scholarly journals Integrated RNA-seq and sRNA-seq revealed differences in transcriptome between susceptible and resistant tomato responding to Fusarium oxysporum

2018 ◽  
Author(s):  
Min Zhao ◽  
Hui-Min Ji ◽  
Ying Gao ◽  
Xin-Xin Cao ◽  
Hui-Ying Mao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Disease Resistance ◽  
Fusarium Oxysporum ◽  
Expression Patterns ◽  
Critical Role ◽  
Mirna Gene ◽  
Initial Point ◽  
Resistant Cultivar ◽  
Post Inoculation ◽  
Rna Seq

ABSTRACTTomato wilt disease caused by Fusarium oxysporum f. sp. lycopersici (FOL) is a worldwide destructive disease of tomato. As exploring gene expression and function approaches constitute an initial point for investigating pathogen-host interaction, we performed RNA-seq and sRNA-seq analysis to unravel regulated genes and miRNAs in tomato infected by FOL. Differentially expressed (DE) protein coding gene and miRNA gene profiles upon inoculation with FOL were presented at twenty-four hours post-inoculation including four treatments. Total of more than 182.6 million and 132.2 million high quality clean reads were obtained by RNA-seq and sRNA-seq, respectively. A large overlap was found in DE mRNAs between susceptible cultivar Moneymaker and resistant cultivar Motelle. All Gene Ontology terms were mainly classified into catalytic activity, metabolic process and binding. Combining with qRT-PCR, five disease resistance genes, Solyc01g095630, Solyc03g059080, Solyc00g174340, Solyc11g071750 and Solyc05g050350, were verified to involved in the disease resistance in the resistant cultivar Motelle treated with FOL. Northern blot analysis further confirmed the results from sRNA-Seq and demonstrated that several miRNAs including Sly-miR477-5p, sly-miR167a, novel_mir_675, novel_mir_504 and novel_mir_762 conferred FOL infection. Our data resulted that pathogen resistant genes/miRNAs may play a critical role with the benefit of a coordinated machinery in prompting the response in prompting FOL response in tomato, which offered us with a future direction and surely help in generating models of mediated resistance responses with assessment of genomic gene expression patterns.

scholarly journals Comparative transcriptome profiling conferring of resistance to Fusarium oxysporum infection between resistant and susceptible tomato

2017 ◽  
Author(s):  
Min Zhao ◽  
Hui-Min Ji ◽  
Yin Gao ◽  
Xin-Xin Cao ◽  
Hui-Yin Mao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
Fusarium Oxysporum ◽  
Expression Patterns ◽  
Critical Role ◽  
Initial Point ◽  
Transcriptional Analysis ◽  
Post Inoculation ◽  
Tomato Cultivar ◽  
Susceptible Tomato

ABASTRCATTomato Fusarium wilt caused by Fusarium oxysporum f. sp. lycopersici (FOL) is a destructive disease of tomato worldwide which causes severe yield loss of the crops. As exploring gene expression and function approaches constitute an initial point for investigating pathogen-host interaction, we performed a transcriptional analysis to unravel regulated genes in tomato infected by FOL. Differentially expressed genes (DEG) upon inoculation with FOL were presented at twenty-four hours post-inoculation including four treatments: Moneymaker_H2O, Moneymaker_FOL, Motelle_H2O and Motelle_FOL. A total of more than 182.6 million high quality clean reads from the four libraries were obtained. A large overlap was found in DEGs between susceptible tomato cultivar Moneymaker and resistant tomato cultivar Motelle. All Gene Ontology terms were mainly classified into catalytic activity, metabolic process and binding. However, Gene Ontology enrichment analysis evidenced specific categories in infected Motelle. Statistics of pathway enrichment of DEGs resulted that the taurine and hypotaurine metabolism, the stibenoid, diarylheptanoid and gingerol biosynthesis, the starch and sucrose metabolism were the top three pathway affected in both groups. Interestingly, plant-pathogen pathway was greatly regulated in Motelle treated with FOL. Combining with qRT-PCR facilitated the identification of regulated pathogenicity associated genes upon infected resistant or susceptible tomato. Our data showed that a coordinated machinery played a critical role in prompting the response, which could help in generating models of mediated resistance responses with assessment of genomic gene expression patterns.

