Transcriptome analysis of rice leaves in response to Rhizoctonia solani infection and reveals a novel regulatory mechanism

2020 ◽  
Vol 14 (5) ◽  
pp. 559-573 ◽  
Author(s):  
De Peng Yuan ◽  
Xiao Feng Xu ◽  
Woo-Jong Hong ◽  
Si Ting Wang ◽  
Xin Tong Jia ◽  
...  
Keyword(s):  
Rhizoctonia Solani ◽  
Transcriptome Analysis ◽  
Regulatory Mechanism ◽  
Rice Leaves

scholarly journals Plant Hormone Metabolome and Transcriptome Analysis of Dwarf and Wild-type Banana

2021 ◽  
Author(s):  
Biao Deng ◽  
Xuan Wang ◽  
Xing Long ◽  
Ren Fang ◽  
Shuangyun Zhou ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcriptome Analysis ◽  
Regulatory Mechanism ◽  
Feedback Regulation ◽  
Wild Type ◽  
Hormone Levels ◽  
Transporter Protein ◽  
Repressor Proteins ◽  
Differential Gene ◽  
The Relationship

AbstractGibberellin (GA), auxin (IAA) and brassinosteroid (BR) are indispensable in the process of plant growth and development. Currently, research on the regulatory mechanism of phytohormones in banana dwarfism is mainly focused on GA, and few studies are focused on IAA and BR. In this study, we measured the contents of endogenous GA, IAA and BR and compared the transcriptomes of wild-type Williams banana and its dwarf mutant across five successive growth periods. We investigated the relationship between hormones and banana dwarfism and explored differential gene expression through transcriptome analysis, thus revealing the possible metabolic regulatory mechanism. We inferred a complex regulatory network of banana dwarfing. In terms of endogenous hormone levels, GA and IAA had significant effects on banana dwarfing, while BR had little effect. The key gene in GA biosynthesis of is GA2ox, and the key genes in IAA biosynthesis are TDC and YUCCA. The differential expression of these genes might be the main factor affecting hormone levels and plant height. In terms of hormone signal transduction, DELLA and AUX/IAA repressor proteins were the core regulators of GA and IAA, respectively. They inhibited the process of signal transduction and had feedback regulation on hormone levels. Finally, the transporter protein PIN, AUX1/LAX protein family and ABCB subfamily played supplementary roles in the transport of IAA. These results provide new insights into GA and IAA regulation of banana growth and a reliable foundation for the improvement of dwarf varieties.

scholarly journals Transcriptome analysis reveals the host selection fitness mechanisms of the Rhizoctonia solani AG1IA pathogen

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Yuan Xia ◽  
Binghong Fei ◽  
Jiayu He ◽  
Menglin Zhou ◽  
Danhua Zhang ◽  
...  
Keyword(s):  
Rhizoctonia Solani ◽  
Transcriptome Analysis ◽  
Host Selection

scholarly journals De novo Transcriptome Assembly and Comparative Analysis Highlight the Primary Mechanism Regulating the Response to Selenium Stimuli in Oats (Avena sativa L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Tao Liu ◽  
Xiaoting Liu ◽  
Rangrang Zhou ◽  
Hong Chen ◽  
Huaigang Zhang ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Regulatory Mechanism ◽  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Processing Technique ◽  
Sodium Selenate ◽  
Control Group ◽  
Primary Mechanism ◽  
High Selenium

Selenium is an essential microelement for humans and animals. The specific processing technique of oats can maximize the preservation of its nutrients. In this study, to understand the genetic response of oats in a high-selenium environment, oats were treated with sodium selenate for 24 h, and transcriptome analysis was performed. A total of 211,485,930 clean reads composing 31.30 Gb of clean data were retained for four samples. After assembly, 186,035 unigenes with an average length of 727 bp were generated, and the N50 length was 1,149 bp. Compared with that in the control group, the expression of 7,226 unigenes in the treatment group was upregulated, and 2,618 unigenes were downregulated. Based on the sulfur assimilation pathway and selenocompound metabolic pathway, a total of 27 unigenes related to selenate metabolism were identified. Among them, the expression of both key genes APS (ATP sulfurylase) and APR (adenosine 5′-phosphosulfate reductase) was upregulated more than 1,000-fold under selenate treatment, while that of CBL (cystathionine-β-synthase) was upregulated 3.12-fold. Based on the transcriptome analysis, we suspect that the high-affinity sulfur transporter Sultr1;2 plays a key role in selenate uptake in oats. A preliminary regulatory mechanism explains the oat response to selenate treatment was ultimately proposed based on the transcriptome analysis and previous research.

