fuels 10:152. https://doi.org/10.1186/s13068-0170841-x
Billingsley JM, DeNicola AB, Tang Y (2016) Technology
development for natural product biosynthesis in
Saccharomyces cerevisiae. Curr Opin Biotechnol
42:74–83.
https://doi.org/10.1016/j.copbio.2016.02.033
Birney E, Clamp M, Durbin R (2004) GeneWise and
genomewise. Genome Res 14:988–995. https://doi.
org/10.1101/gr.1865504
Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ,
Kautsar SA, Suarez Duran HG, de Los Santos
ELC, Kim HU, Nave M, Dickschat JS, Mitchell
DA, Shelest E, Breitling R, Takano E, Lee SY,
Weber T, Medema MH (2017) AntiSMASH 4.0—
improvements in chemistry prediction and gene
cluster boundary identification. Nucleic Acids Res
45:W36–W41. https://doi.org/10.1093/nar/gkx319
Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M,
Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L,
Holmes IH (2016) JBrowse: a dynamic web platform for genome visualization and analysis.
Genome Biol 17:66. https://doi.org/10.1186/
s13059-016-0924-1
Cantarel BL, Korf I, Robb SMC, Parra G, Ross E, Moore
B, Holt C, Sa ´nchez Alvarado A, Yandell M (2008)
MAKER: an easy-to-use annotation pipeline
designed for emerging model organism genomes.
Genome Res 18:188–196. https://doi.org/10.1101/
gr.6743907
Castanera R, Lo ´pez-Varas L, Borgognone A, LaButti K,
Lapidus A, Schmutz J, Grimwood J, Pe ´rez G, Pisabarro AG, Grigoriev IV, Stajich JE, Ramı ´rez L
(2016) Transposable elements versus the fungal
genome: impact on whole-genome architecture
and transcriptional profiles. PLoS Genet 12:
e1006108.
https://doi.org/10.1371/journal.
pgen.1006108
Cerqueira GC, Arnaud MB, Inglis DO, Skrzypek MS,
Binkley G, Simison M, Miyasato SR, Binkley J,
Orvis J, Shah P, Wymore F, Sherlock G, Wortman
JR (2014) The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq
data to improve structural gene annotations.
Nucleic Acids Res 42:D705–D710. https://doi.org/
10.1093/nar/gkt1029
Cherry JM, Hong EL, Amundsen C, Balakrishnan R,
Binkley G, Chan ET, Christie KR, Costanzo MC,
Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz
BC, Karra K, Krieger CJ, Miyasato SR, Nash RS,
Park J, Skrzypek MS, Simison M, Weng S, Wong
ED (2012) Saccharomyces Genome Database: the
genomics resource of budding yeast. Nucleic Acids
Res 40:D700–D705. https://doi.org/10.1093/nar/
gkr1029
Chin C-S, Alexander DH, Marks P, Klammer AA, Drake
J, Heiner C, Clum A, Copeland A, Huddleston J,
Eichler EE, Turner SW, Korlach J (2013) Nonhybrid, finished microbial genome assemblies from
long-read SMRT sequencing data. Nat Methods
10:563–569. https://doi.org/10.1038/nmeth.2474
Cisse ´ OH, Stajich JE (2019) FGMP: assessing fungal
genome completeness. BMC Bioinformatics
20:184. https://doi.org/10.1186/s12859-019-2782-9
Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers
EW (2016) GenBank. Nucleic Acids Res 44:D67–
D72. https://doi.org/10.1093/nar/gkv1276
Clevenger KD, Bok JW, Ye R, Miley GP, Verdan MH,
Velk T, Chen C, Yang K, Robey MT, Gao P, Lamprecht M, Thomas PM, Islam MN, Palmer JM, Wu
CC, Keller NP, Kelleher NL (2017) A scalable platform to identify fungal secondary metabolites and
their gene clusters. Nat Chem Biol 13:895–901.
https://doi.org/10.1038/nchembio.2408
Clutterbuck AJ (2011) Genomic evidence of repeatinduced point mutation (RIP) in filamentous ascomycetes. Fungal Genet Biol 48:306–326. https://
doi.org/10.1016/J.FGB.2010.09.002
Condon BJ, Leng Y, Wu D, Bushley KE, Ohm RA, Otillar
R, Martin J, Schackwitz W, Grimwood J, MohdZainudin N, Xue C, Wang R, Manning VA, Dhillon B,
Tu ZJ, Steffenson BJ, Salamov A, Sun H, Lowry S,
LaButti K, Han J, Copeland A, Lindquist E, Barry
K, Schmutz J, Baker SE, Ciuffetti LM, Grigoriev IV,
Zhong S, Turgeon BG (2013) Comparative genome
structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens. PLoS
Genet 9:e1003233. https://doi.org/10.1371/journal.
