The interaction of fungi with the environment orchestrated by RNAi

Literature cited

• AguirreAMontserratNZacchignaSNivetEHishidaTKrauseMNKurianLOcampoAVazquez-FerrerERodriguez-EstebanCKumarSMorescoJJYatesJRCampistolJMSancho-MartinezIGiaccaMIzpisua BelmonteJCI. 2014. In vivo activation of a conserved microRNA program induces mammalian heart regeneration. Cell Stem Cell 15:589–604, doi:10.1016/j.stem.2014.10.003
   PubMed Web of Science ®Google Scholar
• AlexanderWGRajuNBXiaoHHammondTMPerdueTDMetzenbergRLPukkilaPJShiuPK. 2008. DCL-1 colocalizes with other components of the MSUD machinery and is required for silencing. Fungal Genet Biol 45:719–727, doi:10.1016/j.fgb.2007.10.006
   PubMed Web of Science ®Google Scholar
• AmeresSLZamorePD. 2013. Diversifying microRNA sequence and function. Nat Rev Mol Cell Biol 14:475–488, doi:10.1038/nrm3611
   PubMed Web of Science ®Google Scholar
• AramayoRMetzenbergRL. 1996. Meiotic transvection in fungi. Cell 86:103–113, doi:10.1016/S0092-8674(00)80081-1
   Google Scholar
• Arteaga-VázquezMCaballero-PérezJVielle-CalzadaJ-P. 2006. A family of microRNAs present in plants and animals. Plant Cell 18:3355–3369.
   PubMed Web of Science ®Google Scholar
• AxtellMJWestholmJOLaiEC. 2011. Vive la différence biogenesis and evolution of microRNAs in plants and animals. Genome Biol 12:221, doi:10.1101/gr.101386.109
   PubMed Web of Science ®Google Scholar
• BaiYLanFYangWZhangFYangKLiZGaoPWangS. 2015. sRNA profiling in Aspergillus flavus reveals differentially expressed miRNA-like RNAs response to water activity and temperature. Fungal Genet Biol 81:113–119, doi:10.1016/j.fgb.2015.03.004
   Google Scholar
• BartelDP. 2004. MicroRNAs: genomics, biogenesis, mechanism and function. Cell 116:281–297, doi:10.1016/S0092-8674(04)00045-5
   PubMed Web of Science ®Google Scholar
• BiggarKKStoreyKB. 2015. Insight into post-transcriptional gene regulation: stress-responsive microRNAs and their role in the environmental stress survival of tolerant animals. J Exp Biol 218:1281–1289, doi:10.1242/jeb.104828
   PubMed Web of Science ®Google Scholar
• BillmyreRBCaloSFeretzakiMWangXHeitmanJ. 2013. RNAi function, diversity and loss in the fungal kingdom. Chromosome Res 21:561–572, doi:10.1007/s10577-013-9388-2
   Google Scholar
• BlairCOlsonK. 2015. The role of RNA interference (RNAi) in arbovirus-vector interactions. Viruses 7:820–843, doi:10.3390/v7020820
   Google Scholar
• CaloSNicolásFEVilaATorres-MartínezSRuiz-vázquezRM. 2012. Two distinct RNA-dependent RNA polymerases are required for initiation and amplification of RNA silencing in the basal fungus Mucor circinelloides. Mol Microbiol 83:379–394, doi:10.1111/j.1365-2958.2011.07939.x
   PubMed Web of Science ®Google Scholar
• CaloSShertz-WallCLeeSCBastidasRJNicolásFEGranekJAMieczkowskiPTorres-MartínezSRuiz-VázquezRMCardenasMEHeitmanJ. 2014. Antifungal drug resistance evoked via RNAi-dependent epimutations. Nature 513:555–558, doi:10.1038/nature13575
   PubMed Web of Science ®Google Scholar
• Carreras-VillaseñorNEsquivel-NaranjoEUVillalobos-EscobedoJMAbreu-GoodgerCHerrera-EstrellaA. 2013. The RNAi machinery regulates growth and development in the filamentous fungus Trichoderma atroviride. Mol Microbiol 89:96–112.
