defence against Verticillium wilt disease. J Exp Bot
60:591–602
Esteller M (2011) Non-coding RNAs in human disease.
Nat Rev Genet 12:861–874
Faghihi MA, Wahlestedt C (2009) Regulatory roles of
natural antisense transcripts. Nat Rev Mol Cell
Biol 10:637–643
Feretzaki M, Billmyre RB, Clancey SA, Wang X, Heitman J (2016) Gene network polymorphism illuminates loss and retention of novel RNAi silencing
components in the Cryptococcus pathogenic species complex. PLoS Genet 12:1005868
Francia S, Michelini F, Saxena A, Tang D, De Hoon M,
Mione M, Carninci P (2013) Site-specific DICER
and DROSHA RNA products control the DNA
damage response. Nature 488:231–235
Friedman S, Freitag M (2017) Centrochromatin of
Fungi. In: Black BE (ed) Centromeres and kinetochores. Springer International Publishing AG,
Cham, pp 85–109
Friedman RC, Farh KKH, Burge CB, Bartel DP (2009)
Most mammalian mRNAs are conserved targets of
microRNAs. Genome Res 19:92–105
Gao D, Jiang N, Wing RA, Jiang J, Jackson SA (2015)
Transposons play an important role in the evolution and diversification of centromeres among
closely related species. Front Plant Sci 6:216
Gazzani S, Lawrenson T, Woodward C, Headon D,
Sablowski R (2008) A link between mRNA turnover and RNA interference in Arabidopsis. Science
1046:1046–1049
Ghildiyal M, Zamore PD (2009) Small silencing RNAs:
an expanding universe. Nat Rev Genet 10:94–108
Halic M, Moazed D (2010) Dicer-independent primal
RNAs trigger RNAi and heterochromatin formation. Cell 140:504–516
Hammond TM (2017) Sixteen years of meiotic silencing
by unpaired DNA. Adv Genet 97:1–42
Hammond TM, Andrewski MD, Roossinck MJ, Keller
NP (2008) Aspergillus mycoviruses are targets and
suppressors of RNA silencing. Eukaryot Cell
7:350–357
Hammond TM, Xiao H, Boone EC, Perdue TD, Pukkila
PJ, Shiu PKT (2011) SAD-3, a putative helicase
required for meiotic silencing by unpaired DNA,
interacts with other components of the silencing
machinery. G3 (Bethesda) 1:369–376
Hammond TM, Xiao H, Boone EC, Decker LM, Lee SA,
Perdue TD, Pukkila PJ, Shiu PKT (2013a) Novel
proteins required for meiotic silencing by
unpaired DNA and siRNA generation in Neurospora crassa. Genetics 194:91–100
Hammond TM, Spollen WG, Decker LM, Blake SM,
Springer GK, Shiu PKT (2013b) Identification of
small RNAs associated with meiotic silencing by
unpaired DNA. Genetics 194:279–284
Harvey JJW, Lewsey MG, Patel K, Westwood J,
Heimsta ¨dt S, Carr JP, Baulcombe DC (2011) An
antiviral defense role of AGO2 in plants. PLoS One
6:e14639
Harvey AM, Rehard DG, Groskreutz KM, Kuntz DR,
Sharp K, Shiu PK, Hammond TM (2014) A critical
component of meiotic drive in Neurospora is
located near a chromosome rearrangement.
