Appl Microbiol Biotechnol 101:7435–7443. https://
doi.org/10.1007/s00253-017-8497-9
Shi-Kunne X, Faino L, van den Berg GCM, Thomma
BPHJ, Seidl MF (2018) Evolution within the fungal
genus Verticillium is characterized by chromosomal rearrangement and gene loss. Environ
Microbiol 20:1362–1373. https://doi.org/10.1111/
1462-2920.14037
Sima ˜o FA, Waterhouse RM, Ioannidis P, Kriventseva
EV, Zdobnov EM (2015) BUSCO: assessing
genome assembly and annotation completeness
with single-copy orthologs. Bioinformatics
31:3210–3212.
https://doi.org/10.1093/bioinformatics/btv351
Simpson JT, Wong K, Jackman SD, Schein JE, Jones
SJM, Birol I (2009) ABySS: a parallel assembler for
short read sequence data. Genome Res 19:1117–
1123. https://doi.org/10.1101/gr.089532.108
Sipos G, Prasanna AN, Walter MC, O’Connor E, Ba ´lint
B, Krizsa ´n K, Kiss B, Hess J, Varga T, Slot J, Riley
R, Bo ´ka B, Rigling D, Barry K, Lee J, Mihaltcheva S,
LaButti K, Lipzen A, Waldron R, Moloney NM,
Sperisen C, Kredics L, Va ´gvo ¨lgyi C, Patrignani A,
Fitzpatrick D, Nagy I, Doyle S, Anderson JB, Grigoriev IV, Gu ¨ldener U, Mu ¨nsterko ¨tter M, Nagy LG
(2017) Genome expansion and lineage-specific
genetic innovations in the forest pathogenic fungi
Armillaria. Nat Ecol Evol 1:1931–1941. https://doi.
org/10.1038/s41559-017-0347-8
Smit AFA, Hubley R, Green P (2015) RepeatMasker
Open-4.0 2013-2015. http://www.repeatmasker.org
Stanke M, Waack S (2003) Gene prediction with a
hidden Markov model and a new intron submodel.
Bioinformatics 19:ii215–ii225. https://doi.org/
10.1093/bioinformatics/btg1080
Stein LD (2013) Using GBrowse 2.0 to visualize and
share next-generation sequence data. Brief Bioinform 14:162–171. https://doi.org/10.1093/bib/
bbt001
Sugano SS, Suzuki H, Shimokita E, Chiba H, Noji S,
Osakabe Y, Osakabe K (2017) Genome editing in
the mushroom-forming basidiomycete Coprinopsis cinerea, optimized by a high-throughput transformation system. Sci Rep 7:1260. https://doi.org/
10.1038/s41598-017-00883-5
Terashima K, Yuki K, Muraguchi H, Akiyama M,
Kamada T (2005) The dst1 gene involved in mushroom photomorphogenesis of Coprinus cinereus
encodes a putative photoreceptor for blue light.
Genetics 171:101–108. https://doi.org/10.1534/
genetics.104.040048
Testa AC, Oliver RP, Hane JK (2016) OcculterCut: a
comprehensive survey of AT-rich regions in fungal
genomes. Genome Biol Evol 8:2044–2064. https://
doi.org/10.1093/gbe/evw121
The C elegans Sequencing Consortium (1998) Genome
sequence of the nematode C. elegans: a platform
for investigating biology. Science 282:2012–2018.
https://doi.org/10.1126/SCIENCE.282.5396.2012
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
(2014) Genome sequencing provides insight into
the reproductive biology, nutritional mode and
ploidy of the fern pathogen Mixia osmundae.
New Phytol 202:554–564. https://doi.org/10.1111/
nph.12653
Varga T, Krizsa ´n K, Fo ¨ldi C, Dima B, Sa ´nchez-Garcı ´a M,
Sa ´nchez-Ramı ´rez S, Szo ¨llo ˝si GJ, Szarka ´ndi JG,
Papp V, Albert L, Andreopoulos W, Angelini C,
Antonı ´n V, Barry KW, Bougher NL, Buchanan P,
Buyck B, Bense V, Catcheside P, Chovatia M, Cooper J, Da ¨mon W, Desjardin D, Finy P, Geml J,
Haridas S, Hughes K, Justo A, Karasin ´ski D, Kautmanova I, Kiss B, Kocsube ´ S, Kotiranta H, LaButti
KM, Lechner BE, Liimatainen K, Lipzen A, Luka ´cs
Z, Mihaltcheva S, Morgado LN, Niskanen T, Noordeloos ME, Ohm RA, Ortiz-Santana B, Ovrebo C,
Ra ´cz N, Riley R, Savchenko A, Shiryaev A, Soop K,
Spirin V, Szebenyi C, Toms ˇovsky ´ M, Tulloss RE,
Uehling J, Grigoriev IV, Va ´gvo ¨lgyi C, Papp T,
Martin FM, Miettinen O, Hibbett DS, Nagy LG
(2019) Megaphylogeny resolves global patterns of
mushroom evolution. Nat Ecol Evol 3:668–678.