   PubMed Web of Science ®Google Scholar
• Carreras-VillaseñorNSánchez-ArreguinJAHerrera-EstrellaAH. 2012. Trichoderma: sensing the environment for survival and dispersal. Microbiology 158:3–16.
   Google Scholar
• CarthewRWSontheimerEJ. 2009. Origins and mechanisms of miRNAs and siRNAs. Cell 136:642–655, doi:10.1016/j.cell.2009.01.035
   PubMed Web of Science ®Google Scholar
• CatalanottoCAzzalinGMacinoGCogoniC. 2000. Gene silencing in worms and fungi. Nature 404:245, doi:10.1038/35005169
   PubMed Web of Science ®Google Scholar
• CatalanottoCAzzalinGMacinoGCogoniC. 2002. Involvement of small RNAs and role of the qde genes in the gene-silencing pathway in Neurospora. Genes Dev 16:790–795.
   PubMed Web of Science ®Google Scholar
• CatalanottoCPallottaMReFaloPSachsMSVayssieLMacinoGCogoniC. 2004. Redundancy of the two dicer genes in transgene-induced posttranscriptional gene silencing in Neurospora crassa. Mol Cell Biol 24:2536–2545.
   PubMed Web of Science ®Google Scholar
• CervantesMVilaANicolásFEMoxonSde HaroJPDalmayTTorres-MartínezSRuiz-VázquezRM. 2013. A single argonaute gene participates in exogenous and endogenous RNAi and controls cellular functions in the basal fungus Mucor circinelloides. PLoS One 8: e69283, doi:10.1371/journal.pone.0069283.s015
   PubMed Web of Science ®Google Scholar
• ChangSSZhangZLiuY. 2012. RNA interference path ways in fungi: mechanisms and functions. Annu Rev Microbiol 66:305–323, doi:10.1146/annurev-micro-092611-150138
   Google Scholar
• Chávez-MontesRARosas-CárdenasFFde PaoliEAccerbiMRymarquisLAMahalingamGMarsch-MartínezNMeyersBCGreenPJde FolterS. 2014. Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs. Nat Commun 5:3722.
   Google Scholar
• ChenHKobayashiKMiyaoAHirochikaHYamaokaNNishiguchiM. 2013. Both OsRecQ1 and OsRDR1 are required for the production of small RNA in response to DNA damage in rice. PLoS One 8:e55252, doi:10.1371/journal.pone.0055252.g005
   PubMed Web of Science ®Google Scholar
• ChenRJiangNJiangQSunXWangYZhangHHuZ. 2014. Exploring microRNA-like small RNAs in the filamentous fungus Fusarium oxysporum. PLoS One 9: e104956, doi:10.1371/journal.pone.0104956.s012
   Google Scholar
• ChicasACogoniCMacinoG. 2004. RNAi-dependent and RNAi-independent mechanisms contribute to the silencing of RIPed sequences in Neurospora crassa. Nucleic Acids Res 32:4237–4243.
   PubMedGoogle Scholar
• ChoiJKimKTJeonJWuJSongHAsiegbuFOLeeYH. 2014. funRNA: a fungi-centered genomics platform for genes encoding key components of RNAi. BMC Genomics 15:S14, doi:10.1101/gr.849004
   Google Scholar
• CogoniCMacinoG. 1997. Isolation of quelling-defective (qde) mutants impaired in posttranscriptional transgene-induced gene silencing in Neurospora crassa. Proc Natl Acad Sci U S A 94:10233–10238, doi:10.1073/pnas.94.19.10233
   PubMed Web of Science ®Google Scholar
• CogoniCMacinoG. 1999. Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature 399:166–169.