scholarly journals Transcriptomic analysis reveals distinct resistant response by physcion and chrysophanol against cucumber powdery mildew

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1991 ◽  
Author(s):  
Yanping Li ◽  
Shilin Tian ◽  
Xiaojun Yang ◽  
Xin Wang ◽  
Yuhai Guo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Disease Resistance ◽  
Powdery Mildew ◽  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Defense Responses ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Sequencing Data ◽  
Transcriptional Change

Physcion and chrysophanol induce defense responses against powdery mildew in cucumbers. The combination of these two compounds has synergistic interaction against the disease. We performed RNA-seq on cucumber leaf samples treated with physcion and chrysophanol alone and with their combination. We generated 17.6 Gb of high-quality sequencing data (∼2 Gb per sample) and catalogued the expressions profiles of 12,293 annotated cucumber genes in each sample. We identified numerous differentially expressed genes that exhibited distinct expression patterns among the three treatments. The gene expression patterns of the Chr and Phy treatments were more similar to each other than to the Phy × Chr treatment. The Phy × Chr treatment induced the highest number of differentially expressed genes. This dramatic transcriptional change after Phy × Chr treatment leaves reflects that physcion combined with chrysophanol treatment was most closely associated with induction of disease resistance. The analysis showed that the combination treatment caused expression changes of numerous defense-related genes. These genes have known or potential roles in structural, chemical and signaling defense responses and were enriched in functional gene categories potentially responsible for cucumber resistance. These results clearly demonstrated that disease resistance in cucumber leaves was significantly influenced by the combined physcion and chrysophanol treatment. Thus, physcion and chrysophanol are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to the defense response.

scholarly journals RNA-Seq-Based Gene Expression Pattern and Morphological Alterations in Chick Thymus during Postnatal Development

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Zhouyiyuan Xue ◽  
Abdur Rahman Ansari ◽  
Xing Zhao ◽  
Kun Zang ◽  
Yu Liang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signaling Pathways ◽  
Postnatal Development ◽  
Expression Pattern ◽  
Expression Patterns ◽  
Critical Role ◽  
Gene Expression Pattern ◽  
Receptor Interaction ◽  
Rna Seq ◽  
Morphological Alterations

The thymus is a lobulated unique lymphoid immune organ that plays a critical role in the selection, development, proliferation, and differentiation of T cells. The thymus of developing chickens undergoes continued morphological alterations; however, the biomolecular and transcriptional dynamics of the postnatal thymus in avian species is not clear yet. Therefore, the thymuses from chickens at different stages of development (at weeks 0, 1, 5, 9, 18, and 27) were used in the present study. The RNA-seq method was used to study the gene expression patterns. On average, 24120819 clean reads were mapped, differentially expressed genes (DEGs) were identified on the basis of log values (fold change), including 744 upregulated and 425 downregulated genes. The expression pattern revealed by RNA-seq was validated by quantitative real-time PCR (qPCR) analysis of four important genes, which are PCNA, CCNA2, CCNB2, and CDK1. Thus, the current study revealed that during postnatal development, the thymus undergoes severe atrophy. Thymus structure was damaged and gene expression changed dramatically, especially at the 27th week of age. Moreover, we found significant changes of several signaling pathways such as the cytokine-cytokine receptor interaction and cell cycle signaling pathways. Hence, it may be inferred that those signaling pathways might be closely related to the postnatal chicken thymus development.

scholarly journals Single-Cell RNA-Seq of Mouse Decidual Leukocytes Reveals Intriguing Gestational Changes in the Immune Cell Landscape and Effects of SRC-1/-2 Double-Deficiency

