Comparative RNA-Seq analysis of Nicotiana benthamiana in response to Phytophthora parasitica infection

Shen, Danyu; Chai, Chun-Yue; Ma, Lina; Zhang, Meixiang; Dou, Daolong

doi:10.1007/s10725-016-0163-1

Cited by 20 publications

(18 citation statements)

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“…Foliar application of JA in potato and tomato have been shown to induce resistance against Phytophthora infestans (Cohen et al, 1993). In case of N. benthamiana-P. parasitica interactions, induction of JA and ET pathway is reported but SA pathway was not seen to be activated (Shen et al, 2016). Plants generally activates JA/ET pathway and repress the SA pathway infected by necrotrophic pathogens.…”

Section: Discussionmentioning

confidence: 95%

“…The mechanism of plant's response to pathogens and development of resistance or tolerant response is a complex phenomenon that involves interconnected network of changes in several regular physiological processes(Jones and Dangl, 2006) that is clearly reflected in transcriptome-based studies of several different plant-pathogen systems(Adhikari et al, 2012;Chen et al, 2014;Gao et al, 2013; Judelson et al, 2008;Kunjeti et al, 2012). Consistent with gene expression profiles of Nicotiana benthamiana leaves and A. thaliana roots infected with P. parasitica during compatible interaction(Le Berre et al, 2017;Shen et al, 2016), transmembrane transport, protein kinase activity, iron ion binding, carbohydrate metabolism, phosphotransferase activity and many other daughter terms of biological and molecular processes were significantly enriched among both up and downregulated DETs in citrus roots. Unlike susceptible A. thaliana roots where number of DEGs didn't increase considerably with time during P. parasitica infection (Le Berre et al, 2017), total number of DETs increased in citrus roots from 24 hpi to 48 hpi suggesting induction of stronger defense response towards P. parasitica overtime that can be related to tolerance response during later stages (Figure 7 and Figure S4).Upon perception of pathogen generation of reactive oxygen species (ROS) has been reported as one of the earliest defense strategies in plants(Elmayan and Simon-Plas, 2007).…”

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confidence: 95%

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Transcriptome profile of Carrizo citrange roots in response toPhytophthora parasiticainfection

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Huguet‐Tapia

Ali

2019

Preprint

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Phytophthora parasitica is one of the most widespread Phytophthora species, which is known to cause root rot, foot rot/gummosis and brown rot of fruits in citrus. In this study, we have analyzed the transcriptome of a commonly used citrus rootstock Carrizo citrange in response to P. parasitica infection using the RNA-seq technology. In total, we have identified 6692 differentially expressed transcripts (DETs) among P. parasitica-inoculated and mock-treated roots. Of these, 3960 genes were differentially expressed at 24 hours post inoculation and 5521 genes were differentially expressed at 48 hours post inoculation. Gene ontology analysis of DETs suggested substantial transcriptional reprogramming of diverse cellular processes particularly the biotic stress response pathways in Carrizo citrange roots. Many R genes, transcription factors, and several other genes putatively involved in plant immunity were differentially modulated in citrus roots in response to P. parasitica infection. Analysis reported here lays out a strong foundation for future studies aimed at improving resistance of citrus rootstocks to P. parasitica.

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Section: Discussionmentioning

confidence: 95%

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confidence: 95%

Transcriptome profile of Carrizo citrange roots in response toPhytophthora parasiticainfection

Naveed

Huguet‐Tapia

Ali

2019

Preprint

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“…Cell death caused by NL1 on mature leaves of S. babylonica was visualized using the trypan blue staining method (Shen, Chai, Ma, Zhang, & Dou, ) during the symptomless stage. The trypan blue solution was prepared by mixing 10 g of phenol, 10 ml of glycerol, 10 ml of lactic acid, 10 ml of distilled water and 0.02 g of trypan blue.…”

Section: Methodsmentioning

confidence: 99%

Molecular identification and characterization of Elsinoë murrayae (Synonym: Sphaceloma murrayae) from weeping willow