   PubMed Web of Science ®Google Scholar
• DahlmannTAKückU. 2015. Dicer-dependent biogenesis of small RNAs and evidence for microRNA-like RNAs in the penicillin producing fungus Penicillium chrysogenum. PLoS One 10:e0125989, doi:10.1371/journal.pone.0125989.s012
   PubMed Web of Science ®Google Scholar
• DangYLiLGuoWXueZLiuY. 2013. Convergent transcription induces dynamic DNA methylation at disiRNA loci. PLoS Genet 9:e1003761, doi:10.1371/journal.pone.0125989.s012
   Google Scholar
• de HaroJPCaloSCervantesMNicolásFETorres-MartínezSRuiz-VázquezRM. 2009. A single dicer gene is required for efficient gene silencing associated with two classes of small antisense RNAs in Mucor circinelloides. Eukaryot Cell 8:1486–1497, doi:10.1371/journal.pgen.1003761.s012
   Google Scholar
• DeckerLMBooneECXiaoHShankerBSBooneSFKingstonSLLeeSAHammondTMShiuPK. 2015. Complex formation of RNA silencing proteins in the perinuclear region of Neurospora crassa. Genetics 199:1017–1021, doi:10.1534/genetics.115.174623
   Google Scholar
• DrinnenbergIAFinkGRBartelDP. 2011. Compatibility with killer explains the rise of RNAi-deficient fungi. Science 333:1592, doi:10.1126/science.1209575
   Google Scholar
• DrinnenbergIAWeinbergDEXieKTMowerJPWolfeKHFinkGRBartelDP. 2009. RNAi in budding yeast. Science 326:544–550.
   PubMed Web of Science ®Google Scholar
• DriverFMilnerRJTruemanJW. 2000. A taxonomic revision of Metarhizium based on a phylogenetic analysis of rDNA sequence data. Mycol Res 104:134–150.
   Web of Science ®Google Scholar
• DruzhininaISSeidl-SeibothVHerrera-EstrellaAHorwitzBAKenerleyCMMonteEMukherjeePKZeilingerSGrigorievIVKubicekCP. 2011. Trichoderma: the genomics of opportunistic success. Nat Rev Microbiol 9:749–759, doi:10.1038/nrmicro2637
   PubMed Web of Science ®Google Scholar
• DuanGSaintRBHelliwellCABehmCAWangMBWaterhousePMGordonKH. 2013. C. elegans RNA- dependent RNA polymerases rrf-1 and ego-1 silence Drosophila transgenes by differing mechanisms. Cell Mol Life Sci 70:1469–1481, doi:10.1007/s00018-012-1218-8
   PubMed Web of Science ®Google Scholar
• EichhornSWGuoHMcGearySERodriguez-MiasRAShinCBaekDHsuSGhoshalKVillénJBartelDP. 2014. mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol Cell 56:104–115, doi:10.1016/j.molcel.2014.08.028
   PubMed Web of Science ®Google Scholar
• FranciaSMicheliniFSaxenaATangDde HoonMAnelliVMioneMCarninciPdi FagagnaFDA. 2012. Site-specific dicer and drosha RNA products control the DNA damage response. Nature 488:231–235, doi:10.1038/nature11179
   PubMed Web of Science ®Google Scholar
• GeXLeiPWangHZhangAHanZChenXLiSJiangRKangCZhangJ. 2014. miR-21 improves the neurological outcome after traumatic brain injury in rats. Scientific Rep 4:6718, doi:10.1038/srep06718
   PubMed Web of Science ®Google Scholar
• GoodwinSBM’BarekSBDhillonBWittenbergAHCraneCFHaneJKFosterAJvan der LeeTAJGrimwoodJAertsAAntoniwJBaileyABluhmBBowlerJBristowJvan der BurgtACanto-CanchéBChurchillACLConde-FerràezLCoolsHJCoutinhoPMCsukaiMDehalPde WitPDonzelliBvan de GeestHCvan HamRCHJHammond-KosackKEHenrissatBKilianAKobayashiAKKoopmannEKourmpetisYKuzniarALindquistELombardVMaliepaardCMartinsNMehrabiRNapJPHPonomarenkoARuddJJSalamovASchmutzJSchoutenHJShapiroHStergiopoulosITorrianiSFFTuHde VriesRPWaalwijkCWareSBWiebengaAZwiersL-HOliverRPGrigorievIVKemaGHJ. 2011. Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity and stealth pathogenesis. PLoS Genet 7:e1002070, doi:10.1371/journal.pgen.1002070.s022
   PubMed Web of Science ®Google Scholar
• GrimsonASrivastavaMFaheyBWoodcroftBJChiangHRKingNDegnanBMRokhsarDSBartelDP. 2008. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455:1193–1197, doi:10.1038/nature07415
   PubMed Web of Science ®Google Scholar
• HaMKimVN. 2014. Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol 15:509–524, doi:10.1038/nrm3838
   PubMed Web of Science ®Google Scholar
• HammondTMAndrewskiMDRoossinckMJKellerNP. 2008. Aspergillus mycoviruses are targets and suppressors of RNA silencing. Eukaryot Cell 7:350–357, doi:10.1128/EC.00356-07
   PubMed Web of Science ®Google Scholar
• HammondTMXiaoHBooneECPerdueTDPukkilaPJShiuPK. 2011. SAD-3, a putative helicase required for meiotic silencing by unpaired DNA, interacts with other components of the silencing machinery. Genes Genomes Genet 1:369–376.
