scholarly journals fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Roshan Regmi ◽  
Toby E. Newman ◽  
Lars G. Kamphuis ◽  
Mark C. Derbyshire
Keyword(s):  
Disease Resistance ◽  
Small Rnas ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Differentially Expressed ◽  
Disease Resistance Gene ◽  
Ethylene Response Factor ◽  
Post Inoculation ◽  
Necrotrophic Pathogen ◽  
Degradome Sequencing

Abstract Background Small RNAs are short non-coding RNAs that are key gene regulators controlling various biological processes in eukaryotes. Plants may regulate discrete sets of sRNAs in response to pathogen attack. Sclerotinia sclerotiorum is an economically important pathogen affecting hundreds of plant species, including the economically important oilseed B. napus. However, there are limited studies on how regulation of sRNAs occurs in the S. sclerotiorum and B. napus pathosystem. Results We identified different classes of sRNAs from B. napus using high throughput sequencing of replicated mock and infected samples at 24 h post-inoculation (HPI). Overall, 3999 sRNA loci were highly expressed, of which 730 were significantly upregulated during infection. These 730 up-regulated sRNAs targeted 64 genes, including disease resistance proteins and transcriptional regulators. A total of 73 conserved miRNA families were identified in our dataset. Degradome sequencing identified 2124 cleaved mRNA products from these miRNAs from combined mock and infected samples. Among these, 50 genes were specific to infection. Altogether, 20 conserved miRNAs were differentially expressed and 8 transcripts were cleaved by the differentially expressed miRNAs miR159, miR5139, and miR390, suggesting they may have a role in the S. sclerotiorum response. A miR1885-triggered disease resistance gene-derived secondary sRNA locus was also identified and verified with degradome sequencing. We also found further evidence for silencing of a plant immunity related ethylene response factor gene by a novel sRNA using 5′-RACE and RT-qPCR. Conclusions The findings in this study expand the framework for understanding the molecular mechanisms of the S. sclerotiorum and B. napus pathosystem at the sRNA level.

scholarly journals Combined degradome and replicated small RNA sequencing identifies Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

2020 ◽  
Author(s):  
Roshan Regmi ◽  
Toby E. Newman ◽  
Lars G. Kamphuis ◽  
Mark C. Derbyshire
Keyword(s):  
Brassica Napus ◽  
Small Rnas ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Small Rna Sequencing ◽  
Disease Resistance Gene ◽  
Ethylene Response Factor ◽  
Post Inoculation ◽  
Necrotrophic Pathogen ◽  
Degradome Sequencing

AbstractBackgroundSmall RNAs are short non-coding RNAs that are key gene regulators controlling various biological processes in eukaryotes. Plants may regulate discrete sets of sRNAs in response to pathogen attack. Sclerotinia sclerotiorum is an economically important pathogen affecting hundreds of plant species, including the economically important oilseed Brassica napus. However, there are limited studies on how regulation of sRNAs occurs in the S. sclerotiorum and B. napus pathosystem.ResultsWe identified different classes of sRNAs from B. napus by high throughput sequencing of replicated mock and infected samples at 24 hours post-inoculation (HPI). Overall, 3,999 sRNA loci were highly expressed, of which 730 were significantly upregulated during infection. Degradome sequencing identified numerous likely sRNA targets that were enriched for immunity-related GO terms, including those related to jasmonic acid signalling, during infection. A total of 73 conserved miRNA families were identified in our dataset. Degradome sequencing identified 434 unique cleaved mRNA products from these miRNAs, of which 50 were unique to the infected library. A novel miR1885-triggered disease resistance gene-derived secondary sRNA locus was identified and verified with degradome sequencing. We also experimentally validated silencing of a plant immunity related ethylene response factor gene by a novel sRNA using 5’-RACE.ConclusionsThe findings in this study expand the framework for understanding the molecular mechanisms of the S. sclerotiorum and B. napus pathosystem at the sRNA level.

scholarly journals Integration of Transcriptomes, Small RNAs, and Degradome Sequencing to Identify Putative miRNAs and their Targets Related to Eu-Rubber Biosynthesis in Eucommia ulmoides

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 623
Author(s):  
Jing Ye ◽  
Wenjing Han ◽  
Ruisheng Fan ◽  
Minhao Liu ◽  
Long Li ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Vital Role ◽  
Eucommia Ulmoides ◽  
Messenger Rnas ◽  
Rubber Biosynthesis ◽  
Degradome Sequencing ◽  
The Eu