2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. A753-A754
Author(s):  
Jingfei Chen ◽  
Jialei Duan ◽  
Alina Montalbano ◽  
Boxun Li ◽  
Gary Hon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Immune Cell ◽  
Expression Patterns ◽  
Critical Role ◽  
Fetal Lung ◽  
Specific Gene ◽  
Rna Seq ◽  
Cell Clusters ◽  
Pregnant Mice

Abstract Single-cell RNA-seq of Mouse Decidual Leukocytes Reveals Intriguing Gestational Changes in the Immune Cell Landscape and Effects of SRC-1/-2 Double-DeficiencyOur previous findings suggest that the fetus signals the mother when it is ready to be born through secretion of surfactant components/immune modulators, surfactant protein A (SP-A) and platelet-activating factor (PAF) by the fetal lung into amniotic fluid (AF). This occurs with increased proinflammatory cytokine expression by fetal AF macrophages (Mϕ), increased myometrial NF-κB activation and contractile (CAP) gene expression. Steroid receptor coactivator (Src)-1 and Src-2 are critical for developmental induction SP-A and PAF by the fetal lung. The finding that pregnant wild-type (WT) mice carrying Src-1 and Src-2 double-deficient fetuses (Src-1/-2d/d) manifested a marked delay (~38h) in parturition, further suggests that signals for parturition arise from the fetus and that Src-1 and Src-2 serve a critical role. Infiltrating leukocytes at the maternal-fetal interface (MFI)/decidua are known to play a central role in pregnancy maintenance and parturition timing. However, there is limited knowledge regarding gestational changes in immune cell composition toward term. To analyze gestational changes in the composition of immune cells within decidua and effects of Src-1/-2d/d, we conducted single-cell RNA-seq of ~17,000 decidual leukocytes (CD45+) from pregnant mice at 15.5 and 18.5 dpc carrying WT or Src-1/-2d/d fetuses. Unsupervised clustering identified 22 distinct decidual immune cell clusters, comprised of Mϕ, B cells, natural killer cells, neutrophils, dendritic cells and monocytes. Significant differences in cell type composition and transcriptional profiles were found across study groups (WT @ 15.5 dpc vs. 18.5 dpc; Src-1/-2d/dvs. WT @15.5 dpc and 18.5 dpc). Interestingly, in deciduas of pregnant mice carrying WT fetuses, Mϕ and B cell clusters markedly increased between 15.5 and 18.5 dpc, whereas, neutrophils declined; however, these gestational changes did not occur in pregnant mice carrying Src-1/-2d/d fetuses. Differential gene expression and gene ontology enrichment analyses revealed specific gene expression patterns distinguishing these immune cell subtypes to uncover their putative functions. These findings highlight the complexity and dynamics of the decidual immune cell landscape during the transition from myometrial quiescence to contractility, and the fetal-maternal interactions leading to parturition. Support: NIH grants R01-HL050022 (CRM) and P01-HD087150 (CRM), Burroughs Wellcome Preterm Birth Grant #1019823 (CRM).

scholarly journals Combined Metabolome and Transcriptome Profiling Reveal Optimal Harvest Strategy Model Based on Different Production Purposes in Olive

Foods ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 360
Author(s):  
Guodong Rao ◽  
Jianguo Zhang ◽  
Xiaoxia Liu ◽  
Xue Li ◽  
Chenhe Wang
Keyword(s):  
Gene Expression ◽  
Olive Oil ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Minor Components ◽  
Harvest Time ◽  
Rna Seq ◽  
Optimal Harvest ◽  
Harvest Strategy ◽  
Different Color

Olive oil has been favored as high-quality edible oil because it contains balanced fatty acids (FAs) and high levels of minor components. The contents of FAs and minor components are variable in olive fruits of different color at harvest time, which render it difficult to determine the optimal harvest strategy for olive oil producing. Here, we combined metabolome, Pacbio Iso-seq, and Illumina RNA-seq transcriptome to investigate the association between metabolites and gene expression of olive fruits at harvest time. A total of 34 FAs, 12 minor components, and 181 other metabolites (including organic acids, polyols, amino acids, and sugars) were identified in this study. Moreover, we proposed optimal olive harvesting strategy models based on different production purposes. In addition, we used the combined Pacbio Iso-seq and Illumina RNA-seq gene expression data to identify genes related to the biosynthetic pathways of hydroxytyrosol and oleuropein. These data lay the foundation for future investigations of olive fruit metabolism and gene expression patterns, and provide a method to obtain olive harvesting strategies for different production purposes.