https://doi.org/10.1038/s41559-019-0834-1
Vesth TC, Nybo JL, Theobald S, Frisvad JC, Larsen TO,
Nielsen KF, Hoof JB, Brandl J, Salamov A, Riley R,
Gladden JM, Phatale P, Nielsen MT, Lyhne EK,
Kogle ME, Strasser K, McDonnell E, Barry K,
Clum A, Chen C, LaButti K, Haridas S, Nolan M,
Sandor L, Kuo A, Lipzen A, Hainaut M, Drula E,
Tsang A, Magnuson JK, Henrissat B, Wiebenga A,
Simmons BA, Ma ¨kela ¨ MR, de Vries RP, Grigoriev
IV, Mortensen UH, Baker SE, Andersen MR (2018)
Investigation of inter- and intraspecies variation
through genome sequencing of Aspergillus section
Nigri. Nat Genet 50:1688–1695. https://doi.org/
10.1038/s41588-018-0246-1
Vonk PJ, Escobar N, Wo ¨sten HAB, Lugones LG, Ohm
RA (2019) High-throughput targeted gene deletion
in the model mushroom Schizophyllum commune
using pre-assembled Cas9 ribonucleoproteins. Sci
Rep 9(1):7632. https://doi.org/10.1038/s41598-01944133-2
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A,
Sakthikumar S, Cuomo CA, Zeng Q, Wortman J,
Young SK, Earl AM (2014) Pilon: an integrated
tool for comprehensive microbial variant detection and genome assembly improvement. PLoS
One 9:e112963. https://doi.org/10.1371/journal.
pone.0112963
Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P,
Chalhoub B, Flavell A, Leroy P, Morgante M,
9 Fungal Genomics
223
doi.org/10.1007/s00253-017-8497-9
Shi-Kunne X, Faino L, van den Berg GCM, Thomma
BPHJ, Seidl MF (2018) Evolution within the fungal
genus Verticillium is characterized by chromosomal rearrangement and gene loss. Environ
Microbiol 20:1362–1373. https://doi.org/10.1111/
1462-2920.14037
Sima ˜o FA, Waterhouse RM, Ioannidis P, Kriventseva
EV, Zdobnov EM (2015) BUSCO: assessing
genome assembly and annotation completeness
with single-copy orthologs. Bioinformatics
31:3210–3212.
https://doi.org/10.1093/bioinformatics/btv351
Simpson JT, Wong K, Jackman SD, Schein JE, Jones
SJM, Birol I (2009) ABySS: a parallel assembler for
short read sequence data. Genome Res 19:1117–
1123. https://doi.org/10.1101/gr.089532.108
Sipos G, Prasanna AN, Walter MC, O’Connor E, Ba ´lint
B, Krizsa ´n K, Kiss B, Hess J, Varga T, Slot J, Riley
R, Bo ´ka B, Rigling D, Barry K, Lee J, Mihaltcheva S,
LaButti K, Lipzen A, Waldron R, Moloney NM,
Sperisen C, Kredics L, Va ´gvo ¨lgyi C, Patrignani A,
Fitzpatrick D, Nagy I, Doyle S, Anderson JB, Grigoriev IV, Gu ¨ldener U, Mu ¨nsterko ¨tter M, Nagy LG
(2017) Genome expansion and lineage-specific
genetic innovations in the forest pathogenic fungi
Armillaria. Nat Ecol Evol 1:1931–1941. https://doi.
org/10.1038/s41559-017-0347-8
Smit AFA, Hubley R, Green P (2015) RepeatMasker
Open-4.0 2013-2015. http://www.repeatmasker.org
Stanke M, Waack S (2003) Gene prediction with a
hidden Markov model and a new intron submodel.