Eucommia ulmoides has attracted much attention as a valuable natural rubber (Eu-rubber) production tree. As a strategic material, Eu-rubber plays a vital role in general and defence industries. However, the study of Eu-rubber biosynthesis at a molecular level is scarce, and the regulatory network between microRNAs (miRNAs) and messenger RNAs (mRNAs) in Eu-rubber biosynthesis has not been assessed. In this study, we comprehensively analyzed the transcriptomes, small RNAs (sRNAs) and degradome to reveal the regulatory network of Eu-rubber biosynthesis in E. ulmoides. A total of 82,065 unigenes and 221 miRNAs were identified using high-throughput sequencing; 20,815 targets were predicted using psRNATarget software. Of these targets, 779 miRNA-target pairs were identified via degradome sequencing. Thirty-one miRNAs were differentially expressed; 22 targets of 34 miRNAs were annotated in the terpenoid backbone biosynthesis pathway (ko00900) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG). These miRNAs were putatively related to Eu-rubber biosynthesis. A regulatory network was constructed according to the expression profiles of miRNAs and their targets. These results provide a comprehensive analysis of transcriptomics, sRNAs and degradome to reveal the Eu-rubber accumulation, and provide new insights into genetic engineering techniques which may improve the content of Eu-rubber in E. ulmoides.

scholarly journals Identification of Differentially Expressed Proteins in Sugarcane in Response to Infection by Xanthomonas albilineans Using iTRAQ Quantitative Proteomics

2020 ◽  
Vol 8 (1) ◽  
pp. 76
Author(s):  
Jian-Yu Meng ◽  
Mbuya Sylvain Ntambo ◽  
Philippe C. Rott ◽  
Hua-Ying Fu ◽  
Mei-Ting Huang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Vascular System ◽  
Lipid Transfer Protein ◽  
Differentially Expressed ◽  
Post Inoculation ◽  
Differentially Expressed Proteins ◽  
Lipid Transfer ◽  
Leaf Scald ◽  
Improvement Programs ◽  
Xanthomonas Albilineans

Sugarcane can suffer severe yield losses when affected by leaf scald, a disease caused by Xanthomonas albilineans. This bacterial pathogen colonizes the vascular system of sugarcane, which can result in reduced plant growth and plant death. In order to better understand the molecular mechanisms involved in the resistance of sugarcane to leaf scald, a comparative proteomic study was performed with two sugarcane cultivars inoculated with X. albilineans: one resistant (LCP 85-384) and one susceptible (ROC20) to leaf scald. The iTRAQ (isobaric tags for relative and absolute quantification) approach at 0 and 48 h post-inoculation (hpi) was used to identify and annotate differentially expressed proteins (DEPs). A total of 4295 proteins were associated with 1099 gene ontology (GO) terms by GO analysis. Among those, 285 were DEPs during X. albilineans infection in cultivars LCP 85-384 and ROC20. One hundred seventy-two DEPs were identified in resistant cultivar LCP 85-384, and 113 of these proteins were upregulated and 59 were downregulated. One hundred ninety-two DEPs were found in susceptible cultivar ROC20 and half of these (92) were upregulated, whereas the other half corresponded to downregulated proteins. The significantly upregulated DEPs in LCP 85-384 were involved in metabolic pathways, the biosynthesis of secondary metabolites, and the phenylpropanoid biosynthesis pathway. Additionally, the expression of seven candidate genes related to photosynthesis and glycolytic pathways, plant innate immune system, glycosylation process, plant cytochrome P450, and non-specific lipid transfer protein was verified based on transcription levels in sugarcane during infection by X. albilineans. Our findings shed new light on the differential expression of proteins in sugarcane cultivars in response to infection by X. albilineans. The identification of these genes provides important information for sugarcane variety improvement programs using molecular breeding strategies.

scholarly journals Identification of the Genetic Basis for the Large-tailed Phenotypic Trait in Han Sheep Through Integrated mRNA and miRNA Analysis of Tail Fat Tissue Samples

2020 ◽  
Author(s):  
Yang Guangli ◽  
Zhang Huan ◽  
Zhang Shuhong ◽  
Li Zhiqiang ◽  
Gao Fengyi ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Future Research ◽  
Phenotypic Trait ◽  
Fatty Tissue ◽  
Fat Tissue ◽  
Tissue Samples

