scholarly journals Integration of small RNA, degradome and proteome sequencing in Oryza sativa reveals a delayed senescence network in tetraploid rice seed

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242260
Author(s):  
Baosheng Huang ◽  
Lu Gan ◽  
Dongjie Chen ◽  
Yachun Zhang ◽  
Yujie Zhang ◽  
...  
Keyword(s):  
Antioxidant Enzymes ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Economic Losses ◽  
Rice Seed ◽  
Sequencing Analysis ◽  
Delayed Senescence ◽  
Degradome Sequencing ◽  
Rice Seeds ◽  
Diploid Rice

Seed of rice is an important strategic resource for ensuring the security of China's staple food. Seed deterioration as a result of senescence is a major problem during seed storage, which can cause major economic losses. Screening among accessions in rice germplasm resources for traits such as slow senescence and increased seed longevity during storage is, therefore, of great significance. However, studies on delayed senescence in rice have been based mostly on diploid rice seed to date. Despite better tolerance have been verified by the artificial aging treatment for polyploid rice seed, the delayed senescence properties and delayed senescence related regulatory mechanisms of polyploid rice seed are rarely reported, due to the lack of polyploid rice materials with high seed set. High-throughput sequencing was applied to systematically investigate variations in small RNAs, the degradome, and the proteome between tetraploid and diploid rice seeds. Degradome sequencing analysis of microRNAs showed that expression of miR-164d, which regulates genes encoding antioxidant enzymes, was changed significantly, resulting in decreased miRNA-mediated cleavage of target genes in tetraploid rice. Comparisons of the expression levels of small RNAs (sRNAs) in the tetraploid and diploid libraries revealed that 12 sRNAs changed significantly, consistent with the findings from degradome sequencing. Furthermore, proteomics also showed that antioxidant enzymes were up-regulated in tetraploid rice seeds, relative to diploids.

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 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 Unique Glutelin Expression Patterns and Seed Endosperm Structure Facilitate Glutelin Accumulation in Polyploid Rice Seed

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Lu Gan ◽  
Baosheng Huang ◽  
Zhaojian Song ◽  
Yachun Zhang ◽  
Yujie Zhang ◽  
...  
Keyword(s):  
Nutritional Value ◽  
Expression Patterns ◽  
Initial Time ◽  
Rice Seed ◽  
Temporal Expression ◽  
Time Duration ◽  
Protein Storage Vacuoles ◽  
Proteomic Analyses ◽  
Rice Seeds ◽  
Diploid Rice

Abstract Background Rice is not only an essential food but also a source of high quality protein. Polyploidy is an evolutionary trajectory in plants, and enhancing glutelin by polyploidization is an attractive strategy for improving the nutritional value of rice seeds and presents a great potential for enhancing the commercial value of rice. Elucidating the mechanisms underlying glutelin synthesis and accumulation in tetraploid rice is of great significance. Results To enhance the nutritional value of rice, we developed tetraploid rice and evaluated the contents of various nutrient elements in mature seeds. The results revealed a significant increase in protein contents, including the total seed storage proteins, glutelins, and amino acids in tetraploid rice when compared with those in diploid rice. Tandem mass tag-based quantitative proteomic analyses of seeds revealed that glutelins regulated by several glutelin genes in 9311-4x were significantly up-regulated (≥1.5-fold), which was further verified by immunoblot analyses. In addition, temporal expression patterns of various glutelin subunits in different rice lines were investigated. The results revealed significant differences in the expression patterns between diploid and tetraploid rice seeds. Cytohistological analyses results revealed that the thickness of aleurone cell layers increased significantly by 32% in tetraploid rice, the structures of protein storage vacuoles (PSVs) in sub-aleurone cells were more diverse and abundant than those of diploid rice. Temporal expression and proteomic analyses results revealed that protein disulfide isomerase-like 1–1 expression levels were higher in tetraploid rice than in diploid rice, and that the gene responded to oxidative folding with increased levels of proglutelin and appropriate distribution of seed glutelins in tetraploid rice. Conclusion The results of the present study revealed that polyploidization increased glutelin content by influencing glutelin biosynthesis, transport, and deposition, while variations in glutelin accumulation between tetraploid and diploid rice were largely manifested in the initial time, duration, and relative levels of various glutelin gene expressions during seed filling stages. These findings provide novel insights into improving the protein quality and nutritional value of rice seeds by polyploid breeding.