Zhao

Zhang

Xiao

et al. 2017

Journal of Phytopathology

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Sphaceloma murrayae is a significant fungal pathogen of Salix spp. It causes greyish‐white leaf spots, which were reported worldwide except in China. Its morphological characteristics were described in the early literature; however, there is a lack of molecular information pertaining to this fungus. This study identified and characterized three fungal isolates that obtained from weeping willow leaf spots in China. Based on disease symptoms, morphological characteristics and single nomenclature rules for fungi, these isolates are proposed to be new combinations of Elsinoë murrayae (Synonym: S. murrayae). Phylogenetic analysis that combined internal transcribed spacer (ITS), large subunit (LSU), RBP2 and TEF1‐α DNA sequences indicated that E. murrayae isolates and Elsinoë salicina—another Elsinoë sp. isolated from Salix sp.—were distinguishable species. With trypan blue staining and stereomicroscopic observation, we found that large‐scale cell death occurred at 2 days postinoculation (dpi) and slight disease symptoms started at 3 dpi when the conidia were inoculated on Salix babylonica leaves. Pathogenicity analysis revealed that three isolates can successfully infect mature leaves of S. babylonica, Salix fragilis and Salix suchowensis, but not Salix matsudana. In addition, a necrosis‐ and ethylene‐inducing‐like proteins’ (NLP) gene, named EmNLP1, was cloned. The cytotoxicity of EmNLP1 was confirmed by transient assay in tobacco. During infection, EmNLP1 dramatically peaked at 2 dpi and maintained a high‐level expression in the necrosis lesion growing stage.

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“…We also present three papers which investigate the plant transcriptome response to microbial interactions and translate this into validation of the impact of these transcripts on the beneficial trait (Shen et al 2016;Sun et al 2016;Luo et al 2016). Shen et al (2016) investigate plant responses to Phytophthora parasitica, a broad spectrum fungal pathogen, by quantifying differential gene expressions between inoculated and mock-treated Nicotiana benthamiana leaves using RNA-Seq approaches.…”

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confidence: 99%

“…Shen et al (2016) investigate plant responses to Phytophthora parasitica, a broad spectrum fungal pathogen, by quantifying differential gene expressions between inoculated and mock-treated Nicotiana benthamiana leaves using RNA-Seq approaches. A total of 5375 and 3614 genes were found to be upregulated and downregulated, respectively.…”

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confidence: 99%

Plant–microbe interactions: manipulating signals to enhance agricultural sustainability and environmental security

2016

Self Cite

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Microorganisms are involved in many functions which impact plant growth, productivity and tissue quality and the signals that control this interaction with plants is critical. These interactions have global implications for the ecology of natural ecosystems and food security through impacts on crops. Some plant-microbe interactions are beneficial, such as those with nitrogen fixing bacteria or mycorrhizal fungi, while others are detrimental such as those with pathogenic bacteria and fungi. The presence of microorganisms in some cases (i.e. mycorrhizal fungi) is critical in order for plants to survive under extremely P-deficient conditions. For these and other reasons, the impact of plant signals on the survival, success, community behavior and function of species of microorganisms and vice versa is of great interest. Study of impacts on the biodiversity and functionality of the microbial biomass in soils and on plant surfaces such as root and leaves yields insight into such systems. If we can gain understanding into how plants and microorganisms communicate with each other, or how their individual signaling pathways interfere with one another at a biochemical, protein and transcriptional level, then we may be able to manipulate both beneficial and detrimental interactions. If we can do this successfully, we may have a range of opportunities to improve agricultural sustainability and environmental security into the future. This special issue will concentrate on the cutting-edge research in this field of plant-microbe interactions with a view to making recommendations that will enhance agricultural sustainability and food security.In this special issue we present eight papers, which demonstrate how specific individual and communities of microorganisms, including bacteria and fungi, have profound effects on the traits expressed by, biosynthetic pathways regulated by and transcriptional responses of the host plant. We then go on to present some research which harnesses this understanding to enhance plants resistance to pathogens. The papers present research which is focused on both pathogenic and beneficial microorganisms interacting with a range of host plants including ornamentals, those which produce pharmaceuticals, agricultural plants, both legume and cereals, and model plants. The research also covers the role of microorganisms in general growth promotion and tolerance to biotic stress, disease and fungal infection resistance, and abiotic stress including salt tolerance and promotion of nitrogen fixation. Collectively, this research demonstrates that it is possible to develop a fundamental understanding of the biochemical and molecular signals involved in plant responses to microorganisms and translate this into a predictable plant trait response, which has the potential to enhance a plants tolerance to stress.With respect to how plant traits respond to microbial signals we present two papers (Patil et al. 2016;Tsavkelova et al. 2016). In Patil et al. (2016, 136 Pseudomonas isolates were classified based on pl...

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Comparative RNA-Seq analysis of Nicotiana benthamiana in response to Phytophthora parasitica infection

Cited by 20 publications

References 40 publications

Transcriptome profile of Carrizo citrange roots in response toPhytophthora parasiticainfection

Transcriptome profile of Carrizo citrange roots in response toPhytophthora parasiticainfection

Molecular identification and characterization of Elsinoë murrayae (Synonym: Sphaceloma murrayae) from weeping willow

Plant–microbe interactions: manipulating signals to enhance agricultural sustainability and environmental security

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