The characteristics of mesenteric adipose tissue attached to different intestinal segments and their roles in immune regulation

2022 ◽  
Author(s):  
Haowei Zhang ◽  
Yujin Ding ◽  
Qin Zeng ◽  
Dandan Wang ◽  
Ganglei Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Adipose Tissue ◽  
Immune Regulation ◽  
Expression Profiles ◽  
Critical Role ◽  
Gene Expression Profiles ◽  
Rna Seq ◽  
Mesenteric Adipose Tissue ◽  
Cell Components ◽  
Subsequent Effect

Background: Mesenteric adipose tissue (MAT) plays a critical role in the intestinal physiological ecosystems. Small and large intestines have evidently intrinsic and distinct characteristics. However, whether there exist any mesenteric differences adjacent to the small and large intestines (SMAT and LMAT) has not been properly characterized. We studied the important facets of these differences, such as morphology, gene expression, cell components and immune regulation of MATs, to characterize the mesenteric differences. Methods: The SMAT and LMAT of mice were utilized for comparison of tissue morphology. Paired mesenteric samples were analyzed by RNA-seq to clarify gene expression profiles. MAT partial excision models were constructed to illustrate the immune regulation roles of MATs, and 16S-seq was applied to detect the subsequent effect on microbiota. Results: Our data show that different segments of mesenteries have different morphological structures. SMAT not only has smaller adipocytes but also contains more fat-associated lymphoid clusters than LMAT. The gene expression profile is also discrepant between these two MATs in mice. B-cell markers were abundantly expressed in SMAT, while development-related genes were highly expressed in LMAT. Adipose-derived stem cells of LMAT exhibited higher adipogenic potential and lower proliferation rates than those of SMAT. In addition, SMAT and LMAT play different roles in immune regulation and subsequently affect microbiota components. Finally, our data clarified the described differences between SMAT and LMAT in humans. Conclusions: There were significant differences in cell morphology, gene expression profiles, cell components, biological characteristics, and immune and microbiota regulation roles between regional MATs.

scholarly journals Visual Display of 5p-arm and 3p-arm miRNA Expression with a Mobile Application

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Chao-Yu Pan ◽  
Wei-Ting Kuo ◽  
Chien-Yuan Chiu ◽  
Wen-chang Lin
Keyword(s):  
Mirna Expression ◽  
Expression Patterns ◽  
Mirna Gene ◽  
Visual Display ◽  
Mature Mirnas ◽  
Mobile App ◽  
The Cancer Genome Atlas ◽  
Rna Seq ◽  
Cancer Genome Atlas ◽  
User Friendly

MicroRNAs (miRNAs) play important roles in human cancers. In previous studies, we have demonstrated that both 5p-arm and 3p-arm of mature miRNAs could be expressed from the same precursor and we further interrogated the 5p-arm and 3p-arm miRNA expression with a comprehensive arm feature annotation list. To assist biologists to visualize the differential 5p-arm and 3p-arm miRNA expression patterns, we utilized a user-friendly mobile App to display. The Cancer Genome Atlas (TCGA) miRNA-Seq expression information. We have collected over 4,500 miRNA-Seq datasets from 15 TCGA cancer types and further processed them with the 5p-arm and 3p-arm annotation analysis pipeline. In order to be displayed with the RNA-Seq Viewer App, annotated 5p-arm and 3p-arm miRNA expression information and miRNA gene loci information were converted into SQLite tables. In this distinct application, for any given miRNA gene, 5p-arm miRNA is illustrated on the top of chromosome ideogram and 3p-arm miRNA is illustrated on the bottom of chromosome ideogram. Users can then easily interrogate the differentially 5p-arm/3p-arm expressed miRNAs with their mobile devices. This study demonstrates the feasibility and utility of RNA-Seq Viewer App in addition to mRNA-Seq data visualization.

