ment of CRISPR/Cas9 across the fungal kingdom (Shi et al. 2017). I expect that in the coming years, large improvements will be made in
techniques related to functional genomics, further accelerating discoveries across the fungal
kingdom.
Fungal genome sequencing, comparative
genomics and functional genomics are Big
Data sciences and require a specific skill set:
most bioinformatics tools run in a Linux environment and programming skills (e.g. in
Python and R) are essential for advanced analyses. Most universities now include these
aspects in their curriculum, ensuring that the
next generation of researchers will be skilled in
both experimental lab work and computational
biology.
References
Alma ´si E ´ , Sahu N, Krizsa ´n K, Ba ´lint B, Kova ´cs GM, Kiss
B, Cseklye J, Drula E, Henrissat B, Nagy I, Chovatia
M, Adam C, LaButti K, Lipzen A, Riley R, Grigoriev IV, Nagy LG (2019) Comparative genomics
reveals unique wood-decay strategies and fruiting
body development in the Schizophyllaceae. New
Phytol. https://doi.org/10.1111/nph.16032
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ
(1990) Basic local alignment search tool. J Mol Biol
215:403–410. https://doi.org/10.1016/S0022-2836
(05)80360-2
Aparicio S, Chapman J, Stupka E, Putnam N, Chia J-M,
Dehal P, Christoffels A, Rash S, Hoon S, Smit A,
Gelpke MDS, Roach J, Oh T, Ho IY, Wong M,
Detter C, Verhoef F, Predki P, Tay A, Lucas S,
Richardson P, Smith SF, Clark MS, Edwards YJK,
Doggett N, Zharkikh A, Tavtigian SV, Pruss D,
Barnstead M, Evans C, Baden H, Powell J, Glusman
G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T,
Venkatesh B, Rokhsar D, Brenner S (2002) Wholegenome shotgun assembly and analysis of the
genome of Fugu rubripes. Science 297:1301–1310.
https://doi.org/10.1126/science.1072104
Arabidopsis Genome Initiative (2000) Analysis of the
genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815. https://doi.org/
10.1038/35048692
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H,
Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig
JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis
A, Lewis S, Matese JC, Richardson JE, Ringwald M,
Rubin GM, Sherlock G (2000) Gene ontology: tool
for the unification of biology. Nat Genet 25:25–29.
https://doi.org/10.1038/75556
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin
M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S,
Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N,
Tesler G, Alekseyev MA, Pevzner PA (2012)
SPAdes: a new genome assembly algorithm and
its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/
cmb.2012.0021
Basenko EY, Pulman JA, Shanmugasundram A, Harb
OS, Crouch K, Starns D, Warrenfeltz S, Aurrecoechea C, Stoeckert CJ, Kissinger JC, Roos DS, HertzFowler C (2018) FungiDB: an integrated bioinformatic resource for fungi and oomycetes. J Fungi
4:39. https://doi.org/10.3390/jof4010039
Bateman A, Martin MJ, O’Donovan C, Magrane M, Alpi
E, Antunes R, Bely B, Bingley M, Bonilla C, Britto
R, Bursteinas B, Bye-A-Jee H, Cowley A, Da Silva
A, De Giorgi M, Dogan T, Fazzini F, Castro LG,
Figueira L, Garmiri P, Georghiou G, Gonzalez D,
Hatton-Ellis E, Li W, Liu W, Lopez R, Luo J, Lussi
Y, MacDougall A, Nightingale A, Palka B, Pichler
K, Poggioli D, Pundir S, Pureza L, Qi G, Renaux A,
