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Nehls U, Niculita-Hirzel H, Oudot-Le Secq MP,
Peter M, Quesneville H, Rajashekar B, Reich M,
Rouhier N, Schmutz J, Yin T, Chalot M, Henrissat
B, Ku ¨es U, Lucas S, Van de Peer Y, Podila GK, Polle
A, Pukkila PJ, Richardson PM, Rouze ´ P, Sanders
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Percudani R, Porcel B, Rubini A, Amicucci A,
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A, Bue ´e M, Cantarel B, Chevalier G, Couloux A, Da
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M, Pacioni G, Quesneville H, Riccioni C, Ruotolo
R, Splivallo R, Stocchi V, Tisserant E, Viscomi AR,
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Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EGJ, Grigoriev IV,
Harris P, Jackson M, Kubicek CP, Han CS, Ho I,
Larrondo LF, de Leon AL, Magnuson JK, Merino S,
Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N,
Westerholm-Parvinen A, Schoch CL, Yao J, Barabote R, Nelson MA, Detter C, Bruce D, Kuske CR,
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analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol
26:553–560.
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Martino E, Morin E, Grelet G-A, Kuo A, Kohler A,
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Lindquist EA, Lipzen A, Khouja H-R, Magnuson J,
Murat C, Ohm RA, Singer SW, Spatafora JW,
Wang M, Veneault-Fourrey C, Henrissat B, Grigoriev IV, Martin FM, Perotto S (2018) Comparative
genomics and transcriptomics depict ericoid
mycorrhizal fungi as versatile saprotrophs and
plant mutualists. New Phytol 217:1213–1229.
https://doi.org/10.1111/nph.14974
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genome annotation pipeline using evidence-based
gene model evaluation. Bioinformatics 33:2936–
2937.
https://doi.org/10.1093/bioinformatics/
btx353
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Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen
Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu
Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H,
Wang J, Lam T-W, Wang J (2012) SOAPdenovo2:
an empirically improved memory-efficient shortread de novo assembler. Gigascience 1:18. https://
doi.org/10.1186/2047-217X-1-18
Ma L-J, van der Does HC, Borkovich KA, Coleman JJ,
Daboussi M-J, Di Pietro A, Dufresne M, Freitag M,
Grabherr M, Henrissat B, Houterman PM, Kang S,
Shim W-B, Woloshuk C, Xie X, Xu J-R, Antoniw J,
Baker SE, Bluhm BH, Breakspear A, Brown DW,
Butchko RAE, Chapman S, Coulson R, Coutinho
PM, Danchin EGJ, Diener A, Gale LR, Gardiner
DM, Goff S, Hammond-Kosack KE, Hilburn K,
Hua-Van A, Jonkers W, Kazan K, Kodira CD,
Koehrsen M, Kumar L, Lee Y-H, Li L, Manners
JM, Miranda-Saavedra D, Mukherjee M, Park G,
Park J, Park S-Y, Proctor RH, Regev A, RuizRoldan MC, Sain D, Sakthikumar S, Sykes S,
Schwartz DC, Turgeon BG, Wapinski I, Yoder O,
Young S, Zeng Q, Zhou S, Galagan J, Cuomo CA,
Kistler HC, Rep M (2010) Comparative genomics
reveals mobile pathogenicity chromosomes in
Fusarium. Nature 464:367–373. https://doi.org/
10.1038/nature08850
Mardis ER (2017) DNA sequencing technologies: 2006–
2016. Nat Protoc 12:213–218. https://doi.org/
10.1038/nprot.2016.182
Margulies M, Egholm M, Altman WE, Attiya S, Bader
JS, Bemben LA, Berka J, Braverman MS, Chen Y-J,
Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV,
Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP,
Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim
J-B, Knight JR, Lanza JR, Leamon JH, Lefkowitz
SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB,
McDade KE, McKenna MP, Myers EW, Nickerson
E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT,
Sarkis GJ, Simons JF, Simpson JW, Srinivasan M,
Tartaro KR, Tomasz A, Vogt KA, Volkmer GA,
Wang SH, Wang Y, Weiner MP, Yu P, Begley RF,
Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature
437:376–380. https://doi.org/10.1038/nature03959
Martin F, Aerts A, Ahre ´n D, Brun A, Danchin EGJ,
Duchaussoy F, Gibon J, Kohler A, Lindquist E,
Pereda V, Salamov A, Shapiro HJ, Wuyts J, Blaudez D, Bue ´e M, Brokstein P, Canba ¨ck B, Cohen D,
Courty PE, Coutinho PM, Delaruelle C, Detter JC,
Deveau A, DiFazio S, Duplessis S, FraissinetTachet L, Lucic E, Frey-Klett P, Fourrey C, Feussner I, Gay G, Grimwood J, Hoegger PJ, Jain P,
Kilaru S, Labbe ´ J, Lin YC, Legue ´ V, Le Tacon F,
Marmeisse R, Melayah D, Montanini B, Muratet M,
Nehls U, Niculita-Hirzel H, Oudot-Le Secq MP,
Peter M, Quesneville H, Rajashekar B, Reich M,
Rouhier N, Schmutz J, Yin T, Chalot M, Henrissat
B, Ku ¨es U, Lucas S, Van de Peer Y, Podila GK, Polle
A, Pukkila PJ, Richardson PM, Rouze ´ P, Sanders
IR, Stajich JE, Tunlid A, Tuskan G, Grigoriev IV
(2008) The genome of Laccaria bicolor provides
insights into mycorrhizal symbiosis. Nature
452:88–92. https://doi.org/10.1038/nature06556
Martin F, Kohler A, Murat C, Balestrini R, Coutinho
PM, Jaillon O, Montanini B, Morin E, Noel B,
Percudani R, Porcel B, Rubini A, Amicucci A,
Amselem J, Anthouard V, Arcioni S, Artiguenave
F, Aury J-M, Ballario P, Bolchi A, Brenna A, Brun
A, Bue ´e M, Cantarel B, Chevalier G, Couloux A, Da
Silva C, Denoeud F, Duplessis S, Ghignone S, Hilselberger B, Iotti M, Marc ¸ais B, Mello A, Miranda
M, Pacioni G, Quesneville H, Riccioni C, Ruotolo
R, Splivallo R, Stocchi V, Tisserant E, Viscomi AR,
Zambonelli A, Zampieri E, Henrissat B, Lebrun MH, Paolocci F, Bonfante P, Ottonello S, Wincker P
(2010) Pe ´rigord black truffle genome uncovers
evolutionary origins and mechanisms of symbiosis. Nature 464:1033–1038. https://doi.org/10.1038/
nature08867
Martinez D, Berka RM, Henrissat B, Saloheimo M,
Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EGJ, Grigoriev IV,
Harris P, Jackson M, Kubicek CP, Han CS, Ho I,
Larrondo LF, de Leon AL, Magnuson JK, Merino S,
Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N,
Westerholm-Parvinen A, Schoch CL, Yao J, Barabote R, Nelson MA, Detter C, Bruce D, Kuske CR,
Xie G, Richardson P, Rokhsar DS, Lucas SM,
Rubin EM, Dunn-Coleman N, Ward M, Brettin
TS, Brettin TS (2008) Genome sequencing and
analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol
26:553–560.
https://doi.org/10.1038/
nbt1403
Martino E, Morin E, Grelet G-A, 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 H-R, Magnuson J,
Murat C, Ohm RA, Singer SW, Spatafora JW,
Wang M, Veneault-Fourrey C, Henrissat B, Grigoriev IV, Martin FM, Perotto S (2018) Comparative
genomics and transcriptomics depict ericoid
mycorrhizal fungi as versatile saprotrophs and
plant mutualists. New Phytol 217:1213–1229.
https://doi.org/10.1111/nph.14974
Min B, Grigoriev IV, Choi I-G (2017) FunGAP: fungal
genome annotation pipeline using evidence-based
gene model evaluation. Bioinformatics 33:2936–
2937.
https://doi.org/10.1093/bioinformatics/
btx353
Nu ¨tzmann H-W, Scazzocchio C, Osbourn A (2018)
Metabolic gene clusters in eukaryotes. Annu Rev
9 Fungal Genomics
221