in Repbase. Nat Rev Genet 9:411–412. https://doi.
org/10.1038/nrg2165-c1
Keller NP (2019) Fungal secondary metabolism: regulation, function and drug discovery. Nat Rev Microbiol 17:167–180. https://doi.org/10.1038/s41579018-0121-1
Keller NP, Turner G, Bennett JW (2005) Fungal secondary metabolism—from biochemistry to genomics.
Nat Rev Microbiol 3:937–947. https://doi.org/
10.1038/nrmicro1286
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle
TH, Zahler AM, Haussler D (2002) The human
genome browser at UCSC. Genome Res 12:996–
1006. https://doi.org/10.1101/gr.229102
Khaldi N, Seifuddin FT, Turner G, Haft D, Nierman
WC, Wolfe KH, Fedorova ND (2010) SMURF:
genomic mapping of fungal secondary metabolite
clusters. Fungal Genet Biol 47:736–741. https://doi.
org/10.1016/j.fgb.2010.06.003
Klosterman SJ, Subbarao KV, Kang S, Veronese P, Gold
SE, Thomma BPHJ, Chen Z, Henrissat B, Lee Y-H,
Park J, Garcia-Pedrajas MD, Barbara DJ, Anchieta
A, de Jonge R, Santhanam P, Maruthachalam K,
Atallah Z, Amyotte SG, Paz Z, Inderbitzin P, Hayes
RJ, Heiman DI, Young S, Zeng Q, Engels R, Galagan J, Cuomo CA, Dobinson KF, Ma L-J (2011)
Comparative genomics yields insights into niche
adaptation of plant vascular wilt pathogens. PLoS
Pathog 7:e1002137. https://doi.org/10.1371/journal.ppat.1002137
Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot
F, Canba ¨ck 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, Ho ¨gberg N, Johansson T, Khouja H-R, 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, VeneaultFourrey C, Zuccaro A, Tunlid A, Grigoriev IV,
Hibbett DS, Martin F, Martin F (2015) Convergent
losses of decay mechanisms and rapid turnover of
symbiosis genes in mycorrhizal mutualists. Nat
Genet 47:410–415. https://doi.org/10.1038/ng.3223
Krizsa ´n K, Alma ´si E ´ , Mere ´nyi Z, Sahu N, Vira ´gh M,
Ko ´szo ´ T, Mondo S, Kiss B, Ba ´lint B, Ku ¨es U, Barry
K, Cseklye J, Hegedu ¨s B, Henrissat B, Johnson J,
Lipzen A, Ohm RA, Nagy I, Pangilinan J, Yan J,
Xiong Y, Grigoriev IV, Hibbett DS, Nagy LG (2019)
Transcriptomic atlas of mushroom development
reveals conserved genes behind complex multicellularity in fungi. Proc Natl Acad Sci USA 116:7409–
7418. https://doi.org/10.1073/PNAS.1817822116
Krogh A, Larsson B, von Heijne G, Sonnhammer EL
(2001) Predicting transmembrane protein topology with a hidden Markov model: application to
complete genomes. J Mol Biol 305:567–580.
https://doi.org/10.1006/JMBI.2000.4315
Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S,
Casas-Flores S, Horwitz BA, Mukherjee PK,
Mukherjee M, Kredics L, Alcaraz LD, Aerts A,
Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F,
Deshpande N, von Do ¨hren H, Ebbole DJ, EsquivelNaranjo EU, Fekete E, Flipphi M, Glaser F, Go ´mezRodrı ´guez EY, Gruber S, Han C, Henrissat B, Hermosa R, Herna ´ndez-On ˜ate M, Karaffa L, Kosti I, Le
Crom S, Lindquist E, Lucas S, Lu ¨beck M, Lu ¨beck
PS, Margeot A, Metz B, Misra M, Nevalainen H,
Omann M, Packer N, Perrone G, Uresti-Rivera EE,
Salamov A, Schmoll M, Seiboth B, Shapiro H,
Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A,
Wilkinson HH, Zhang M, Coutinho PM, Kenerley
CM, Monte E, Baker SE, Grigoriev IV (2011) Comparative genome sequence analysis underscores
mycoparasitism as the ancestral life style of Trichoderma. Genome Biol 12:R40. https://doi.org/
10.1186/gb-2011-12-4-r40
Ku ¨es U, Liu Y (2000) Fruiting body production in
basidiomycetes. Appl Microbiol Biotechnol
54:141–152.
https://doi.org/10.1007/
s002530000396
Ku ¨es U, Navarro-Gonza ´lez M (2015) How do Agaricomycetes shape their fruiting bodies? 1. Morphological aspects of development. Fungal Biol Rev
29:63–97.
https://doi.org/10.1016/J.