Rosanoff S, Saidi R, Sawford T, Shypitsyna A,
Speretta E, Turner E, Tyagi N, Volynkin V, Wardell T, Warner K, Watkins X, Zaru R, Zellner H,
Xenarios I, Bougueleret L, Bridge A, Poux S,
Redaschi N, Aimo L, Argoud-Puy G, Auchincloss
A, Axelsen K, Bansal P, Baratin D, Blatter M-C,
Boeckmann B, Bolleman J, Boutet E, Breuza L,
Casal-Casas C, de Castro E, Coudert E, Cuche B,
Doche M, Dornevil D, Duvaud S, Estreicher A,
Famiglietti L, Feuermann M, Gasteiger E, Gehant
S, Gerritsen V, Gos A, Gruaz-Gumowski N, Hinz
U, Hulo C, Jungo F, Keller G, Lara V, Lemercier P,
Lieberherr D, Lombardot T, Martin X, Masson P,
Morgat A, Neto T, Nouspikel N, Paesano S, Pedruzzi I, Pilbout S, Pozzato M, Pruess M, Rivoire C,
Roechert B, Schneider M, Sigrist C, Sonesson K,
Staehli S, Stutz A, Sundaram S, Tognolli M, Verbregue L, Veuthey A-L, Wu CH, Arighi CN,
Arminski L, Chen C, Chen Y, Garavelli JS, Huang
H, Laiho K, McGarvey P, Natale DA, Ross K,
Vinayaka CR, Wang Q, Wang Y, Yeh L-S, Zhang
J (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res 45:D158–D169. https://doi.
org/10.1093/nar/gkw1099
Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S,
Mauceli E, Berger B, Mesirov JP, Lander ES
(2002) ARACHNE: a whole-genome shotgun
assembler. Genome Res 12:177–189. https://doi.
org/10.1101/gr.208902
Bennett S (2004) Solexa Ltd. Pharmacogenomics 5:433–
438. https://doi.org/10.1517/14622416.5.4.433
Bennett JW, Chung KT (2001) Alexander Fleming and
the discovery of penicillin. Adv Appl Microbiol
49:163–184
Benocci T, Aguilar-Pontes MV, Zhou M, Seiboth B, de
Vries RP (2017) Regulators of plant biomass degradation in ascomycetous fungi. Biotechnol Bio216
R. A. Ohm
techniques related to functional genomics, further accelerating discoveries across the fungal
kingdom.
Fungal genome sequencing, comparative
genomics and functional genomics are Big
Data sciences and require a specific skill set:
most bioinformatics tools run in a Linux environment and programming skills (e.g. in
Python and R) are essential for advanced analyses. Most universities now include these
aspects in their curriculum, ensuring that the
next generation of researchers will be skilled in
both experimental lab work and computational
biology.
References
Alma ´si E ´ , Sahu N, Krizsa ´n K, Ba ´lint B, Kova ´cs GM, Kiss
B, Cseklye J, Drula E, Henrissat B, Nagy I, Chovatia
M, Adam C, LaButti K, Lipzen A, Riley R, Grigoriev IV, Nagy LG (2019) Comparative genomics
reveals unique wood-decay strategies and fruiting
body development in the Schizophyllaceae. New
Phytol. https://doi.org/10.1111/nph.16032
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ
(1990) Basic local alignment search tool. J Mol Biol
215:403–410. https://doi.org/10.1016/S0022-2836
(05)80360-2
Aparicio S, Chapman J, Stupka E, Putnam N, Chia J-M,
Dehal P, Christoffels A, Rash S, Hoon S, Smit A,
Gelpke MDS, Roach J, Oh T, Ho IY, Wong M,
Detter C, Verhoef F, Predki P, Tay A, Lucas S,
Richardson P, Smith SF, Clark MS, Edwards YJK,
Doggett N, Zharkikh A, Tavtigian SV, Pruss D,
Barnstead M, Evans C, Baden H, Powell J, Glusman
G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T,
Venkatesh B, Rokhsar D, Brenner S (2002) Wholegenome shotgun assembly and analysis of the
genome of Fugu rubripes. Science 297:1301–1310.
