Identification of MiRNA from Eggplant (Solanum melongena L.) by Small RNA Deep Sequencing and Their Response to Verticillium dahliae Infection

Liu, Yang; Jue, Dengwei; Li, Wang; Zhang, Ruijie; Chen, Min; Yang, Qing

doi:10.1371/journal.pone.0072840

Cited by 69 publications

(51 citation statements)

References 64 publications

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“…Previously, a set of miRNAs were identified to be involved in plant immunity against bacterial and viral pathogens (Navarro et al, 2006;Du et al, 2011;Radwan et al, 2011;Seo et al, 2013). Recently, host miRNAs were also found to be responsive to the infection of an increasing list of filamentous pathogens, such as Cronartium quercuum (Lu et al, 2007), Erysiphe graminis (Xin et al, 2010), Fusarium virguliforme (Radwan et al, 2011), Phytophthora sojae (Guo et al, 2011), and Verticillium dahliae (Yin et al, 2012;Yang et al, 2013). In this study, small RNA accumulation in rice seedlings of susceptible and resistant lines upon M. oryzae infection was systemically assayed by deep sequencing.…”

Section: Discussionmentioning

confidence: 99%

Multiple Rice MicroRNAs Are Involved in Immunity against the Blast Fungus Magnaporthe oryzae

Shi

et al. 2013

Plant Physiol.

282

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MicroRNAs (miRNAs) are indispensable regulators for development and defense in eukaryotes. However, the miRNA species have not been explored for rice (Oryza sativa) immunity against the blast fungus Magnaporthe oryzae, the most devastating fungal pathogen in rice production worldwide. Here, by deep sequencing small RNA libraries from susceptible and resistant lines in normal conditions and upon M. oryzae infection, we identified a group of known rice miRNAs that were differentially expressed upon M. oryzae infection. They were further classified into three classes based on their expression patterns in the susceptible japonica line Lijiangxin Tuan Hegu and in the resistant line International Rice Blast Line Pyricularia-Kanto51-m-Tsuyuake that contains a single resistance gene locus, Pyricularia-Kanto 51-m (Pikm), within the Lijiangxin Tuan Hegu background. RNA-blot assay of nine of them confirmed sequencing results. Real-time reverse transcription-polymerase chain reaction assay showed that the expression of some target genes was negatively correlated with the expression of miRNAs. Moreover, transgenic rice plants overexpressing miR160a and miR398b displayed enhanced resistance to M. oryzae, as demonstrated by decreased fungal growth, increased hydrogen peroxide accumulation at the infection site, and up-regulated expression of defense-related genes. Taken together, our data indicate that miRNAs are involved in rice immunity against M. oryzae and that overexpression of miR160a or miR398b can enhance rice resistance to the disease.

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Section: Discussionmentioning

confidence: 99%

Multiple Rice MicroRNAs Are Involved in Immunity against the Blast Fungus Magnaporthe oryzae

Shi

et al. 2013

Plant Physiol.

282

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“…More recently, functions of RNA silencing in plant resistance to fungal pathogens are being revealed. Plant miRNAs are differentially expressed in response to inoculation with fungal pathogens, such as Erysiphe graminis (Xin et al, 2010), Fusarium virguliforme (Radwan et al, 2011), V. dahliae (Yin et al, 2012; Yang et al, 2013), V. longisporum (Shen et al, 2014), M. oryzae (Li et al, 2014), and B. cinerea (Jin and Wu, 2015). More importantly, mutants of key components of the RNA silencing machinery exhibit altered susceptibility to fungal pathogens including two species of Verticillium (Ellendorff et al, 2009; Shen et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification of Dicer-Like, Argonaute, and RNA-Dependent RNA Polymerase Gene Families in Brassica Species and Functional Analyses of Their Arabidopsis Homologs in Resistance to Sclerotinia sclerotiorum

Cao

Wen

et al. 2016

Front. Plant Sci.