   Google Scholar
• Hernández-OñateMAEsquivel-NaranjoEUMendoza-MendozaAStewartAHerrera-EstrellaA. 2012. An injury response mechanism conserved across kingdoms determines entry of the fungus Trichoderma atroviride into development. Proc Natl Acad Sci U S A 109:14918–14923.
   Google Scholar
• Hernández-OñateMAHerrera-EstrellaA. 2015. Damage response involves mechanisms conserved across plants, animals and fungi. Curr Genet 61:359–372.
   Google Scholar
• HertelJStadlerPF. 2015. The expansion of animal microRNA families revisited. Life 5:905–920, doi:10.3390/life5010905
   Google Scholar
• JanbonGMaengSYangDHKoYJJungKWMoyrandFFloydAHeitmanJBahnYS. 2010. Characterizing the role of RNA silencing components in Cryptococcus neoformans. Fungal Genet Biol 47:1070–1080, doi:10.1016/j.fgb.2010.10.005
   Google Scholar
• JiangNYangYJanbonGPanJZhuX. 2012. Identification and functional demonstration of miRNAs in the fungus Cryptococcus neoformans. PLoS One 7:e52734, doi:10.1371/journal.pone.0052734.t004
   Google Scholar
• KangKZhongJJiangLLiuGGouCYWuQWangYLuoJGouD. 2013. Identification of microRNA-like RNAs in the filamentous fungus Trichoderma reesei by Solexa sequencing. PloS one 8:e76288.
   PubMed Web of Science ®Google Scholar
• KatoAAkamatsuYSakurabaYInoueH. 2004. The Neurospora crassa mus-19 gene is identical to the qde-3 gene, which encodes a ReqQ homolog and is involved in recombination repair and postreplication repair. Curr Genet 45:37–44, doi:10.1371/journal.pone.0076288.s008
   Google Scholar
• KruszkaKPieczynskiMWindelsDBielewiczDJarmolowskiASzweykowska-KulinskaZVazquezF. 2012. Role of microRNAs and other sRNAs of plants in their changing environments. J Plant Physiol 169:1664–1672, doi:10.1016/j.jplph.2012.03.009
   PubMed Web of Science ®Google Scholar
• KubicekCPHerrera-EstrellaASeidlVle CromSZeilingerSDruzhininaISHermosaRCasas-FloresSHorwitzBAMukherjeePKMukherjeeMKredicsLAlcarazLDAertsAAntalZAtanasovaLCervantes-BadilloMGChallacombeJChertkovOMcCluskeyKCoulpierFDeshpandeNvon DöhrenHEbboleDJEsquivel-NaranjoEUFeketeEFlipphiMGlaserFGómez-RodríguezEYGruberSHansCHenrissatBHernández-OñateMKaraffaLKostiILindquistELucasSLübeckMLübeckPSMargeotAMetzBMisraMNevalainenHOmannMPackerNPerroneGUresti-RiveraEESalamovASchmollMSeibothBShapiroHSuknoSTamayo-RamosJAThonMTischDWiestAWilkinsonHHZhangMCoutinhoPMKenerleyCMMonteEBakerSEGrigorievIV. 2011. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol 12:R40, doi:10.1093/bioinformatics/btm076
   PubMed Web of Science ®Google Scholar
• LauSKChowWNWongAYYeungJMBaoJZhangNLokSWooPCYuenKY. 2013. Identification of microRNA-like RNAs in mycelial and yeast phases of the thermal dimorphic fungus Penicillium marneffei. PLoS Negl Trop Dis 7:e2398.
