tive analysis with A. fumigatus and A. oryzae.
Nature 438:1105–1115. https://doi.org/10.1038/
nature04341
Ghurye J, Pop M (2019) Modern technologies and algorithms for scaffolding assembled genomes. PLoS
Comput Biol 15:e1006994. https://doi.org/10.1371/
journal.pcbi.1006994
Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B,
Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG (1996) Life with
6000 genes. Science 274(546):563–567. https://doi.
org/10.1126/SCIENCE.274.5287.546
Goodwin SB, Ben M’Barek S, Dhillon B, Wittenberg
AHJ, Crane CF, Hane JK, Foster AJ, Van der Lee
TAJ, Grimwood J, Aerts A, Antoniw J, Bailey A,
Bluhm B, Bowler J, Bristow J, van der Burgt A,
Canto-Canche ´ B, Churchill ACL, Conde-Ferra `ez
L, Cools HJ, Coutinho PM, Csukai M, Dehal P, De
Wit P, Donzelli B, van de Geest HC, van Ham
RCHJ, Hammond-Kosack KE, Henrissat B, Kilian
A, Kobayashi AK, Koopmann E, Kourmpetis Y,
Kuzniar A, Lindquist E, Lombard V, Maliepaard
C, Martins N, Mehrabi R, Nap JPH, Ponomarenko
A, Rudd JJ, Salamov A, Schmutz J, Schouten HJ,
Shapiro H, Stergiopoulos I, Torriani SFF, Tu H, de
Vries RP, Waalwijk C, Ware SB, Wiebenga A,
Zwiers L-H, Oliver RP, Grigoriev IV, Kema GHJ
(2011) Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and
stealth pathogeness. PLoS Genet 7:e1002070.
https://doi.org/10.1371/journal.pgen.1002070
Grigoriev IV, Cullen D, Goodwin SB, Hibbett D, Jeffries
TW, Kubicek CP, Kuske C, Magnuson JK, Martin
F, Spatafora JW, Tsang A, Baker SE (2011) Fueling
the future with fungal genomics. Mycology 2:192–
209. https://doi.org/10.1080/21501203.2011.584577
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 (2014) MycoCosm portal: gearing up
for 1000 fungal genomes. Nucleic Acids Res 42:
D699–D704. https://doi.org/10.1093/nar/gkt1183
Grimm D, Wo ¨sten HAB (2018) Mushroom cultivation
in the circular economy. Appl Microbiol Biotechnol
102:7795–7803.
https://doi.org/10.1007/
s00253-018-9226-8
Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith
RK Jr, Hannick LI, Maiti R, Ronning CM, Rusch
DB, Town CD, Salzberg SL, White O (2003)
Improving the Arabidopsis genome annotation
using maximal transcript alignment assemblies.
Nucleic Acids Res 31:5654–5666. https://doi.org/
10.1093/nar/gkg770
Hane JK, Rouxel T, Howlett BJ, Kema GHJ, Goodwin
SB, Oliver RP (2011) A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi. Genome Biol 12:R45. https://doi.org/
10.1186/gb-2011-12-5-r45
Haridas S, Salamov A, Grigoriev IV (2018) Fungal
genome annotation. Methods Mol Biol 1775:171–
184
Harvey CJB, Tang M, Schlecht U, Horecka J, Fischer CR,
Lin H-C, Li J, Naughton B, Cherry J, Miranda M, Li
YF, Chu AM, Hennessy JR, Vandova GA, Inglis D,
Aiyar RS, Steinmetz LM, Davis RW, Medema MH,
Sattely E, Khosla C, St Onge RP, Tang Y, Hillenmeyer ME (2018) HEx: a heterologous expression
platform for the discovery of fungal natural products. Sci Adv 4:eaar5459. https://doi.org/10.1126/
sciadv.aar5459
Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke
M (2016) BRAKER1: unsupervised RNA-Seqbased genome annotation with GeneMark-ET and
AUGUSTUS. Bioinformatics 32:767–769. https://
doi.org/10.1093/bioinformatics/btv661
Horton P, Park K-J, Obayashi T, Fujita N, Harada H,
Adams-Collier CJ, Nakai K (2007) WoLF PSORT:
protein localization predictor. Nucleic Acids Res
35:W585–W587.