FBR.2015.05.001
Lee E, Helt GA, Reese JT, Munoz-Torres MC, Childers
CP, Buels RM, Stein L, Holmes IH, Elsik CG, Lewis
SE (2013) Web Apollo: a web-based genomic
annotation editing platform. Genome Biol 14:R93.
https://doi.org/10.1186/gb-2013-14-8-r93
Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P,
Bruno D, Vamathevan J, Miranda M, Anderson IJ,
Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R,
Doering TL, Donlin MJ, D’Souza CA, Fox DS,
Grinberg V, Fu J, Fukushima M, Haas BJ, Huang
JC, Janbon G, Jones SJM, Koo HL, Krzywinski MI,
Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA,
Marra RE, Mathewson CA, Mitchell TG, Pertea M,
Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A,
Shin H, Shumway M, Specht CA, Suh BB, Tenney
A, Utterback TR, Wickes BL, Wortman JR, Wye
NH, Kronstad JW, Lodge JK, Heitman J, Davis RW,
Fraser CM, Hyman RW (2005) The genome of the
basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 307:1321–1324.
https://doi.org/10.1126/science.1103773
Lombard V, Golaconda Ramulu H, Drula E, Coutinho
PM, Henrissat B (2014) The carbohydrate-active
enzymes database (CAZy) in 2013. Nucleic Acids
Res 42:D490–D495. https://doi.org/10.1093/nar/
gkt1178
Lomsadze A, Burns PD, Borodovsky M (2014) Integration of mapped RNA-Seq reads into automatic
training of eukaryotic gene finding algorithm.
220
R. A. Ohm
org/10.1038/nrg2165-c1
Keller NP (2019) Fungal secondary metabolism: regulation, function and drug discovery. Nat Rev Microbiol 17:167–180. https://doi.org/10.1038/s41579018-0121-1
Keller NP, Turner G, Bennett JW (2005) Fungal secondary metabolism—from biochemistry to genomics.
Nat Rev Microbiol 3:937–947. https://doi.org/
10.1038/nrmicro1286
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle
TH, Zahler AM, Haussler D (2002) The human
genome browser at UCSC. Genome Res 12:996–
1006. https://doi.org/10.1101/gr.229102
Khaldi N, Seifuddin FT, Turner G, Haft D, Nierman
WC, Wolfe KH, Fedorova ND (2010) SMURF:
genomic mapping of fungal secondary metabolite
clusters. Fungal Genet Biol 47:736–741. https://doi.
org/10.1016/j.fgb.2010.06.003
Klosterman SJ, Subbarao KV, Kang S, Veronese P, Gold
SE, Thomma BPHJ, Chen Z, Henrissat B, Lee Y-H,
Park J, Garcia-Pedrajas MD, Barbara DJ, Anchieta
A, de Jonge R, Santhanam P, Maruthachalam K,
Atallah Z, Amyotte SG, Paz Z, Inderbitzin P, Hayes
RJ, Heiman DI, Young S, Zeng Q, Engels R, Galagan J, Cuomo CA, Dobinson KF, Ma L-J (2011)
Comparative genomics yields insights into niche
adaptation of plant vascular wilt pathogens. PLoS
Pathog 7:e1002137. https://doi.org/10.1371/journal.ppat.1002137
Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot
F, Canba ¨ck 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, Ho ¨gberg N, Johansson T, Khouja H-R, 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, VeneaultFourrey C, Zuccaro A, Tunlid A, Grigoriev IV,
Hibbett DS, Martin F, Martin F (2015) Convergent
losses of decay mechanisms and rapid turnover of
symbiosis genes in mycorrhizal mutualists. Nat
Genet 47:410–415. https://doi.org/10.1038/ng.3223
Krizsa ´n K, Alma ´si E ´ , Mere ´nyi Z, Sahu N, Vira ´gh M,
Ko ´szo ´ T, Mondo S, Kiss B, Ba ´lint B, Ku ¨es U, Barry
K, Cseklye J, Hegedu ¨s B, Henrissat B, Johnson J,
Lipzen A, Ohm RA, Nagy I, Pangilinan J, Yan J,
Xiong Y, Grigoriev IV, Hibbett DS, Nagy LG (2019)
Transcriptomic atlas of mushroom development
reveals conserved genes behind complex multicellularity in fungi. Proc Natl Acad Sci USA 116:7409–
7418. https://doi.org/10.1073/PNAS.1817822116
Krogh A, Larsson B, von Heijne G, Sonnhammer EL
(2001) Predicting transmembrane protein topology with a hidden Markov model: application to
complete genomes. J Mol Biol 305:567–580.