Bioinformatics 19:ii215–ii225. https://doi.org/
10.1093/bioinformatics/btg1080
Stein LD (2013) Using GBrowse 2.0 to visualize and
share next-generation sequence data. Brief Bioinform 14:162–171. https://doi.org/10.1093/bib/
bbt001
Sugano SS, Suzuki H, Shimokita E, Chiba H, Noji S,
Osakabe Y, Osakabe K (2017) Genome editing in
the mushroom-forming basidiomycete Coprinopsis cinerea, optimized by a high-throughput transformation system. Sci Rep 7:1260. https://doi.org/
10.1038/s41598-017-00883-5
Terashima K, Yuki K, Muraguchi H, Akiyama M,
Kamada T (2005) The dst1 gene involved in mushroom photomorphogenesis of Coprinus cinereus
encodes a putative photoreceptor for blue light.
Genetics 171:101–108. https://doi.org/10.1534/
genetics.104.040048
Testa AC, Oliver RP, Hane JK (2016) OcculterCut: a
comprehensive survey of AT-rich regions in fungal
genomes. Genome Biol Evol 8:2044–2064. https://
doi.org/10.1093/gbe/evw121
The C elegans Sequencing Consortium (1998) Genome
sequence of the nematode C. elegans: a platform
for investigating biology. Science 282:2012–2018.
https://doi.org/10.1126/SCIENCE.282.5396.2012
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
(2014) Genome sequencing provides insight into
the reproductive biology, nutritional mode and
ploidy of the fern pathogen Mixia osmundae.
New Phytol 202:554–564. https://doi.org/10.1111/
nph.12653
Varga T, Krizsa ´n K, Fo ¨ldi C, Dima B, Sa ´nchez-Garcı ´a M,
Sa ´nchez-Ramı ´rez S, Szo ¨llo ˝si GJ, Szarka ´ndi JG,
Papp V, Albert L, Andreopoulos W, Angelini C,
Antonı ´n V, Barry KW, Bougher NL, Buchanan P,
Buyck B, Bense V, Catcheside P, Chovatia M, Cooper J, Da ¨mon W, Desjardin D, Finy P, Geml J,
Haridas S, Hughes K, Justo A, Karasin ´ski D, Kautmanova I, Kiss B, Kocsube ´ S, Kotiranta H, LaButti
KM, Lechner BE, Liimatainen K, Lipzen A, Luka ´cs
Z, Mihaltcheva S, Morgado LN, Niskanen T, Noordeloos ME, Ohm RA, Ortiz-Santana B, Ovrebo C,
Ra ´cz N, Riley R, Savchenko A, Shiryaev A, Soop K,
Spirin V, Szebenyi C, Toms ˇovsky ´ M, Tulloss RE,
Uehling J, Grigoriev IV, Va ´gvo ¨lgyi C, Papp T,
Martin FM, Miettinen O, Hibbett DS, Nagy LG
(2019) Megaphylogeny resolves global patterns of
mushroom evolution. Nat Ecol Evol 3:668–678.
https://doi.org/10.1038/s41559-019-0834-1
Vesth TC, Nybo JL, Theobald S, Frisvad JC, Larsen TO,
Nielsen KF, Hoof JB, Brandl J, Salamov A, Riley R,
Gladden JM, Phatale P, Nielsen MT, Lyhne EK,
Kogle ME, Strasser K, McDonnell E, Barry K,
Clum A, Chen C, LaButti K, Haridas S, Nolan M,
Sandor L, Kuo A, Lipzen A, Hainaut M, Drula E,
Tsang A, Magnuson JK, Henrissat B, Wiebenga A,
Simmons BA, Ma ¨kela ¨ MR, de Vries RP, Grigoriev
IV, Mortensen UH, Baker SE, Andersen MR (2018)
Investigation of inter- and intraspecies variation
through genome sequencing of Aspergillus section
Nigri. Nat Genet 50:1688–1695. https://doi.org/
10.1038/s41588-018-0246-1
Vonk PJ, Escobar N, Wo ¨sten HAB, Lugones LG, Ohm
RA (2019) High-throughput targeted gene deletion
in the model mushroom Schizophyllum commune
using pre-assembled Cas9 ribonucleoproteins. Sci
Rep 9(1):7632. https://doi.org/10.1038/s41598-01944133-2
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A,
Sakthikumar S, Cuomo CA, Zeng Q, Wortman J,
Young SK, Earl AM (2014) Pilon: an integrated
tool for comprehensive microbial variant detection and genome assembly improvement. PLoS
One 9:e112963. https://doi.org/10.1371/journal.
pone.0112963
Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P,
Chalhoub B, Flavell A, Leroy P, Morgante M,
9 Fungal Genomics
223