev IV, Wo ¨sten
HAB (2010) Genome sequence of the model mushroom Schizophyllum commune. Nat Biotechnol
28:957–963
Ohm RA, de Jong JF, de Bekker C, Wo ¨sten HAB,
Lugones LG (2011) Transcription factor genes of
Schizophyllum commune involved in regulation of
mushroom formation. Mol Microbiol 81:1433–
1445.
https://doi.org/10.1111/j.13652958.2011.07776.x
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 GHJ, Lawrence C, Scott JA,
Spatafora JW, Turgeon BG, de Wit PJGM, 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. https://doi.org/10.1371/journal.ppat.1003037
Ohm RA, Aerts D, Wo ¨sten HAB, Lugones LG (2013)
The blue light receptor complex WC-1/2 of Schizophyllum commune is involved in mushroom
formation and protection against phototoxicity.
Environ Microbiol 15:943–955. https://doi.org/
10.1111/j.1462-2920.2012.02878.x
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. https://doi.org/
10.1016/J.FGB.2014.05.001
Parra G, Bradnam K, Korf I (2007) CEGMA: a pipeline
to accurately annotate core genes in eukaryotic
genomes. Bioinformatics 23:1061–1067. https://
doi.org/10.1093/bioinformatics/btm071
Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G,
Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JAE,
van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EGJ,
Debets AJM, Dekker P, van Dijck PWM, van Dijk
A, Dijkhuizen L, Driessen AJM, d’Enfert C, Geysens S, Goosen C, Groot GSP, de Groot PWJ, Guillemette T, Henrissat B, Herweijer M, van den
Hombergh JPTW, van den Hondel CAMJJ, van
der Heijden RTJM, van der Kaaij RM, Klis FM,
Kools HJ, Kubicek CP, van Kuyk PA, Lauber J,
Lu X, van der Maarel MJEC, Meulenberg R,
Menke H, Mortimer MA, Nielsen J, Oliver SG,
Olsthoorn M, Pal K, van Peij NNME, Ram AFJ,
Rinas U, Roubos JA, Sagt CMJ, Schmoll M, Sun J,
Ussery D, Varga J, Vervecken W, van de Vondervoort PJJ, Wedler H, Wo ¨sten HAB, Zeng A-P, van
Ooyen AJJ, Visser J, Stam H (2007) Genome
sequencing and analysis of the versatile cell factory
Aspergillus niger CBS 513.88. Nat Biotechnol
25:221–231. https://doi.org/10.1038/nbt1282
Peter M, Kohler A, Ohm RA, Kuo A, Kru ¨tzmann 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, Po ¨ggeler 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. https://doi.org/10.1038/
ncomms12662
Petersen TN, Brunak S, von Heijne G, Nielsen H (2011)
SignalP 4.0: discriminating signal peptides from
transmembrane regions. Nat Methods 8:785–786.
https://doi.org/10.1038/nmeth.1701
Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in large genomes. Bioinformatics 21:i351–i358. https://doi.org/10.1093/
bioinformatics/bti1018
Rawlings ND, Waller M, Barrett AJ, Bateman A (2014)
MEROPS: the database of proteolytic enzymes,
their substrates and inhibitors. Nucleic Acids Res
42:D503–D509. https://doi.org/10.1093/nar/gkt953
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 GHJ,
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 M-H, Howlett BJ (2011)
Effector diversification within compartments of
the Leptosphaeria maculans genome affected by
repeat-induced point mutations. Nat Commun
2:202. https://doi.org/10.1038/ncomms1189
Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR,
Fiddes JC, Hutchison CA, Slocombe PM, Smith M
(1977a) Nucleotide sequence of bacteriophage
jX174 DNA. Nature 265:687–695. https://doi.org/
10.1038/265687a0
Sanger F, Nicklen S, Coulson AR (1977b) DNA sequencing with chain-terminating inhibitors. Proc Natl
Acad Sci USA 74:5463–5467. https://doi.org/
10.1073/PNAS.74.12.5463
Shi T-Q, Liu G-N, Ji R-Y, Shi K, Song P, Ren L-J, Huang
H, Ji X-J (2017) CRISPR/Cas9-based genome editing of the filamentous fungi: the state of the art.