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 High-Throughput Sequencing Reveals the Regulatory Networks of Transcriptome and Small RNAs During the Defense Against Marssonina brunnea in Poplar

2021 ◽  
Vol 12 ◽  
Author(s):  
Yangwenke Liao ◽  
Qingyue Zhang ◽  
Rongrong Cui ◽  
Xin Xu ◽  
Fuyuan Zhu ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Small Rnas ◽  
Regulatory Networks ◽  
High Throughput Sequencing ◽  
Mapk Pathway ◽  
Lignin Biosynthesis ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Marssonina Brunnea ◽  
Anti Fungal

MicroRNAs are implicated in the adjustment of gene expression in plant response to biotic stresses. However, the regulatory networks of transcriptome and miRNAs are still poorly understood. In the present study, we ascertained the induction of genes for small RNA biosynthesis in poplar defense to a hemibiotrophic fungus Marssonina brunnea and afterward investigated the molecular regulatory networks by performing comprehensive sequencing analysis of mRNAs and small RNAs in M. brunnea-inoculated leaves. Differentially expressed genes in M. brunnea-infected poplar are mainly involved in secondary metabolisms, phytohormone pathways, the recognition of pathogens, and MAPK pathway in the plant, with real-time quantitative PCR (qPCR) validating the mRNA-seq results. Furthermore, differentially expressed miRNAs, such as MIR167_1-6, MIR167_1-12, MIR171_2-3, MIR395-13, MIR396-3, MIR396-16, MIR398-8, and MIR477-6, were identified. Through psRobot and TargetFinder programs, MIR167-1-6, MIR395-13, MIR396-3, MIR396-16, and MIR398-8 were annotated to modulate the expression of genes implicated in transportation, signaling, and biological responses of phytohormones and activation of antioxidants for plant immunity. Besides, validated differentially expressed genes involved in lignin generation, which were phenylalanine ammonia-lyase, ferulate-5-hydroxylase, cinnamyl alcohol dehydrogenase, and peroxidase 11, were selected as targets for the identification of novel miRNAs. Correspondingly, novel miRNAs, such as Novel MIR8567, Novel MIR3228, Novel MIR5913, and Novel MIR6493, were identified using the Mireap online program, which functions in the transcriptional regulation of lignin biosynthesis for poplar anti-fungal response. The present study underlines the roles of miRNAs in the regulation of transcriptome in the anti-fungal response of poplar and provides a new idea for molecular breeding of woody plants.

scholarly journals High-Throughput Sequencing Analysis of Small RNAs Derived from Coleus Blumei Viroids

Viruses ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 619
Author(s):  
Dong-Mei Jiang ◽  
Meng Wang ◽  
Shi-Fang Li ◽  
Zhi-Xiang Zhang
Keyword(s):  
Small Rnas ◽  
High Throughput Sequencing ◽  
Sequencing Analysis ◽  
Primary Sequence ◽  
Host Interactions ◽  
Coleus Blumei ◽  
The Right ◽  
Insight Into

Characterization of viroid-derived small RNAs (vd-sRNAs) is important to understand viroid–host interactions; however, vd-sRNAs belonging to the genus Coleviroid are yet to be identified and characterized. Herein, we used coleus plants singly infected with coleus blumei viroid (CbVd)-1, -5, or -6 and doubly infected with CbVd-1 and -5 to identify and analyze their vd-sRNAs. We found sense and antisense vd-sRNAs for CbVd-1, -5 and -6, and 22-nt vd-sRNAs were the most abundant; moreover, the 5′-terminal nucleotides (nts) of CbVd-1, -5, and -6 were biased toward U and C, and sRNAs derived from these three viroids were unevenly distributed along their genomes. We also noted that CbVd-5 and -6 share a fragment that forms the right half of the rod-like secondary structure of these viroids, which implied that they generated almost the same type of vd-sRNAs. This finding indicated that vd-sRNA biogenesis is mainly determined by the primary sequence of their substrates. More importantly, we found two complementary vd-sRNAs (22 nt) that were generated from the central conserved region (CCR) of these three viroids, suggesting an important role of CCR in vd-sRNA biogenesis. In conclusion, our results provide novel insight into the biogenesis of vd-sRNAs and the biological roles of CCR.