Abstract Background: While evolution has led certain breeds of sheep to exhibit large tails composed of fatty tissue, the genetic basis for this fatty large-tailed phenotypic trait remains to be defined in breeds of Han sheep. Here, we employed a high-throughput sequencing approach to identify mRNAs and microRNAs (miRNAs) that were differentially expressed in tail fat tissue samples from large-tailed Han (LTH) and small-tailed Han (STH) sheep in order to identify key genetic determinants of the large-tailed phenotype.Results: In total, we identified 521 mRNAs (237 upregulated, 284 downregulated) and 14 miRNAs (6 upregulated, 8 downregulated) that were differentially expressed between these two sheep breeds. Predictive analytical database tools were subsequently utilized to identify 2,409 putative targets of these differentially expressed miRNAs (DEMs), including 65 which were among the list of differentially expressed genes (DEGs) identified in the present study. By specifically focusing on predicted DEM/DEG pairs with appropriate regulatory directionality, we identified DIRF, HSD17B12, LPL, APOBR, INSIGI, THRSP, ACSL5, FAAH, ACSS2, APOA1, ACLY, and ACSM3 through mRNA analyses and ACSL4, FTO, FGF8, IGF2, GNPDA2, LIPG, PRKAA2, ELOVL7, SOAT2, and SIRT1 through miRNA analyses as candidate genes which may regulate fat deposition and fatty acid metabolism in the adipose tissue from the tails of Han sheep. Conclusion: Together, our data provide insight into the potential genetic basis for the large-tailed phenotype of LTH sheep, suggesting that it may be attributable to specific DEMs and DEGs that regulate one another and thereby control lipid metabolism. These data provide a basis for future research regarding the role of these genes in ovine tail fat deposition, and offer preliminary perspectives on the molecular mechanisms governing the fatty large-tailed phenotype in LTH sheep.

scholarly journals Small RNAs and Gene Network in a Durable Disease Resistance Gene—Mediated Defense Responses in Rice

PLoS ONE ◽  
2015 ◽  
Vol 10 (9) ◽  
pp. e0137360 ◽  
Author(s):  
Hanming Hong ◽  
Yanyan Liu ◽  
Haitao Zhang ◽  
Jinghua Xiao ◽  
Xianghua Li ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Resistance Gene ◽  
Small Rnas ◽  
Gene Network ◽  
Defense Responses ◽  
Disease Resistance Gene ◽  
Durable Disease Resistance

scholarly journals Multi-omics Analysis Reveals Whether and how Naphthylacetic Acid Affects the Quality of Rehmannia Glutinosa

2020 ◽  
Author(s):  
Jianjun LI ◽  
Luying SHAO ◽  
Jialin ZHU ◽  
Jingxiao MA ◽  
Yanqing ZHOU ◽  
...  
Keyword(s):  
Small Rna ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Rehmannia Glutinosa ◽  
Degradome Sequencing ◽  
Differentially Expressed Mirnas ◽  
Naphthylacetic Acid

Abstract Background: Rehmannia glutinosa (R.glutinosa) is an important medicinal plant. The tuberous root of R.glutinosa is often used as herbal medicine. Naphthylacetic acid (NAA) as expansin can improve its yield, but knowledge about gene regulation and metabolome in its root is limited.Results: Full-length transcriptome, next generation transcriptome(NGS), small RNA and degradome sequencing and metabolomics were used to elucidate whether and how NAA affected its quality.30 differential expression metabolites (DEMs) (11 upregulated, 19downregulated) were identified, but catalpol and Rehmannioside D as quality standards were unchanged in its tuberous roots under control and NAA conditions (CKs and NTs); Their NGS identified 1,113 differentially expressed transcripts (DETs) (596 upregulated, 517downregulated) verified by RT-qPCR; Small RNA sequencing identified 78miRNAs (11known, 67 novel), of which 3 were differentially expressed miRNAs (1upregulated, 2downregulated). Among them, 274 differentially expressed miRNAs target transcripts (DEMTs) were predicted found and then validated by degradome sequencing; DETs and DEMTs were mainly related to metabolism. 4 miRNA-mRNA interaction pairs that regulates 4 metabolites (2 negatively correlated, 2 positively correlated) were identified; DETs, DEMs, differentially expressed miRNAs and DEMTs involved in phenylpropanoid biosynthesis regulated metabolites.Conclusions: The identification of DETs, DEMs, differentially expressed miRNAs and DEMTs could help to elucidate the regulatory networks and molecular mechanisms important for NAA-improving root quality of R.glutinosa.

scholarly journals Identification and Characterization of Long Non-Coding RNA in Tomato Roots under Salt Stress

2021 ◽  
Author(s):  
Ning Li ◽  
Zhongyu Wang ◽  
Baike Wang ◽  
Juan Wang ◽  
Ruiqiang Xu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Differentially Expressed ◽  
Vegetable Crops ◽  
Tomato Roots ◽  
Non Coding Rnas

As one of the most important vegetable crops in the world, the production of tomatoes was restricted by salt stress. Therefore, it is of great interest to analyze the salt stress tolerance genes. As the non-coding RNAs (ncRNAs) with a length of more than 200 nucleotides, long non-coding RNAs (lncRNAs) lack the ability of protein-coding, but they can play crucial roles in plant development and response to abiotic stresses by regulating gene expression. Nevertheless, there are few studies on the roles of salt-induced lncRNAs in tomatoes. Therefore, we selected wild tomato Solanum pennellii (S. pennellii) and cultivated tomato M82 to be materials. By high-throughput sequencing, 1044 putative lncRNAs were identified here. Among them, 154 and 137 lncRNAs were differentially expressed in M82 and S. pennellii, respectively. Through functional analysis of target genes of differentially expressed lncRNAs (DE-lncRNAs), some genes were found to respond positively to salt stress by participating in Abscisic Acid (ABA) signaling pathway, brassinosteroid (BR) signaling pathway, ethylene (ETH) signaling pathway and anti-oxidation process. We also construct a salt-induced lncRNA-mRNA co-expression network to dissect the putative mechanisms of high salt tolerance in S. pennellii. We analyze the function of salt-induced lncRNAs in tomato roots at the genome-wide levels for the first time. These results will contribute to understanding the molecular mechanisms of salt tolerance in tomatoes from the perspective of lncRNAs.