https://doi.org/10.1093/nar/
gkm259
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman
A, Binns D, Bork P, Das U, Daugherty L, Duquenne
L, Finn RD, Gough J, Haft D, Hulo N, Kahn D,
Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez
R, Madera M, Maslen J, McAnulla C, McDowall J,
Mistry J, Mitchell A, Mulder N, Natale D, Orengo
C, Quinn AF, Selengut JD, Sigrist CJA, Thimma M,
Thomas PD, Valentin F, Wilson D, Wu CH, Yeats
C (2009) InterPro: the integrative protein signature database. Nucleic Acids Res 37:D211–D215.
https://doi.org/10.1093/nar/gkn785
International Human Genome Sequencing Consortium
(2001) Initial sequencing and analysis of the
human genome. Nature 409:860–921. https://doi.
org/10.1038/35057062
Jain M, Olsen HE, Paten B, Akeson M (2016) The
Oxford Nanopore MinION: delivery of nanopore
sequencing to the genomics community. Genome
Biol 17:239. https://doi.org/10.1186/s13059-0161103-0
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P,
Kohany O, Walichiewicz J (2005) Repbase update,
a database of eukaryotic repetitive elements. Cytogenet Genome Res 110:462–467. https://doi.org/
10.1159/000084979
Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia
of genes and genomes. Nucleic Acids Res 28:27–30.
https://doi.org/10.1093/nar/28.1.27
Kapitonov VV, Jurka J (2001) Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci USA
98:8714–8719.
https://doi.org/10.1073/
pnas.151269298
Kapitonov VV, Jurka J (2008) A universal classification
of eukaryotic transposable elements implemented
9 Fungal Genomics
219
Nature 438:1105–1115. https://doi.org/10.1038/
nature04341
Ghurye J, Pop M (2019) Modern technologies and algorithms for scaffolding assembled genomes. PLoS
Comput Biol 15:e1006994. https://doi.org/10.1371/
journal.pcbi.1006994
Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B,
Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG (1996) Life with
6000 genes. Science 274(546):563–567. https://doi.
org/10.1126/SCIENCE.274.5287.546
Goodwin SB, Ben M’Barek S, Dhillon B, Wittenberg
AHJ, Crane CF, Hane JK, Foster AJ, Van der Lee
TAJ, Grimwood J, Aerts A, Antoniw J, Bailey A,
Bluhm B, Bowler J, Bristow J, van der Burgt A,
Canto-Canche ´ B, Churchill ACL, Conde-Ferra `ez
L, Cools HJ, Coutinho PM, Csukai M, Dehal P, De
Wit P, Donzelli B, van de Geest HC, van Ham
RCHJ, Hammond-Kosack KE, Henrissat B, Kilian
A, Kobayashi AK, Koopmann E, Kourmpetis Y,
Kuzniar A, Lindquist E, Lombard V, Maliepaard
C, Martins N, Mehrabi R, Nap JPH, Ponomarenko
A, Rudd JJ, Salamov A, Schmutz J, Schouten HJ,
Shapiro H, Stergiopoulos I, Torriani SFF, Tu H, de
Vries RP, Waalwijk C, Ware SB, Wiebenga A,
Zwiers L-H, Oliver RP, Grigoriev IV, Kema GHJ
(2011) Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and
stealth pathogeness. PLoS Genet 7:e1002070.