https://doi.org/10.1006/JMBI.2000.4315
Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S,
Casas-Flores S, Horwitz BA, Mukherjee PK,
Mukherjee M, Kredics L, Alcaraz LD, Aerts A,
Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F,
Deshpande N, von Do ¨hren H, Ebbole DJ, EsquivelNaranjo EU, Fekete E, Flipphi M, Glaser F, Go ´mezRodrı ´guez EY, Gruber S, Han C, Henrissat B, Hermosa R, Herna ´ndez-On ˜ate M, Karaffa L, Kosti I, Le
Crom S, Lindquist E, Lucas S, Lu ¨beck M, Lu ¨beck
PS, Margeot A, Metz B, Misra M, Nevalainen H,
Omann M, Packer N, Perrone G, Uresti-Rivera EE,
Salamov A, Schmoll M, Seiboth B, Shapiro H,
Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A,
Wilkinson HH, Zhang M, Coutinho PM, Kenerley
CM, Monte E, Baker SE, Grigoriev IV (2011) Comparative genome sequence analysis underscores
mycoparasitism as the ancestral life style of Trichoderma. Genome Biol 12:R40. https://doi.org/
10.1186/gb-2011-12-4-r40
Ku ¨es U, Liu Y (2000) Fruiting body production in
basidiomycetes. Appl Microbiol Biotechnol
54:141–152.
https://doi.org/10.1007/
s002530000396
Ku ¨es U, Navarro-Gonza ´lez M (2015) How do Agaricomycetes shape their fruiting bodies? 1. Morphological aspects of development. Fungal Biol Rev
29:63–97.
https://doi.org/10.1016/J.
FBR.2015.05.001
Lee E, Helt GA, Reese JT, Munoz-Torres MC, Childers
CP, Buels RM, Stein L, Holmes IH, Elsik CG, Lewis
SE (2013) Web Apollo: a web-based genomic
annotation editing platform. Genome Biol 14:R93.
https://doi.org/10.1186/gb-2013-14-8-r93
Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P,
Bruno D, Vamathevan J, Miranda M, Anderson IJ,
Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R,
Doering TL, Donlin MJ, D’Souza CA, Fox DS,
Grinberg V, Fu J, Fukushima M, Haas BJ, Huang
JC, Janbon G, Jones SJM, Koo HL, Krzywinski MI,
Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA,
Marra RE, Mathewson CA, Mitchell TG, Pertea M,
Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A,
Shin H, Shumway M, Specht CA, Suh BB, Tenney
A, Utterback TR, Wickes BL, Wortman JR, Wye
NH, Kronstad JW, Lodge JK, Heitman J, Davis RW,
Fraser CM, Hyman RW (2005) The genome of the
basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 307:1321–1324.
https://doi.org/10.1126/science.1103773
Lombard V, Golaconda Ramulu H, Drula E, Coutinho
PM, Henrissat B (2014) The carbohydrate-active
enzymes database (CAZy) in 2013. Nucleic Acids
Res 42:D490–D495. https://doi.org/10.1093/nar/
gkt1178
Lomsadze A, Burns PD, Borodovsky M (2014) Integration of mapped RNA-Seq reads into automatic
training of eukaryotic gene finding algorithm.
220
R. A. Ohm