https://doi.org/10.1126/science.1072104
Arabidopsis Genome Initiative (2000) Analysis of the
genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815. https://doi.org/
10.1038/35048692
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H,
Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig
JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis
A, Lewis S, Matese JC, Richardson JE, Ringwald M,
Rubin GM, Sherlock G (2000) Gene ontology: tool
for the unification of biology. Nat Genet 25:25–29.
https://doi.org/10.1038/75556
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin
M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S,
Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N,
Tesler G, Alekseyev MA, Pevzner PA (2012)
SPAdes: a new genome assembly algorithm and
its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/
cmb.2012.0021
Basenko EY, Pulman JA, Shanmugasundram A, Harb
OS, Crouch K, Starns D, Warrenfeltz S, Aurrecoechea C, Stoeckert CJ, Kissinger JC, Roos DS, HertzFowler C (2018) FungiDB: an integrated bioinformatic resource for fungi and oomycetes. J Fungi
4:39. https://doi.org/10.3390/jof4010039
Bateman A, Martin MJ, O’Donovan C, Magrane M, Alpi
E, Antunes R, Bely B, Bingley M, Bonilla C, Britto
R, Bursteinas B, Bye-A-Jee H, Cowley A, Da Silva
A, De Giorgi M, Dogan T, Fazzini F, Castro LG,
Figueira L, Garmiri P, Georghiou G, Gonzalez D,
Hatton-Ellis E, Li W, Liu W, Lopez R, Luo J, Lussi
Y, MacDougall A, Nightingale A, Palka B, Pichler
K, Poggioli D, Pundir S, Pureza L, Qi G, Renaux A,
Rosanoff S, Saidi R, Sawford T, Shypitsyna A,
Speretta E, Turner E, Tyagi N, Volynkin V, Wardell T, Warner K, Watkins X, Zaru R, Zellner H,
Xenarios I, Bougueleret L, Bridge A, Poux S,
Redaschi N, Aimo L, Argoud-Puy G, Auchincloss
A, Axelsen K, Bansal P, Baratin D, Blatter M-C,
Boeckmann B, Bolleman J, Boutet E, Breuza L,
Casal-Casas C, de Castro E, Coudert E, Cuche B,
Doche M, Dornevil D, Duvaud S, Estreicher A,
Famiglietti L, Feuermann M, Gasteiger E, Gehant
S, Gerritsen V, Gos A, Gruaz-Gumowski N, Hinz
U, Hulo C, Jungo F, Keller G, Lara V, Lemercier P,
Lieberherr D, Lombardot T, Martin X, Masson P,
Morgat A, Neto T, Nouspikel N, Paesano S, Pedruzzi I, Pilbout S, Pozzato M, Pruess M, Rivoire C,
Roechert B, Schneider M, Sigrist C, Sonesson K,
Staehli S, Stutz A, Sundaram S, Tognolli M, Verbregue L, Veuthey A-L, Wu CH, Arighi CN,
Arminski L, Chen C, Chen Y, Garavelli JS, Huang
H, Laiho K, McGarvey P, Natale DA, Ross K,
Vinayaka CR, Wang Q, Wang Y, Yeh L-S, Zhang
J (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res 45:D158–D169. https://doi.
org/10.1093/nar/gkw1099
Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S,
Mauceli E, Berger B, Mesirov JP, Lander ES
(2002) ARACHNE: a whole-genome shotgun
assembler. Genome Res 12:177–189. https://doi.
org/10.1101/gr.208902
Bennett S (2004) Solexa Ltd. Pharmacogenomics 5:433–
438. https://doi.org/10.1517/14622416.5.4.433
Bennett JW, Chung KT (2001) Alexander Fleming and
the discovery of penicillin. Adv Appl Microbiol
49:163–184
Benocci T, Aguilar-Pontes MV, Zhou M, Seiboth B, de
Vries RP (2017) Regulators of plant biomass degradation in ascomycetous fungi. Biotechnol Bio216
R. A. Ohm