222
R. A. Ohm
52:159–183.
https://doi.org/10.1146/
annurev-genet-120417-031237
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, Ku ¨es U, Lilly WW, Lindquist E, Lucas S, Magnuson JK, Piumi F, Raudaskoski M, Salamov A, Schmutz J, Schwarze FWMR,
vanKuyk PA, Horton JS, Grigoriev IV, Wo ¨sten
HAB (2010) Genome sequence of the model mushroom Schizophyllum commune. Nat Biotechnol
28:957–963
Ohm RA, de Jong JF, de Bekker C, Wo ¨sten HAB,
Lugones LG (2011) Transcription factor genes of
Schizophyllum commune involved in regulation of
mushroom formation. Mol Microbiol 81:1433–
1445.
https://doi.org/10.1111/j.13652958.2011.07776.x
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 GHJ, Lawrence C, Scott JA,
Spatafora JW, Turgeon BG, de Wit PJGM, 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. https://doi.org/10.1371/journal.ppat.1003037
Ohm RA, Aerts D, Wo ¨sten HAB, Lugones LG (2013)
The blue light receptor complex WC-1/2 of Schizophyllum commune is involved in mushroom
formation and protection against phototoxicity.
Environ Microbiol 15:943–955. https://doi.org/
10.1111/j.1462-2920.2012.02878.x
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. https://doi.org/
10.1016/J.FGB.2014.05.001
Parra G, Bradnam K, Korf I (2007) CEGMA: a pipeline
to accurately annotate core genes in eukaryotic
genomes. Bioinformatics 23:1061–1067. https://
doi.org/10.1093/bioinformatics/btm071
Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G,
Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JAE,
van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EGJ,
Debets AJM, Dekker P, van Dijck PWM, van Dijk
A, Dijkhuizen L, Driessen AJM, d’Enfert C, Geysens S, Goosen C, Groot GSP, de Groot PWJ, Guillemette T, Henrissat B, Herweijer M, van den
Hombergh JPTW, van den Hondel CAMJJ, van
der Heijden RTJM, van der Kaaij RM, Klis FM,
Kools HJ, Kubicek CP, van Kuyk PA, Lauber J,
Lu X, van der Maarel MJEC, Meulenberg R,
Menke H, Mortimer MA, Nielsen J, Oliver SG,
Olsthoorn M, Pal K, van Peij NNME, Ram AFJ,
Rinas U, Roubos JA, Sagt CMJ, Schmoll M, Sun J,
Ussery D, Varga J, Vervecken W, van de Vondervoort PJJ, Wedler H, Wo ¨sten HAB, Zeng A-P, van
Ooyen AJJ, Visser J, Stam H (2007) Genome
sequencing and analysis of the versatile cell factory
Aspergillus niger CBS 513.88. Nat Biotechnol
25:221–231. https://doi.org/10.1038/nbt1282
Peter M, Kohler A, Ohm RA, Kuo A, Kru ¨tzmann 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, Po ¨ggeler 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. https://doi.org/10.1038/
ncomms12662
Petersen TN, Brunak S, von Heijne G, Nielsen H (2011)
SignalP 4.0: discriminating signal peptides from
transmembrane regions. Nat Methods 8:785–786.
https://doi.org/10.1038/nmeth.1701
Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in large genomes. Bioinformatics 21:i351–i358. https://doi.org/10.1093/
bioinformatics/bti1018
Rawlings ND, Waller M, Barrett AJ, Bateman A (2014)
MEROPS: the database of proteolytic enzymes,
their substrates and inhibitors. Nucleic Acids Res
42:D503–D509. https://doi.org/10.1093/nar/gkt953
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 GHJ,
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 M-H, Howlett BJ (2011)
Effector diversification within compartments of
the Leptosphaeria maculans genome affected by
repeat-induced point mutations. Nat Commun
2:202. https://doi.org/10.1038/ncomms1189
Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR,
Fiddes JC, Hutchison CA, Slocombe PM, Smith M
(1977a) Nucleotide sequence of bacteriophage
jX174 DNA. Nature 265:687–695. https://doi.org/
10.1038/265687a0
Sanger F, Nicklen S, Coulson AR (1977b) DNA sequencing with chain-terminating inhibitors. Proc Natl
Acad Sci USA 74:5463–5467. https://doi.org/
10.1073/PNAS.74.12.5463
Shi T-Q, Liu G-N, Ji R-Y, Shi K, Song P, Ren L-J, Huang
H, Ji X-J (2017) CRISPR/Cas9-based genome editing of the filamentous fungi: the state of the art.
222
R. A. Ohm