Genetics 197:1165–1174
Janbon G, Maeng S, Yang DH, Ko YJ, Jung KW, Moyrand F, Floyd A, Heitman J, Bahn YS (2010) Characterizing the role of RNA silencing components
in Cryptococcus neoformans. Fungal Genet Biol
47:1070–1080
Jeang KT (2012) RNAi in the regulation of mammalian
viral infections. BMC Biol 10:58
Jiang X, Qiao F, Long Y, Cong H, Sun H (2017)
MicroRNA-like RNAs in plant pathogenic fungus
Fusarium oxysporum f. sp. niveum are involved in
toxin gene expression fine tuning. 3 Biotech 7:354
Kadotani N, Nakayashiki H, Tosa Y, Mayama S (2004)
One of the two dicer-like proteins in the filamentous fungi Magnaporthe oryzae genome is responsible for hairpin RNA-triggered RNA silencing and
related small interfering RNA accumulation. J Biol
Chem 279:44467–44474
Kang K, Zhong J, Jiang L, Liu G, Gou CY, Wu Q, Wang
Y, Luo J, Gou D (2013) Identification of
microRNA-like RNAs in the filamentous fungus
Trichoderma reesei by Solexa sequencing. PLoS
One 8:e76288
Koch A, Kumar N, Weber L, Keller H, Imani J, Kogel KH (2013) Host-induced gene silencing of cytochrome P450 lanosterol C14 -demethylase-encoding genes confers strong resistance to Fusarium
species. Proc Natl Acad Sci 110:19324–19329
Kronholm I, Johannesson H, Ketola T (2016) Epigenetic
control of phenotypic plasticity in the filamentous
fungus Neurospora crassa. G3 (Bethesda) 6:4009–
4022
Kuan T, Zhai Y, Ma W (2016) Small RNAs regulate
plant responses to filamentous pathogens. Semin
Cell Dev Biol 56:190–200
Lau SKP, Chow WN, Wong AYP, Yeung JMY, Bao J,
Zhang N, Lok S, Woo PCY, Yuen KY (2013) Identification of microRNA-like RNAs in mycelial and
yeast phases of the thermal dimorphic fungus Penicillium marneffei. PLoS Negl Trop Dis 7:e2398
Lau AYT, Cheng X, Cheng CK, Nong W, Cheung MK,
Chan RHF, Hui JHL, Kwan HS (2018) Discovery of
microRNA-like RNAs during early fruiting body
development in the model mushroom Coprinopsis
cinerea. PLoS One 13:e0198234
Laurie JD, Linning R, Bakkeren G (2008) Hallmarks of
RNA silencing are found in the smut fungus Ustilago hordei but not in its close relative Ustilago
maydis. Curr Genet 53:49–58
Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small
RNAs with antisense complementarity to lin-14.
Cell 75:843–854
Lee DW, Pratt RJ, McLaughlin M, Aramayo R (2003) An
Argonaute-like protein is required for meiotic
silencing. Genetics 164:821–828
5 Small RNAs in Fungi
119
60:591–602
Esteller M (2011) Non-coding RNAs in human disease.
Nat Rev Genet 12:861–874
Faghihi MA, Wahlestedt C (2009) Regulatory roles of
natural antisense transcripts. Nat Rev Mol Cell
Biol 10:637–643
Feretzaki M, Billmyre RB, Clancey SA, Wang X, Heitman J (2016) Gene network polymorphism illuminates loss and retention of novel RNAi silencing
components in the Cryptococcus pathogenic species complex. PLoS Genet 12:1005868
Francia S, Michelini F, Saxena A, Tang D, De Hoon M,
Mione M, Carninci P (2013) Site-specific DICER
and DROSHA RNA products control the DNA
damage response. Nature 488:231–235
Friedman S, Freitag M (2017) Centrochromatin of
Fungi. In: Black BE (ed) Centromeres and kinetochores. Springer International Publishing AG,
Cham, pp 85–109
Friedman RC, Farh KKH, Burge CB, Bartel DP (2009)
Most mammalian mRNAs are conserved targets of
microRNAs. Genome Res 19:92–105
Gao D, Jiang N, Wing RA, Jiang J, Jackson SA (2015)
Transposons play an important role in the evolution and diversification of centromeres among
closely related species. Front Plant Sci 6:216
Gazzani S, Lawrenson T, Woodward C, Headon D,
Sablowski R (2008) A link between mRNA turnover and RNA interference in Arabidopsis. Science
1046:1046–1049
Ghildiyal M, Zamore PD (2009) Small silencing RNAs:
an expanding universe. Nat Rev Genet 10:94–108
Halic M, Moazed D (2010) Dicer-independent primal
RNAs trigger RNAi and heterochromatin formation. Cell 140:504–516
Hammond TM (2017) Sixteen years of meiotic silencing
by unpaired DNA. Adv Genet 97:1–42
Hammond TM, Andrewski MD, Roossinck MJ, Keller
NP (2008) Aspergillus mycoviruses are targets and
suppressors of RNA silencing. Eukaryot Cell
7:350–357
Hammond TM, Xiao H, Boone EC, Perdue TD, Pukkila
PJ, Shiu PKT (2011) SAD-3, a putative helicase
required for meiotic silencing by unpaired DNA,
interacts with other components of the silencing
machinery. G3 (Bethesda) 1:369–376
Hammond TM, Xiao H, Boone EC, Decker LM, Lee SA,
Perdue TD, Pukkila PJ, Shiu PKT (2013a) Novel
proteins required for meiotic silencing by
unpaired DNA and siRNA generation in Neurospora crassa. Genetics 194:91–100
Hammond TM, Spollen WG, Decker LM, Blake SM,
Springer GK, Shiu PKT (2013b) Identification of
small RNAs associated with meiotic silencing by
unpaired DNA. Genetics 194:279–284
Harvey JJW, Lewsey MG, Patel K, Westwood J,
Heimsta ¨dt S, Carr JP, Baulcombe DC (2011) An
antiviral defense role of AGO2 in plants. PLoS One
6:e14639
Harvey AM, Rehard DG, Groskreutz KM, Kuntz DR,
Sharp K, Shiu PK, Hammond TM (2014) A critical
component of meiotic drive in Neurospora is
located near a chromosome rearrangement.