   PubMed Web of Science ®Google Scholar
• LeeDWPrattRJMcLaughlinMAramayoR. 2003. An Argonaute-like protein is required for meiotic silencing. Genetics 164:821–828, doi:10.1371/journal.pntd.0002398.s001
   PubMed Web of Science ®Google Scholar
• LeeHCAaltoAPYangQChangSSHuangGFisherDChaJPoranenMMBamfordDHLiuY. 2010. The DNA/RNA-dependent RNA polymerase QDE-1 generates aberrantRNA and dsRNA for RNAi in a process requiring replication protein A and a DNA helicase. PLoS Biol 8:e1000496.
   Google Scholar
• LeeHCChangSSChoudharySAaltoAPMaitiMBamfordDHLiuY. 2009. qiRNA is a new type of small interfering RNA induced by DNA damage. Nature 459:274–277, doi:10.1371/journal.pbio.1000496.s003
   PubMed Web of Science ®Google Scholar
• LeeHCLiLGuWXueZCrosthwaiteSKPertsemlidisALewisZAFreitagMSelkerEUMelloCCLiuY. 2010. Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol Cell 38:803–814.
   PubMed Web of Science ®Google Scholar
• LinJSLinCCLinHHChenYCJengST. 2012. microR828 regulates lignin and H2O2 accumulation in sweet potato on wounding. New Phytol 196:427–440, doi:10.1111/j.1469-8137.2012.04277.x
   PubMed Web of Science ®Google Scholar
• LinYLMaLTLeeYRLinSSWangS-YChangTTShawJFLiWHChuFH. 2015. microRNA-like small RNAs prediction in the development of Antrodia cinnamomea. PLoS One . 10:e0123245, 10.1371/journal.pone.0123245.s005
   PubMed Web of Science ®Google Scholar
• LuoJQiuHCaiGWagnerNEBhattacharyaDZhangN. 2015. Phylogenomic analysis uncovers the evolutionary history of nutrition and infection mode in rice-blast fungus and other Magnaporthales. Sci Rep 5:9448, doi:10.1038/srep09448
   Web of Science ®Google Scholar
• MaitiMLeeHCLiuY. 2007. QIP, a putative exonuclease, interacts with the Neurospora Argonaute protein and facilitates conversion of duplex siRNA into single strands. Genes Dev 21:590–600, doi:10.1101/gad.1497607
   PubMed Web of Science ®Google Scholar
• Medina-CastellanosEEsquivel-NaranjoEUHeilMHerrera-EstrellaA. 2014. Extracellular ATP activates MAPK and ROS signaling during injury response in the fungus Trichoderma atroviride. Front Plant Sci 5:659.
   Google Scholar
• MichalikKMBöttcherRFörstemannK. 2012. A small RNA response at DNA ends in Drosophila. Nucleic Acids Res 40:9596–9603, doi:10.1093/nar/gks711
   PubMed Web of Science ®Google Scholar
• MolnarASchwachFStudholmeDJThuenemannECBaulcombeDC. 2007. miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii.Nature 447:1126–1129.
   PubMed Web of Science ®Google Scholar
• MukherjeePKHorwitzBAHerrera-EstrellaASchmollMKenerleyCM. 2013. Trichoderma research in the genome era. Annu Rev Phytopathol 51:105–129, doi:10.1146/annurev-phyto-082712-102353
   PubMed Web of Science ®Google Scholar
• MurataTKadotaniNYamaguchiMTosaYMayamaSNakayashikiH. 2007. siRNA-dependent and independent post-transcriptional cosuppression of the LTR-retrotransposon MAGGY in the phytopathogenic fungus Magnaporthe oryzae. Nucleic Acids Res 35:5987–5994, doi:10.1093/nar/gkm646
   Google Scholar
• NapoliCLemieuxCJorgensenR. 1990. Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2:279–289, doi:10.1105/tpc.2.4.279
   PubMed Web of Science ®Google Scholar
• NicolásFEde HaroJPTorres-MartínezSRuiz-VázquezRM. 2007. Mutants defective in a Mucor circinelloides dicer-like gene are not compromised in siRNA silencing but display developmental defects. Fungal Genet Biol 44:504–516.
   PubMed Web of Science ®Google Scholar
• NicolásFEMoxonSde HaroJCaloSGrigorievIVTorres-MartínezSMoultonVRuiz-VázquezRMDalmayT. 2010. Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides. Nucleic Acids Res 38:5535–5541.