scholarly journals Integrative transcriptome analysis discloses the molecular basis of a heterogeneous fungal phytopathogen complex, Rhizoctonia solani AG-1 subgroups

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Naoki Yamamoto ◽  
Yanran Wang ◽  
Runmao Lin ◽  
Yueyang Liang ◽  
Yao Liu ◽  
...  
Keyword(s):  
Rhizoctonia Solani ◽  
Transcriptome Analysis ◽  
Molecular Basis ◽  
Ethylene Biosynthesis ◽  
Fungal Species ◽  
Detoxification Enzymes ◽  
Secreted Proteins ◽  
Evolutionary Trajectory ◽  
Pathogenic Factors ◽  
Allergen Protein

AbstractRhizoctonia solani is a fungal species complex that causes necrotrophic crop diseases. It comprises several anastomosis groups, some of which include intra-subgroups, such as AG-1 IA and AG-1 IB, exhibiting varying pathogenicity. Owing to its heterozygous and multinucleate features, genomic analyses of R. solani are still challenging, and understanding of its genetic diversity and genic components is limited. In this study, in order to elucidate the molecular basis of this phytopathogen complex, an integrated transcriptome analysis was undertaken for three subgroups of AG-1, i.e. AG-1 IA, AG-1 IB, and AG-1 IC. Sequence variations suggested substantial evolutionary distances within AG-1. Transcript simple sequence repeats showed comparable characteristics among AG-1, but contained polymorphic sites. Intra-subgroup polymorphisms suggested varying genic heterozygosity within AG-1, suggesting their independent evolutionary trajectory. Sequences of pathogenic factors, phytotoxin biosynthesis pathway enzymes, secreted lignocellulosic enzymes, secreted reactive oxygen species detoxification enzymes, apoplastic/cytoplasmic effector candidates, were conserved among those subgroups. dN/dS ratios of a secretome subset suggested core secreted proteins in AG-1 and distinct evolution of Cys-rich small secreted proteins after differentiation of AG-1 subgroups. Identification of likely pathogenic factors including allergen protein homologues, oxidative phosphorylation and ethylene biosynthesis pathways, and diversification of polysaccharide monooxygenases provides molecular insight into key genomic components that play a role in R. solani pathogenesis.

scholarly journals Transcriptome analysis of two inflorescence branching mutants reveals cytokinin is an important regulator in controlling inflorescence architecture in the woody plant Jatropha curcas

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Mao-Sheng Chen ◽  
Mei-Li Zhao ◽  
Gui-Juan Wang ◽  
Hui-Ying He ◽  
Xue Bai ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Metabolic Pathway ◽  
Jatropha Curcas ◽  
Woody Plant ◽  
Regulatory Mechanism ◽  
Adenosine Kinase ◽  
Inflorescence Architecture ◽  
Inflorescence Development ◽  
Order Branch ◽  
Important Regulator

Abstract Background In higher plants, inflorescence architecture is an important agronomic trait directly determining seed yield. However, little information is available on the regulatory mechanism of inflorescence development in perennial woody plants. Based on two inflorescence branching mutants, we investigated the transcriptome differences in inflorescence buds between two mutants and wild-type (WT) plants by RNA-Seq to identify the genes and regulatory networks controlling inflorescence architecture in Jatropha curcas L., a perennial woody plant belonging to Euphorbiaceae. Results Two inflorescence branching mutants were identified in germplasm collection of Jatropha. The duo xiao hua (dxh) mutant has a seven-order branch inflorescence, and the gynoecy (g) mutant has a three-order branch inflorescence, while WT Jatropha has predominantly four-order branch inflorescence, occasionally the three- or five-order branch inflorescences in fields. Using weighted gene correlation network analysis (WGCNA), we identified several hub genes involved in the cytokinin metabolic pathway from modules highly associated with inflorescence phenotypes. Among them, Jatropha ADENOSINE KINASE 2 (JcADK2), ADENINE PHOSPHORIBOSYL TRANSFERASE 1 (JcAPT1), CYTOKININ OXIDASE 3 (JcCKX3), ISOPENTENYLTRANSFERASE 5 (JcIPT5), LONELY GUY 3 (JcLOG3) and JcLOG5 may participate in cytokinin metabolic pathway in Jatropha. Consistently, exogenous application of cytokinin (6-benzyladenine, 6-BA) on inflorescence buds induced high-branch inflorescence phenotype in both low-branch inflorescence mutant (g) and WT plants. These results suggested that cytokinin is an important regulator in controlling inflorescence branching in Jatropha. In addition, comparative transcriptome analysis showed that Arabidopsis homologous genes Jatropha AGAMOUS-LIKE 6 (JcAGL6), JcAGL24, FRUITFUL (JcFUL), LEAFY (JcLFY), SEPALLATAs (JcSEPs), TERMINAL FLOWER 1 (JcTFL1), and WUSCHEL-RELATED HOMEOBOX 3 (JcWOX3), were differentially expressed in inflorescence buds between dxh and g mutants and WT plants, indicating that they may participate in inflorescence development in Jatropha. The expression of JcTFL1 was downregulated, while the expression of JcLFY and JcAP1 were upregulated in inflorescences in low-branch g mutant. Conclusions Cytokinin is an important regulator in controlling inflorescence branching in Jatropha. The regulation of inflorescence architecture by the genes involved in floral development, including TFL1, LFY and AP1, may be conservative in Jatropha and Arabidopsis. Our results provide helpful information for elucidating the regulatory mechanism of inflorescence architecture in Jatropha.