pgen.1003233
Contreras-Cornejo HA, Macı ´as-Rodrı ´guez L, del-Val E,
Larsen J (2016) Ecological functions of Trichoderma spp. and their secondary metabolites in
the rhizosphere: interactions with plants. FEMS
Microbiol Ecol 92:fiw036. https://doi.org/10.1093/
femsec/fiw036
Coutinho PM, Andersen MR, Kolenova K, vanKuyk PA,
Benoit I, Gruben BS, Trejo-Aguilar B, Visser H,
van Solingen P, Pakula T, Seiboth B, Battaglia E,
Aguilar-Osorio G, de Jong JF, Ohm RA, Aguilar M,
Henrissat B, Nielsen J, Sta ˚lbrand H, de Vries RP
(2009) Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus
nidulans and comparison to Aspergillus niger and
Aspergillus oryzae. Fungal Genet Biol 46(Suppl 1):
S161–S169
Cuomo CA, Birren BW (2010) The fungal genome initiative and lessons learned from genome sequencing. Methods Enzymol 470:833–855. https://doi.
org/10.1016/S0076-6879(10)70034-3
Cuomo CA, Guldener U, Xu J-R, Trail F, Turgeon BG,
Di Pietro A, Walton JD, Ma L-J, Baker SE, Rep M,
Adam G, Antoniw J, Baldwin T, Calvo S, Chang YL, DeCaprio D, Gale LR, Gnerre S, Goswami RS,
Hammond-Kosack K, Harris LJ, Hilburn K, Kennell JC, Kroken S, Magnuson JK, Mannhaupt G,
Mauceli E, Mewes H-W, Mitterbauer R, Muehlbauer G, Munsterkotter M, Nelson D, O’Donnell
K, Ouellet T, Qi W, Quesneville H, Roncero MIG,
9 Fungal Genomics
217
Billingsley JM, DeNicola AB, Tang Y (2016) Technology
development for natural product biosynthesis in
Saccharomyces cerevisiae. Curr Opin Biotechnol
42:74–83.
https://doi.org/10.1016/j.copbio.2016.02.033
Birney E, Clamp M, Durbin R (2004) GeneWise and
genomewise. Genome Res 14:988–995. https://doi.
org/10.1101/gr.1865504
Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ,
Kautsar SA, Suarez Duran HG, de Los Santos
ELC, Kim HU, Nave M, Dickschat JS, Mitchell
DA, Shelest E, Breitling R, Takano E, Lee SY,
Weber T, Medema MH (2017) AntiSMASH 4.0—
improvements in chemistry prediction and gene
cluster boundary identification. Nucleic Acids Res
45:W36–W41. https://doi.org/10.1093/nar/gkx319
Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M,
Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L,
Holmes IH (2016) JBrowse: a dynamic web platform for genome visualization and analysis.
Genome Biol 17:66. https://doi.org/10.1186/
s13059-016-0924-1
Cantarel BL, Korf I, Robb SMC, Parra G, Ross E, Moore
B, Holt C, Sa ´nchez Alvarado A, Yandell M (2008)
MAKER: an easy-to-use annotation pipeline
designed for emerging model organism genomes.
Genome Res 18:188–196. https://doi.org/10.1101/
gr.6743907
Castanera R, Lo ´pez-Varas L, Borgognone A, LaButti K,
Lapidus A, Schmutz J, Grimwood J, Pe ´rez G, Pisabarro AG, Grigoriev IV, Stajich JE, Ramı ´rez L
(2016) Transposable elements versus the fungal
genome: impact on whole-genome architecture
and transcriptional profiles. PLoS Genet 12:
e1006108.
https://doi.org/10.1371/journal.
pgen.1006108
Cerqueira GC, Arnaud MB, Inglis DO, Skrzypek MS,
Binkley G, Simison M, Miyasato SR, Binkley J,
Orvis J, Shah P, Wymore F, Sherlock G, Wortman
JR (2014) The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq
data to improve structural gene annotations.