   PubMed Web of Science ®Google Scholar
• NicolásFETorres-MartínezSRuiz-VázquezRM. 2003. Two classes of small antisense RNAs in fungal RNA silencing triggered by non-integrative transgenes. EMBO J 22: 3983–3991.
   Web of Science ®Google Scholar
• NicolásFEVilaAMoxonSCascalesMDTorres-MartínezSRuiz-VázquezRMGarreV. 2015. The RNAi machinery controls distinct responses to environmental signals in the basal fungus Mucor circinelloides. BMC Genomics 16:1–14.
   Google Scholar
• NolanTBracciniLAzzalinGDe ToniAMacinoGCogoniC. 2005. The post-transcriptional gene silencing machinery functions independently of DNA methylation to repress a LINE1-like retrotransposon in Neurospora crassa. Nucleic Acids Res 33:1564–1573, doi:10.1093/nar/gki300
   PubMedGoogle Scholar
• NunesCCGowdaMSailsberyJXueMChenFBrownDEOhYMitchellTKDeanRA. 2011. Diverse and tissue-enriched small RNAs in the plant pathogenic fungus Magnaporthe oryzae. BMC Genomics 12:288, doi:10.1101/gr.849004
   Google Scholar
• PandaSKSunkarR. 2015. Nutrient-and other stress-responsive microRNAs in plants: role for thiol-based redox signaling. Plant Signaling Behavior 10:e1010916.
   PubMed Web of Science ®Google Scholar
• RamanVSimonSARomagADemirciFMathioniSMZhaiJMeyersBCDonofrioNM. 2013. Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus, Magnaporthe oryzae. BMC Genomics 14:326, doi:10.1002/yea.817
   Google Scholar
• RomanoNMacinoG. 1992. Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol Microbiol 6:3343–3353, doi:10.1111/j.1365-2958.1992.tb02202.x
   PubMed Web of Science ®Google Scholar
• SamarajeewaDASaulsPASharpKJSmithZJXiaoHGroskreutzKMMaloneTLBooneECEdwardsKAShiuPKTLarsonEDHammondTM. 2014. Efficient detection of unpaired DNA requires a member of the rad54-like family of homologous recombination proteins. Genetics 198:895–904.
   PubMed Web of Science ®Google Scholar
• SaugstadJA. 2010. MicroRNAs as effectors of brain function with roles in ischemia and injury, neuroprotection and neurodegeneration. J Cereb Blood Flow Metab 30: 1564–1576, doi:10.1038/jcbfm.2010.101
   PubMed Web of Science ®Google Scholar
• SchommerCPalatnikJFAggarwalPChételatACubasPFarmerEENathUWeigelD. 2008. Control of jasmonate biosynthesis and senescence by miR319 targets. PLoS Biol . 6:1991–2001.
   Google Scholar
• SegersGCZhangXDengFSunQNussDL. 2007. Evidence that RNA silencing functions as an antiviral defense mechanism in fungi. Proc Natl Acad Sci U S A 104:12902–12906, doi:10.1073/pnas.0702500104
   PubMed Web of Science ®Google Scholar
• ShiuPKRajuNBZicklerDMetzenbergRL. 2001. Meiotic silencing by unpaired DNA. Cell 107:905–916, doi:10.1016/S0092-8674(01)00609-2
   PubMed Web of Science ®Google Scholar
• ShiuPKZicklerDRajuNBRuprich-RobertGMetzenbergRL. 2006. SAD-2 is required for meiotic silencing by unpaired DNA and perinuclear localization of SAD-1 RNA-directed RNA polymerase. Proc Natl Acad Sci U S A 103:2243–2248.
   PubMedGoogle Scholar
• SunQChoiGHNussDL. 2009. A single Argonaute gene is required for induction of RNA silencing antiviral defense and promotes viral RNA recombination. Proc Natl Acad Sci U S A . 106:17927–17932, 10.1073/pnas.0907552106
   PubMed Web of Science ®Google Scholar
• TabachYBilliACHayesGDNewmanMAZukOGabelHKamathRYacobyKChapmanBGarciaSMBorowskyMKimJKRuvkunG. 2013. Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence. Nature 493:694–698.