https://doi.org/10.1371/journal.pgen.1002070
Grigoriev IV, Cullen D, Goodwin SB, Hibbett D, Jeffries
TW, Kubicek CP, Kuske C, Magnuson JK, Martin
F, Spatafora JW, Tsang A, Baker SE (2011) Fueling
the future with fungal genomics. Mycology 2:192–
209. https://doi.org/10.1080/21501203.2011.584577
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 (2014) MycoCosm portal: gearing up
for 1000 fungal genomes. Nucleic Acids Res 42:
D699–D704. https://doi.org/10.1093/nar/gkt1183
Grimm D, Wo ¨sten HAB (2018) Mushroom cultivation
in the circular economy. Appl Microbiol Biotechnol
102:7795–7803.
https://doi.org/10.1007/
s00253-018-9226-8
Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith
RK Jr, Hannick LI, Maiti R, Ronning CM, Rusch
DB, Town CD, Salzberg SL, White O (2003)
Improving the Arabidopsis genome annotation
using maximal transcript alignment assemblies.
Nucleic Acids Res 31:5654–5666. https://doi.org/
10.1093/nar/gkg770
Hane JK, Rouxel T, Howlett BJ, Kema GHJ, Goodwin
SB, Oliver RP (2011) A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi. Genome Biol 12:R45. https://doi.org/
10.1186/gb-2011-12-5-r45
Haridas S, Salamov A, Grigoriev IV (2018) Fungal
genome annotation. Methods Mol Biol 1775:171–
184
Harvey CJB, Tang M, Schlecht U, Horecka J, Fischer CR,
Lin H-C, Li J, Naughton B, Cherry J, Miranda M, Li
YF, Chu AM, Hennessy JR, Vandova GA, Inglis D,
Aiyar RS, Steinmetz LM, Davis RW, Medema MH,
Sattely E, Khosla C, St Onge RP, Tang Y, Hillenmeyer ME (2018) HEx: a heterologous expression
platform for the discovery of fungal natural products. Sci Adv 4:eaar5459. https://doi.org/10.1126/
sciadv.aar5459
Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke
M (2016) BRAKER1: unsupervised RNA-Seqbased genome annotation with GeneMark-ET and
AUGUSTUS. Bioinformatics 32:767–769. https://
doi.org/10.1093/bioinformatics/btv661
Horton P, Park K-J, Obayashi T, Fujita N, Harada H,
Adams-Collier CJ, Nakai K (2007) WoLF PSORT:
protein localization predictor. Nucleic Acids Res
35:W585–W587.
https://doi.org/10.1093/nar/
gkm259
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman
A, Binns D, Bork P, Das U, Daugherty L, Duquenne
L, Finn RD, Gough J, Haft D, Hulo N, Kahn D,
Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez
R, Madera M, Maslen J, McAnulla C, McDowall J,
Mistry J, Mitchell A, Mulder N, Natale D, Orengo
C, Quinn AF, Selengut JD, Sigrist CJA, Thimma M,
Thomas PD, Valentin F, Wilson D, Wu CH, Yeats
C (2009) InterPro: the integrative protein signature database. Nucleic Acids Res 37:D211–D215.
https://doi.org/10.1093/nar/gkn785
International Human Genome Sequencing Consortium
(2001) Initial sequencing and analysis of the
human genome. Nature 409:860–921. https://doi.
org/10.1038/35057062
Jain M, Olsen HE, Paten B, Akeson M (2016) The
Oxford Nanopore MinION: delivery of nanopore
sequencing to the genomics community. Genome
Biol 17:239. https://doi.org/10.1186/s13059-0161103-0
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P,
Kohany O, Walichiewicz J (2005) Repbase update,
a database of eukaryotic repetitive elements. Cytogenet Genome Res 110:462–467. https://doi.org/
10.1159/000084979
Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia
of genes and genomes. Nucleic Acids Res 28:27–30.
https://doi.org/10.1093/nar/28.1.27
Kapitonov VV, Jurka J (2001) Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci USA
98:8714–8719.
https://doi.org/10.1073/
pnas.151269298
Kapitonov VV, Jurka J (2008) A universal classification
of eukaryotic transposable elements implemented
9 Fungal Genomics
219