Identification of Soybean MicroRNAs Involved in Soybean Cyst Nematode Infection by Deep Sequencing

Li, Xiaoyan; Wang, Xue; Zhang, Shaopeng; Liu, Dawei; Duan, Yuxi; Dong, Wei

doi:10.1371/journal.pone.0039650

Cited by 118 publications

(113 citation statements)

References 67 publications

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“…Genome sequences, together with data generated by next-generation sequencing technologies, have enabled the identification and quantification of small RNAs on a genome-wide scale. To date, hundreds of miRNAs have been identified in soybean (Song et al, 2011;Li et al, 2012). However, many newly annotated miRNAs and their targets have not been well verified, and even annotated miRNAs are often later corrected based on more robust experimental data (Jeong et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes

et al. 2014

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Small RNAs are ubiquitous, versatile repressors and include (1) microRNAs (miRNAs), processed from mRNA forming stem-loops; and (2) small interfering RNAs (siRNAs), the latter derived in plants by a process typically requiring an RNAdependent RNA polymerase. We constructed and analyzed an expression atlas of soybean (Glycine max) small RNAs, identifying over 500 loci generating 21-nucleotide phased siRNAs (phasiRNAs; from PHAS loci), of which 483 overlapped annotated protein-coding genes. Via the integration of miRNAs with parallel analysis of RNA end (PARE) data, 20 miRNA triggers of 127 PHAS loci were detected. The primary class of PHAS loci (208 or 41% of the total) corresponded to NB-LRR genes; some of these small RNAs preferentially accumulate in nodules. Among the PHAS loci, novel representatives of TAS3 and noncanonical phasing patterns were also observed. A noncoding PHAS locus, triggered by miR4392, accumulated preferentially in anthers; the phasiRNAs are predicted to target transposable elements, with their peak abundance during soybean reproductive development. Thus, phasiRNAs show tremendous diversity in dicots. We identified novel miRNAs and assessed the veracity of soybean miRNAs registered in miRBase, substantially improving the soybean miRNA annotation, facilitating an improvement of miRBase annotations and identifying at high stringency novel miRNAs and their targets.

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Section: Introductionmentioning

confidence: 99%

An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes

et al. 2014

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“…Compelling evidence indicates that cyst nematodes target and manipulate the expression of several main components of epigenetic machinery, including small interfering RNAs, microRNAs, and DNA methylation (Hewezi et al, 2008Li et al, 2012;Rambani et al, 2015). This raises the question of how nematodes use their effectors to modify the epigenome of infected host cells.…”

Section: Discussionmentioning

confidence: 99%

Cellular Signaling Pathways and Posttranslational Modifications Mediated by Nematode Effector Proteins

Hewezi

2015

Plant Physiol.

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Plant-parasitic cyst and root-knot nematodes synthesize and secrete a suite of effector proteins into infected host cells and tissues. These effectors are the major virulence determinants mediating the transformation of normal root cells into specialized feeding structures. Compelling evidence indicates that these effectors directly hijack or manipulate refined host physiological processes to promote the successful parasitism of host plants. Here, we provide an update on recent progress in elucidating the molecular functions of nematode effectors. In particular, we emphasize how nematode effectors modify plant cell wall structure, mimic the activity of host proteins, alter auxin signaling, and subvert defense signaling and immune responses. In addition, we discuss the emerging evidence suggesting that nematode effectors target and recruit various components of host posttranslational machinery in order to perturb the host signaling networks required for immunity and to regulate their own activity and subcellular localization.The root-knot (Meloidogyne spp.) and cyst (Globodera and Heterodera spp.) nematodes are sedentary endoparasites of the root system in a wide range of plant species. These obligate parasites engage in intricate relationships with their host plants that result in the transformation of normal root cells into specialized feeding sites, which provide the nematodes with all the