   PubMed Web of Science ®Google Scholar
• ThomsonRCPlachetzkiDCMahlerDLMooreBR. 2014. A critical appraisal of the use of microRNA data in phylogenetics. Proc Natl Acad Sci U S A 111:E3659–E3668, doi:10.1073/pnas.1407207111
   Google Scholar
• TrieuTACaloSNicolásFEVilaAMoxonSDalmayTTorres-MartínezSGarreVRuiz-VázquezRM. 2015. A non-canonical RNA silencing pathway promotes mRNA degradation in basal fungi. PLOS Genet 11:e1005168.
   Google Scholar
• WangXHsuehYPLiWFloydASkalskyRHeitmanJ. 2010. Sex-induced silencing defends the genome of Cryptococcus neoformans via RNAi. Genes Dev 24:2566–2582, doi:10.1371/journal.pgen.1005168.s022
   Google Scholar
• WangXWangPSunSDarwicheSIdnurmAHeitmanJ. 2012. Transgene induced co-suppression during vegetative growth in Cryptococcus neoformans. PLoS Genet 8:1–13.
   Google Scholar
• WeiWBaZGaoMWuYMaYAmiardSWhiteCIDanielsenJMRYangYGQiY. 2012. A role for small RNAs in DNA double-strand break repair. Cell 149:101–112, doi:10.1016/j.cell.2012.03.002
   PubMed Web of Science ®Google Scholar
• WeibergAWangMLinF-MZhaoHZhangZKaloshianIHuangH-DJinH. 2013. Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways. Science 342:118–123, doi:10.1126/science.1239705
   PubMed Web of Science ®Google Scholar
• XiaoHAlexanderWGHammondTMBooneECPerdueTDPukkilaPJShiuPK. 2010. QIP, a protein that converts duplex siRNA into single strands, is required for meiotic silencing by unpaired DNA. Genetics 186:119–126, doi:10.1534/genetics.110.118273
   PubMed Web of Science ®Google Scholar
• YangQYeQALiuY. 2015. Mechanism of siRNA production from repetitive DNA. Genes Dev 29:526–537, doi:10.1101/gad.255828.114
   Google Scholar
• ZhangDXNussDL. 2008. A host dicer is required for defective viral RNA production and recombinant virus vector RNA instability for a positive sense RNA virus. Proc Natl Acad Sci U S A 105:16749–16754, doi:10.1073/pnas.0807225105
   PubMed Web of Science ®Google Scholar
• ZhangDXSpieringMJNussDL. 2014a. Characterizing the roles of Cryphonectria parasitica RNA-dependent RNA polymerase-like genes in antiviral defense, viral recombination and transposon transcript accumulation. PLoS One 9:e108653.
   Google Scholar
• ZhangZChangSSZhangZXueZZhangHLiSLiuY. 2013. Homologous recombination as a mechanism to recognize repetitive DNA sequences in an RNAi pathway. Genes Dev 27:145–150.
   PubMed Web of Science ®Google Scholar
• ZhangZYangQSunGChenSHeQLiSLiuY. 2014b. Histone H3K56 acetylation is required for quelling-induced small RNA production through its role in homologous recombination. J Biol Chem 289:9365–9371.
   PubMed Web of Science ®Google Scholar
• ZhouJFuYXieJLiBJiangDLiGChengJ. 2012a. Identification of microRNA-like RNAs in a plant pathogenic fungus Sclerotinia sclerotiorum by high-throughput sequencing. Mol Genet Genomics 287:275–282, doi:10.1007/s00438-012-0678-8
   Google Scholar
• ZhouQWangZZhangJMengHHuangB. 2012b. Genomewide identification and profiling of microRNA-like RNAs from Metarhizium anisopliae during development. Fungal Biol 116:1156–1162, doi:10.1016/j.funbio.2012.09.001
   PubMedGoogle Scholar
• ZongJYaoXYinJZhangDMaH. 2009. Evolution of the RNA-dependent RNA polymerase (RdRP) genes: duplications and possible losses before and after the divergence of major eukaryotic groups. Gene 447:29–39, doi:10.1016/j.gene.2009.07.004
   PubMed Web of Science ®Google Scholar