scholarly journals Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples

2020 ◽  
pp. 160-170
Author(s):  
John Vivian ◽  
Jordan M. Eizenga ◽  
Holly C. Beale ◽  
Olena M. Vaske ◽  
Benedict Paten
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Rna Seq ◽  
Single Patient ◽  
Tissue Samples ◽  
Composite Tissue ◽  
Patient Sample ◽  
Statistical Framework ◽  
Therapeutic Leads ◽  
Upregulated Genes

PURPOSE Many antineoplastics are designed to target upregulated genes, but quantifying upregulation in a single patient sample requires an appropriate set of samples for comparison. In cancer, the most natural comparison set is unaffected samples from the matching tissue, but there are often too few available unaffected samples to overcome high intersample variance. Moreover, some cancer samples have misidentified tissues of origin or even composite-tissue phenotypes. Even if an appropriate comparison set can be identified, most differential expression tools are not designed to accommodate comparisons to a single patient sample. METHODS We propose a Bayesian statistical framework for gene expression outlier detection in single samples. Our method uses all available data to produce a consensus background distribution for each gene of interest without requiring the researcher to manually select a comparison set. The consensus distribution can then be used to quantify over- and underexpression. RESULTS We demonstrate this method on both simulated and real gene expression data. We show that it can robustly quantify overexpression, even when the set of comparison samples lacks ideally matched tissue samples. Furthermore, our results show that the method can identify appropriate comparison sets from samples of mixed lineage and rediscover numerous known gene-cancer expression patterns. CONCLUSION This exploratory method is suitable for identifying expression outliers from comparative RNA sequencing (RNA-seq) analysis for individual samples, and Treehouse, a pediatric precision medicine group that leverages RNA-seq to identify potential therapeutic leads for patients, plans to explore this method for processing its pediatric cohort.

scholarly journals Megakaryocytes differentially sort mRNAs for matrix metalloproteinases and their inhibitors into platelets: a mechanism for regulating synthetic events

Blood ◽  
2011 ◽  
Vol 118 (7) ◽  
pp. 1903-1911 ◽  
Author(s):  
Luca Cecchetti ◽  
Neal D. Tolley ◽  
Noemi Michetti ◽  
Loredana Bury ◽  
Andrew S. Weyrich ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Matrix Metalloproteinases ◽  
Mrna Expression ◽  
Vascular Remodeling ◽  
Differentially Express ◽  
Expression Patterns ◽  
Critical Role ◽  
Rna Seq ◽  
Next Generation ◽  
Generation Sequencing

Abstract Megakaryocytes transfer a diverse and functional transcriptome to platelets during the final stages of thrombopoiesis. In platelets, these transcripts reflect the expression of their corresponding proteins and, in some cases, serve as a template for translation. It is not known, however, if megakaryocytes differentially sort mRNAs into platelets. Given their critical role in vascular remodeling and inflammation, we determined whether megakaryocytes selectively dispense transcripts for matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs) into platelets. Next-generation sequencing (RNA-Seq) revealed that megakaryocytes express mRNA for 10 of the 24 human MMP family members. mRNA for all of these MMPs are present in platelets with the exception of MMP-2, 14, and 15. Megakaryocytes and platelets also express mRNA for TIMPs 1-3, but not TIMP-4. mRNA expression patterns predicted the presence and, in most cases, the abundance of each corresponding protein. Nonetheless, exceptions were observed: MMP-2 protein is present in platelets but not its transcript. In contrast, quiescent platelets express TIMP-2 mRNA but only traces of TIMP-2 protein. In response to activating signals, however, platelets synthesize significant amounts of TIMP-2 protein. These results demonstrate that megakaryocytes differentially express mRNAs for MMPs and TIMPs and selectively transfer a subset of these into platelets. Among the platelet messages, TIMP-2 serves as a template for signal-dependent translation.

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