Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae

Nunes, Cristiano C.; Gowda, Malali; Sailsbery, Joshua; Xue, Minfeng; Chen, Feng; Brown, Douglas; Oh, Yeonyee; Mitchell, Thomas K.; Dean, Ralph A.

doi:10.1186/1471-2164-12-288

Cited by 106 publications

(108 citation statements)

References 60 publications

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“…Filamentous fungi, with one billion years of evolution, are an important group of multicellular eukaryotes (Hedges et al 2004). Small RNA pathway also had been proved in filamentous fungi in different researches (Nicolas et al 2010;Nunes et al 2011). Recently, Lee et al (2010) reported that miRNA-like small RNAs (milRNAs) also exist in the filamentous fungus Neurospora crassa.…”

Section: Introductionmentioning

confidence: 99%

Identification of microRNA-like RNAs in a plant pathogenic fungus Sclerotinia sclerotiorum by high-throughput sequencing

et al. 2012

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MicroRNAs are small non-coding RNAs of approximately 22 nt with important regulatory roles in post-transcriptional regulation of gene expression. To date, no miRNAs have been reported in plant pathogenic fungi. Here we used Solexa sequencing to find new miRNAs in a plant pathogenic fungus Sclerotinia sclerotiorum. 13,229,401 high-quality reads were obtained, a total of 5,645,718 reads were mapped to the S. sclerotiorum genome corresponding to 348,108 unique sRNAs. Among the sRNAs, 2 microRNA-like RNAs (milRNAs) and 42 mil-RNA candidates were identified by sequence analysis. Northern blot and RT-PCR results showed that some milRNAs and candidates are differentially expressed in sclerotial development suggesting the role of these milRNAs and candidates in this biological process. Our results provide new insights into the functional roles of small RNAs and add new resources for the study of plant pathogenic fungi.

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Section: Introductionmentioning

confidence: 99%

Identification of microRNA-like RNAs in a plant pathogenic fungus Sclerotinia sclerotiorum by high-throughput sequencing

et al. 2012

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“…Sequencing of sRNAs from many species of fungi has led to the discovery of many classes of them, e.g., siRNAs in Schizosaccharomyces pombe, Saccharomyces castellii, Candida albicans, Cryptococcus neoformans, and Magnaporthe oryzae; qiRNAs (QDE-2-interacting RNAs) in N. crassa; priRNAs (primal small RNAs) in S. pombe; ex-siRNAs (exonic-siRNAs) in Mucor circinelloides and T. atroviride; disiRNAs (Dicer-independent small interfering RNAs) in N. crassa, and milRNAs (miRNAslike small RNAs) in N. crassa, Sclerotinia sclerotiorum, Metharizium anisopliae, C. neoformans, and T. reesei. The functional role of some of these classes of sRNAs has been proven, but for many others it still remains to be shown (50,(55)(56)(57)(58)(59)(60)(61)(62)(63)(64)(65)(66)(67). For T. atroviride, however, a functional characterization of the components of the RNAi machinery is already available.…”

Section: Genome Integrity Genome Defense Mechanismsmentioning

confidence: 99%

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Schmoll

Dattenböck

Carreras-Villaseñor

et al. 2016

Microbiol Mol Biol Rev

163

195

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SUMMARYThe genusTrichodermacontains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for “hot topic” research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism inT. reesei,T. atroviride, andT. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of eachTrichodermaspecies discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved inN-linked glycosylation was detected, as were indications for the ability ofTrichodermaspp. to generate hybrid galactose-containingN-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique toTrichoderma, and these warrant further investigation. We found interesting expansions in theTrichodermagenus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique toT. atrovirideis the duplication of the alternative sulfur amino acid synthesis pathway.

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“…Based on their RNA precursors and biogenesis mechanisms, these small RNAs can be divided into various types in fungi, including QDE-2-interacting small RNAs (qiRNAs), microRNA-like RNAs (milRNAs), Dicer-independent small interfering RNAs (disiRNAs), small interfering RNAs (siRNAs), long terminal repeat retrotransposon-siRNAs (LTR-siRNAs) and tRNA-derived RNA fragments (tRFs) (Jöchl et al 2008; Lee et al 2009; Nicolas et al 2010; Nunes et al 2011). The maturation of small RNAs in the RNA-silencing pathway is dependent on the RNase III ribonuclease Dicer, RNA-dependent RNA polymerases (RdRps) and Argonaute proteins (Lee et al 2010).…”

Section: Introductionmentioning

confidence: 99%

Qipgene inFusarium oxysporumis required for normal hyphae morphology and virulence

et al. 2015

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Ribonucleic acid (RNA)-silencing mechanisms exist in many eukaryotes to regulate a variety of biological processes. The known molecular components are related to Dicers, Argonautes and RNA-dependent RNA polymerases. Previous biochemical studies have also suggested that Qip, with an exonuclease domain, facilitates the conversion of duplex small interfering RNAs into single strands. In our study, the Qip gene in Fusarium oxysporum was disrupted using homologous recombination technology. The deletion of the Qip gene resulted in a decrease in colony growth rates but increased the number of branches. Additionally, the ΔQip mutant had a reduced pathogenicity in cabbage. Our results show Qip gene in F. oxysporum is required for normal hyphae morphology and virulence. The mutant will be useful for elucidating the relationship between the RNA-silencing mechanism and hyphal growth and development in F. oxysporum.

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Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae

Cited by 106 publications

References 60 publications

Identification of microRNA-like RNAs in a plant pathogenic fungus Sclerotinia sclerotiorum by high-throughput sequencing

Identification of microRNA-like RNAs in a plant pathogenic fungus Sclerotinia sclerotiorum by high-throughput sequencing

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Qipgene inFusarium oxysporumis required for normal hyphae morphology and virulence

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