A New Approach for Predicting the Value of Gene Expression: Two-way Collaborative Filtering

2019 ◽  
Vol 14 (6) ◽  
pp. 480-490 ◽  
Author(s):  
Tuncay Bayrak ◽  
Hasan Oğul
Keyword(s):  
Gene Expression ◽  
Regression Model ◽  
Collaborative Filtering ◽  
High Throughput Sequencing ◽  
Mean Squared Error ◽  
Experimental Studies ◽  
Kernel Functions ◽  
Feature Representation ◽  
Sequencing Analysis ◽  
Computational Systems Biology

Background: Predicting the value of gene expression in a given condition is a challenging topic in computational systems biology. Only a limited number of studies in this area have provided solutions to predict the expression in a particular pattern, whether or not it can be done effectively. However, the value of expression for the measurement is usually needed for further meta-data analysis. Methods: Because the problem is considered as a regression task where a feature representation of the gene under consideration is fed into a trained model to predict a continuous variable that refers to its exact expression level, we introduced a novel feature representation scheme to support work on such a task based on two-way collaborative filtering. At this point, our main argument is that the expressions of other genes in the current condition are as important as the expression of the current gene in other conditions. For regression analysis, linear regression and a recently popularized method, called Relevance Vector Machine (RVM), are used. Pearson and Spearman correlation coefficients and Root Mean Squared Error are used for evaluation. The effects of regression model type, RVM kernel functions, and parameters have been analysed in our study in a gene expression profiling data comprising a set of prostate cancer samples. Results: According to the findings of this study, in addition to promising results from the experimental studies, integrating data from another disease type, such as colon cancer in our case, can significantly improve the prediction performance of the regression model. Conclusion: The results also showed that the performed new feature representation approach and RVM regression model are promising for many machine learning problems in microarray and high throughput sequencing analysis.

scholarly journals Application of vigor indexes to evaluate the cold tolerance in rice seeds germination conditioned in plant extract

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sheila Bigolin Teixeira ◽  
Stefânia Nunes Pires ◽  
Gabriele Espinel Ávila ◽  
Bruna Evelyn Paschoal Silva ◽  
Victoria Novo Schmitz ◽  
...  
Keyword(s):  
Low Temperatures ◽  
Seed Priming ◽  
Dry Mass ◽  
Economic Losses ◽  
Tolerance Index ◽  
Promising Tool ◽  
Germination Speed ◽  
Cold Tolerant ◽  
Rice Seeds ◽  
Carrot Extract

AbstractRice is a crop that presents sensitivity to cold, especially in the germination phase, which leads to high economic losses. Alternative management forms are essential to increase tolerance to low temperatures, and seed priming represents a promising tool. The objective of this study was to investigate the priming effect of the aqueous extract of carrot roots on rice seeds to increase tolerance to low temperatures during germination. Seeds from cultivars BRS Querência (cold-susceptible) and Brilhante (cold-tolerant) were soaked for 24 h in concentrations of 0, 25, 50, and 100% carrot extract, sown on germitest paper and conditioned in BOD for 21 days at 15 °C. As a control, the seeds soaked in water were also germinated at 25 °C. They were evaluated for germination, first germination count, and germination speed index to calculate the stress indices: tolerance index, susceptibility index, and harmonic mean. They were also evaluated for the length and dry mass of shoot and root. The results showed that the rice seeds conditioning in carrot extract effectively reduces the damage caused by cold, significantly increasing the germination speed and the percentage of final germination and the growth evaluations, more expressive at 100% concentration. The stress indexes are efficient in estimating the tolerance of the cultivars and the effect of the different conditions in low-temperature conditions, highlighting the superiority of the Brilhante cultivar.

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