scholarly journals Transcriptome analysis of rice leaves in response to Rhizoctonia solani infection

2019 ◽  
Author(s):  
De Peng Yuan ◽  
Chong Zhang ◽  
Si Ting Wang ◽  
Yang Liu ◽  
Shuang Li ◽  
...  
Keyword(s):  
Rhizoctonia Solani ◽  
Differentially Expressed Genes ◽  
Defense Mechanisms ◽  
Differentially Expressed ◽  
Control Group ◽  
Sequencing Analysis ◽  
Kegg Pathways ◽  
Sheath Blight Disease ◽  
Rice Leaves ◽  
Mapman Analysis

Abstract Background: Sheath blight disease (ShB) is one of the important diseases that severely affects rice production. However, the mechanism of defense against ShB remains unclear. To understand the molecular mechanism of rice defense to ShB, an RNA-sequencing analysis was performed using Rhizoctonia solani AG1-IA-inoculated rice leaves. Results: After 48 hours of inoculation, 6,838 genes were differentially expressed in rice leaves (>2 fold, P<0.05). Among them, 3,802 genes were upregulated, while 3,036 were downregulated compared to the control group. In addition, the differentially expressed genes were classified via GO, KEGG, and Mapman analyses. Thirty GO terms, including biological process, molecular function, and cellular component, were significantly enriched, and 30 KEGG pathways included ribosome, carbon metabolism, and biosynthesis of amino acids. A Mapman analysis demonstrated that the phytohormone and metabolic pathways were significantly altered. Interestingly, the expression levels of 359 transcription factors, including WRKY, MYB, and NAC family members, as well as 239 transporter genes, including ABC, MFS, and SWEET, were significantly changed upon R. solani AG1-IA inoculation. An additional genetic study showed that OsWRKY53 negatively and OsAKT1 positively regulate rice defense to R. solani, respectively. In addition, interestingly, many differentially expressed genes contain R. solani-responsive cis-elements in their promoter region. Conclusions: Taken together, our analyses provide valuable information for the additional study of rice defense mechanisms to ShB, and the genes identified could be useful in the future to breed resistant rice.

scholarly journals Phytotoxin of Rice Aggregate Sheath Spot Pathogen Rhizoctonia oryzae-sativae and Its Biological Activities

2021 ◽  
Author(s):  
Xiaoyu Wang ◽  
Aimin Wang ◽  
Zhiyi Chen ◽  
Lihui Wei
Keyword(s):  
Rhizoctonia Solani ◽  
Biological Activities ◽  
Mass Spectrometry Data ◽  
Gas Chromatography Mass Spectrometry ◽  
Yield Losses ◽  
Growth Status ◽  
Spot Disease ◽  
Detached Leaf ◽  
Rhizoctonia Oryzae ◽  
Rice Leaves

Rice aggregate sheath spot disease occurs in many countries, causing serious yield losses. In China, the disease-causing fungus Rhizoctonia oryzae-sativae was reported in 1985, and since then, it has rarely been reported in major rice-growing areas after almost 30 years. Compared with Rhizoctonia solani, R. oryzae-sativae has a significantly different physiological morphology and growth status, although both fungi affect rice leaves in very similar ways. The optimum temperature for the suitable growth of R. oryzae-sativae is 31 °C, which is consistent with previous reports. We extracted phytotoxins from R. oryzae-sativae and analyzed its biological activity via the detached leaf and radicle inhibition methods. Rhizoctonia solani and R. oryzae-sativae exhibit differences in terms of pathogenicity and toxins activity, which indicates that these fungi may produce different toxins components. Based on gas chromatography–mass spectrometry data, esters, phenols, and other components were present in the crude toxins extract of R. oryzae-sativae. Our research provides a new method for studying the phytotoxins of R. oryzae-sativae. However, further studies are needed to elucidate the pathogenic mechanisms responsible for the aggregate sheath spot disease on rice.

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