Genetics 197:1165–1174
Janbon G, Maeng S, Yang DH, Ko YJ, Jung KW, Moyrand F, Floyd A, Heitman J, Bahn YS (2010) Characterizing the role of RNA silencing components
in Cryptococcus neoformans. Fungal Genet Biol
47:1070–1080
Jeang KT (2012) RNAi in the regulation of mammalian
viral infections. BMC Biol 10:58
Jiang X, Qiao F, Long Y, Cong H, Sun H (2017)
MicroRNA-like RNAs in plant pathogenic fungus
Fusarium oxysporum f. sp. niveum are involved in
toxin gene expression fine tuning. 3 Biotech 7:354
Kadotani N, Nakayashiki H, Tosa Y, Mayama S (2004)
One of the two dicer-like proteins in the filamentous fungi Magnaporthe oryzae genome is responsible for hairpin RNA-triggered RNA silencing and
related small interfering RNA accumulation. J Biol
Chem 279:44467–44474
Kang K, Zhong J, Jiang L, Liu G, Gou CY, Wu Q, Wang
Y, Luo J, Gou D (2013) Identification of
microRNA-like RNAs in the filamentous fungus
Trichoderma reesei by Solexa sequencing. PLoS
One 8:e76288
Koch A, Kumar N, Weber L, Keller H, Imani J, Kogel KH (2013) Host-induced gene silencing of cytochrome P450 lanosterol C14 -demethylase-encoding genes confers strong resistance to Fusarium
species. Proc Natl Acad Sci 110:19324–19329
Kronholm I, Johannesson H, Ketola T (2016) Epigenetic
control of phenotypic plasticity in the filamentous
fungus Neurospora crassa. G3 (Bethesda) 6:4009–
4022
Kuan T, Zhai Y, Ma W (2016) Small RNAs regulate
plant responses to filamentous pathogens. Semin
Cell Dev Biol 56:190–200
Lau SKP, Chow WN, Wong AYP, Yeung JMY, Bao J,
Zhang N, Lok S, Woo PCY, Yuen KY (2013) Identification of microRNA-like RNAs in mycelial and
yeast phases of the thermal dimorphic fungus Penicillium marneffei. PLoS Negl Trop Dis 7:e2398
Lau AYT, Cheng X, Cheng CK, Nong W, Cheung MK,
Chan RHF, Hui JHL, Kwan HS (2018) Discovery of
microRNA-like RNAs during early fruiting body
development in the model mushroom Coprinopsis
cinerea. PLoS One 13:e0198234
Laurie JD, Linning R, Bakkeren G (2008) Hallmarks of
RNA silencing are found in the smut fungus Ustilago hordei but not in its close relative Ustilago
maydis. Curr Genet 53:49–58
Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small
RNAs with antisense complementarity to lin-14.
Cell 75:843–854
Lee DW, Pratt RJ, McLaughlin M, Aramayo R (2003) An
Argonaute-like protein is required for meiotic
silencing. Genetics 164:821–828
5 Small RNAs in Fungi
119