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“…We studied genetic mechanisms of increase of sugar beet, cucumber and potato plant resistance to parasitic nematodes H. schachtii, M. incognita and D. destructor under impact of biostimulants: Radostim-super, Avercom and its derivatives. The experiments we based on the assumption that plants, infected with different types of pathogenic or parasitic organisms, increased the synthesis of si/miRNA specific both to own plant mRNA (which expression rises at the specialized infected plant cells and involves plant developmental processes) and to pathogenic or parasitic highly homologous mRNA (Hewezi et al, 2008;Ithal et al, 2007;Katiyar-Agarwal et al, 2006;Klink et al, 2009;Li et al, 2012;Padmanabhan et al, 2009;Patel et al, 2010). We also assumed that the biostimulants induce synthesis of si/miRNA which improves plant immunity through the specified mechanism of si/miRNA action.…”

Section: Discussionmentioning

confidence: 99%

“…Targets for si/miRNA are mRNA transcripts of plant genes which expression is induced during infection (therefore damage of plants by phytopathogens raises), or highly homologous mRNA of pathogenic organisms Hewezi et al, 2008;Katiyar-Agarwal et al, 2006;Li et al, 2012;Padmanabhan et al, 2009;Patel et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Impact of New Natural Biostimulants on Increasing Synthesis in Plant Cells of Small Regulatory si/miRNA With High Anti-Nematodic Activity

Tsygankova¹,

Iutynska²,

Galkin³

et al. 2013

IJB

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Plant endoparasitic cyst nematode Heterodera schachtii Schmidt, gallic nematode Meloidogyne incognita and stem nematode Ditylenchus destructor damage various agricultural crops. The application of ecologically safe natural biostimulants with bioprotective properties is a newer approach for increasing plant resistance to parasitic nematodes. The molecular-genetic analysis of biostimulants action on plant genome is necessary for creation of new effective bioregulators for plant protection against phytopathogenic organisms. In our field and greenhouse experiments, we investigated the influence of new natural biostimulants Avercom and its derivatives on plant protection against nematodes Meloidogyne incognita and Ditylenchus destructor. Considerable increase of resistance to nematodes and productivity of cucumber and potato were observed for plants treated by biostimulant Avercom and its derivatives. Impact of biostimulants Radostim-super and Avercom on increase of resistance of sugar beet and cucumber sprouts to nematodes Heterodera schachtii and Meloidogyne incognita was studied in the laboratory conditions. Comparative analysis of morpho-physiological signs of control and experimental plants showed that plants treated by Radostim-super and Avercom were more viable and resistant to these nematodes as compared to control sprouts. In the molecular-genetic experiments, we studied the impact of these biostimulants on inducing synthesis of small regulatory si/miRNA, which plays key role in plant immune protection. Using method Dot-blot hybridization we studied degree of homology between si/miRNA with mRNA populations, isolated from plants untreated and treated with new natural biostimulants. We found considerable difference in the degree of homology (6-28%) between populations of mRNA and si/miRNA from nematode-infected plants that were either untreated or treated with biostimulants. We have also investigated silencing of translation of mRNA activity of si/miRNA in the wheat embryo cell-free system of protein synthesis. In these experiments, we found high inhibitory activity (38-65%) of si/miRNA from plants treated by biostimulants as compared to low inhibitory activity (15-20%) of si/miRNA from untreated plants. Obtained differences in the degree of homology between populations of mRNA and si/miRNA from untreated and treated with biostimulants plants, which were infected by nematode, and also the high inhibitory activity of si/miRNA from plants treated by biostimulants confirm that these biostimulants induce synthesis of anti-nematodic si/miRNA in plants, resulting in considerable increase of their resistance to these phytopathogens.Keywords: Heterodera schachtii, Meloidogyne іncognita, Ditylenchus destructor, natural biostimulants, anti-nematodic si/miRNA, the degree of homology between mRNA and si/miRNA, silencing activity of si/miRNA in the wheat embryo cell-free system of protein synthesis, plant resistance to nematodes www.ccsenet.org/ijb

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Identification of Soybean MicroRNAs Involved in Soybean Cyst Nematode Infection by Deep Sequencing

Cited by 118 publications

References 67 publications

An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes

An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes

Cellular Signaling Pathways and Posttranslational Modifications Mediated by Nematode Effector Proteins

Impact of New Natural Biostimulants on Increasing Synthesis in Plant Cells of Small Regulatory si/miRNA With High Anti-Nematodic Activity

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