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RNA silencing is an important mechanism to regulate gene expression and antiviral defense in plants. Nevertheless, RNA silencing machinery in the important oil crop Brassica napus and function in resistance to the devastating fungal pathogen Sclerotinia sclerotiorum are not well-understood. In this study, gene families of RNA silencing machinery in B. napus were identified and their role in resistance to S. sclerotiorum was revealed. Genome of the allopolyploid species B. napus possessed 8 Dicer-like (DCL), 27 Argonaute (AGO), and 16 RNA-dependent RNA polymerase (RDR) genes, which included almost all copies from its progenitor species B. rapa and B. oleracea and three extra copies of RDR5 genes, indicating that the RDR5 group in B. napus appears to have undergone further expansion through duplication during evolution. Moreover, compared with Arabidopsis, some AGO and RDR genes such as AGO1, AGO4, AGO9, and RDR5 had significantly expanded in these Brassica species. Twenty-one out of 51 DCL, AGO, and RDR genes were predicted to contain calmodulin-binding transcription activators (CAMTA)-binding site (CGCG box). S. sclerotiorum inoculation strongly induced the expression of BnCAMTA3 genes while significantly suppressed that of some CGCG-containing RNA silencing component genes, suggesting that RNA silencing machinery might be targeted by CAMTA3. Furthermore, Arabidopsis mutant analyses demonstrated that dcl4-2, ago9-1, rdr1-1, rdr6-11, and rdr6-15 mutants were more susceptible to S. sclerotiorum, while dcl1-9 was more resistant. Our results reveal the importance of RNA silencing in plant resistance to S. sclerotiorum and imply a new mechanism of CAMTA function as well as RNA silencing regulation.

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“…Viewed from pathogens, it is well known that miRNAs are essential components in plant defense to viral (Ding and Voinnet 2007) and bacterial pathogens (Li et al 2010). Host miRNAs were found to be differentially responsive to the infection of fungal and oomycete pathogens, such as Botrytis cinerea (Jin and Wu 2015), Cronartium quercuum (Lu et al 2007), Erysiphe graminis (Xin et al 2010), Fusarium virguliforme (Radwan et al 2011), Phytophthora sojae (Guo et al 2011), Verticillium dahliae (Yin et al 2012;Yang et al 2013), Verticillium longisporum (Shen et al 2014) and Magnaporthe oryzae (Li et al 2014). However, the role and mechanisms of miRNAs in plant defense to fungal pathogens, especially necrotrophic fungal pathogens such as Sclerotinia sclerotiorum remains poorly understood.…”

Section: Introductionmentioning

confidence: 99%

Tight regulation of the interaction between Brassica napus and Sclerotinia sclerotiorum at the microRNA level

Cao

Zhao

et al. 2016

Plant Mol Biol

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MicroRNAs (miRNAs) are multifunctional non-coding short nucleotide molecules. Nevertheless, the role of miRNAs in the interactions between plants and necrotrophic pathogens is largely unknown. Here, we report the identification of the miRNA repertoire of the economically important oil crop oilseed rape (Brassica napus) and those involved in interacting with its most devastating necrotrophic pathogen Sclerotinia sclerotiorum. We identified 280 B. napus miRNA candidates, including 53 novel candidates and 227 canonical members or variants of known miRNA families, by high-throughput deep sequencing of small RNAs from both normal and S. sclerotiorum-inoculated leaves. Target genes of 15 novel candidates and 222 known miRNAs were further identified by sequencing of degradomes from the two types of samples. MiRNA microarray analysis revealed that 68 miRNAs were differentially expressed between S. sclerotiorum-inoculated and uninoculated leaves. A set of these miRNAs target genes involved in plant defense to S. sclerotiorum and/or other pathogens such as nucleotide binding site-leucine-rich repeat (NBS-LRR) R genes and nitric oxygen and reactive oxygen species related genes. Additionally, three miRNAs target AGO1 and AGO2, key components of post-transcriptional gene silencing (PTGS). Expression of several viral PTGS suppressors reduced resistance to S. sclerotiorum. Arabidopsis mutants of AGO1 and AGO2 exhibited reduced resistance while transgenic lines over-expressing AGO1 displayed increased resistance to S. sclerotiorum in an AGO1 expression level-dependent manner. Moreover, transient over-expression of miRNAs targeting AGO1 and AGO2 decreased resistance to S. sclerotiorum in oilseed rape. Our results demonstrate that the interactions between B. napus and S. sclerotiorum are tightly regulated at miRNA level and probably involve PTGS.

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Identification of MiRNA from Eggplant (Solanum melongena L.) by Small RNA Deep Sequencing and Their Response to Verticillium dahliae Infection

Cited by 69 publications

References 64 publications

Multiple Rice MicroRNAs Are Involved in Immunity against the Blast Fungus Magnaporthe oryzae

Multiple Rice MicroRNAs Are Involved in Immunity against the Blast Fungus Magnaporthe oryzae

Genome-Wide Identification of Dicer-Like, Argonaute, and RNA-Dependent RNA Polymerase Gene Families in Brassica Species and Functional Analyses of Their Arabidopsis Homologs in Resistance to Sclerotinia sclerotiorum

Tight regulation of the interaction between Brassica napus and Sclerotinia sclerotiorum at the microRNA level

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