scholarly journals Identification of miRNAs and Their Target Genes Involved in Cucumber Fruit Expansion Using Small RNA and Degradome Sequencing

Biomolecules ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 483 ◽  
Author(s):  
Sun ◽  
Luo ◽  
Chang ◽  
Li ◽  
Zhou ◽  
...  
Keyword(s):  
Small Rna ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Sequencing Data ◽  
Degradome Sequencing ◽  
Complex Biological Process ◽  
Cucumber Fruit ◽  
Differentially Expressed Mirnas

Fruit expansion is an essential and very complex biological process. Regulatory roles of microRNAs (miRNAs) and miRNA–mRNA modules in the cucumber fruit expansion are not yet to be investigated. In this work, 1253 known and 1269 novel miRNAs were identified from nine cucumber fruit small RNA (sRNA) libraries through high-throughput sequencing. A total of 105 highly differentially expressed miRNAs were recognized in the fruit on five days post anthesis with pollination (EXP_5d) sRNA library. Further, expression patterns of 11 differentially expressed miRNAs were validated by quantitative real-time PCR (qRT-PCR). The expression patterns were similar to sRNAs sequencing data. Transcripts of 1155 sequences were predicted as target genes of differentially expressed miRNAs by degradome sequencing. Gene Ontology (GO) enrichment showed that these target genes were involved in 24 biological processes, 15 cell components and nine molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that these target genes were significantly enriched in 19 pathways and the enriched KEGG pathways were associated with environmental adaptation, signal transduction and translation. Based on the functional prediction of miRNAs and target genes, our findings suggest that miRNAs have a potential regulatory role in cucumber fruit expansion by targeting their target genes, which provide important data for understanding the miRNA-mediated regulatory networks controlling fruit expansion in cucumber. Specific miRNAs could be selected for further functional research and molecular breeding in cucumber.

scholarly journals Early Transcriptional Response to DNA Virus Infection in Sclerotinia sclerotiorum

Viruses ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 278 ◽  
Author(s):  
Feng Ding ◽  
Jiasen Cheng ◽  
Yanping Fu ◽  
Tao Chen ◽  
Bo Li ◽  
...  
Keyword(s):  
Signal Transduction ◽  
G Protein ◽  
Sclerotinia Sclerotiorum ◽  
Molecular Mechanisms ◽  
Cell Structure ◽  
Differentially Expressed ◽  
Post Inoculation ◽  
Dna Virus ◽  
Fungal Cell ◽  
Small G Protein

We previously determined that virions of Sclerotinia sclerotiorum hypovirulence associated DNA virus 1 (SsHADV-1) could directly infect hyphae of Sclerotinia sclerotiorum, resulting in hypovirulence of the fungal host. However, the molecular mechanisms of SsHADV-1 virions disruption of the fungal cell wall barrier and entrance into the host cell are still unclear. To investigate the early response of S. sclerotiorum to SsHADV-1 infection, S. sclerotiorum hyphae were inoculated with purified SsHADV-1 virions. The pre- and post-infection hyphae were collected at one–three hours post-inoculation for transcriptome analysis. Further, bioinformatic analysis showed that differentially expressed genes (DEGs) regulated by SsHADV-1 infection were identified in S. sclerotiorum. In total, 187 genes were differentially expressed, consisting of more up-regulated (114) than down-regulated (73) genes. The identified DEGs were involved in several important pathways. Metabolic processes, biosynthesis of antibiotics, and secondary metabolites were the most affected categories in S. sclerotiorum upon SsHADV-1 infection. Cell structure analysis suggested that 26% of the total DEGs were related to membrane tissues. Furthermore, 10 and 27 DEGs were predicted to be located in the cell membrane and mitochondria, respectively. Gene ontology enrichment analyses of the DEGs were performed, followed by functional annotation of the genes. Interestingly, one third of the annotated functional DEGs could be involved in the Ras-small G protein signal transduction pathway. These results revealed that SsHADV-1 virions may be able to bind host membrane proteins and influence signal transduction through Ras-small G protein-coupled receptors during early infection, providing new insight towards the molecular mechanisms of virions infection in S. sclerotiorum.

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