Nucleic Acids Res 42:D705–D710. https://doi.org/
10.1093/nar/gkt1029
Cherry JM, Hong EL, Amundsen C, Balakrishnan R,
Binkley G, Chan ET, Christie KR, Costanzo MC,
Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz
BC, Karra K, Krieger CJ, Miyasato SR, Nash RS,
Park J, Skrzypek MS, Simison M, Weng S, Wong
ED (2012) Saccharomyces Genome Database: the
genomics resource of budding yeast. Nucleic Acids
Res 40:D700–D705. https://doi.org/10.1093/nar/
gkr1029
Chin C-S, Alexander DH, Marks P, Klammer AA, Drake
J, Heiner C, Clum A, Copeland A, Huddleston J,
Eichler EE, Turner SW, Korlach J (2013) Nonhybrid, finished microbial genome assemblies from
long-read SMRT sequencing data. Nat Methods
10:563–569. https://doi.org/10.1038/nmeth.2474
Cisse ´ OH, Stajich JE (2019) FGMP: assessing fungal
genome completeness. BMC Bioinformatics
20:184. https://doi.org/10.1186/s12859-019-2782-9
Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers
EW (2016) GenBank. Nucleic Acids Res 44:D67–
D72. https://doi.org/10.1093/nar/gkv1276
Clevenger KD, Bok JW, Ye R, Miley GP, Verdan MH,
Velk T, Chen C, Yang K, Robey MT, Gao P, Lamprecht M, Thomas PM, Islam MN, Palmer JM, Wu
CC, Keller NP, Kelleher NL (2017) A scalable platform to identify fungal secondary metabolites and
their gene clusters. Nat Chem Biol 13:895–901.
https://doi.org/10.1038/nchembio.2408
Clutterbuck AJ (2011) Genomic evidence of repeatinduced point mutation (RIP) in filamentous ascomycetes. Fungal Genet Biol 48:306–326. https://
doi.org/10.1016/J.FGB.2010.09.002
Condon BJ, Leng Y, Wu D, Bushley KE, Ohm RA, Otillar
R, Martin J, Schackwitz W, Grimwood J, MohdZainudin N, Xue C, Wang R, Manning VA, Dhillon B,
Tu ZJ, Steffenson BJ, Salamov A, Sun H, Lowry S,
LaButti K, Han J, Copeland A, Lindquist E, Barry
K, Schmutz J, Baker SE, Ciuffetti LM, Grigoriev IV,
Zhong S, Turgeon BG (2013) Comparative genome
structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens. PLoS
Genet 9:e1003233. https://doi.org/10.1371/journal.
pgen.1003233
Contreras-Cornejo HA, Macı ´as-Rodrı ´guez L, del-Val E,
Larsen J (2016) Ecological functions of Trichoderma spp. and their secondary metabolites in
the rhizosphere: interactions with plants. FEMS
Microbiol Ecol 92:fiw036. https://doi.org/10.1093/
femsec/fiw036
Coutinho PM, Andersen MR, Kolenova K, vanKuyk PA,
Benoit I, Gruben BS, Trejo-Aguilar B, Visser H,
van Solingen P, Pakula T, Seiboth B, Battaglia E,
Aguilar-Osorio G, de Jong JF, Ohm RA, Aguilar M,
Henrissat B, Nielsen J, Sta ˚lbrand H, de Vries RP
(2009) Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus
nidulans and comparison to Aspergillus niger and
Aspergillus oryzae. Fungal Genet Biol 46(Suppl 1):
S161–S169
Cuomo CA, Birren BW (2010) The fungal genome initiative and lessons learned from genome sequencing. Methods Enzymol 470:833–855. https://doi.
org/10.1016/S0076-6879(10)70034-3
Cuomo CA, Guldener U, Xu J-R, Trail F, Turgeon BG,
Di Pietro A, Walton JD, Ma L-J, Baker SE, Rep M,
Adam G, Antoniw J, Baldwin T, Calvo S, Chang YL, DeCaprio D, Gale LR, Gnerre S, Goswami RS,
Hammond-Kosack K, Harris LJ, Hilburn K, Kennell JC, Kroken S, Magnuson JK, Mannhaupt G,
Mauceli E, Mewes H-W, Mitterbauer R, Muehlbauer G, Munsterkotter M, Nelson D, O’Donnell
K, Ouellet T, Qi W, Quesneville H, Roncero MIG,
9 Fungal Genomics
217