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 Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hangxia Jin ◽  
Xiaomin Yu ◽  
Qinghua Yang ◽  
Xujun Fu ◽  
Fengjie Yuan
Keyword(s):  
Developmental Stage ◽  
Phytic Acid ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Defense Mechanisms ◽  
Developmental Stages ◽  
Sucrose Metabolism ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Seed Developmental Stage

AbstractPhytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3–InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.

scholarly journals PSVII-2 Differentially expressed genes and their biological function in skeletal muscle of calves born from cows with or without protein supplementation during mid-gestation

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 165-166
Author(s):  
Elisa B Carvalho ◽  
Letícia P Sanglard ◽  
Karolina B Nascimento ◽  
Javier M Meneses ◽  
Daniel R Casagrande ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Differentially Expressed Genes ◽  
Muscle Development ◽  
Negative Binomial ◽  
Muscle Protein ◽  
Basal Diet ◽  
Protein Supplementation ◽  
Differentially Expressed ◽  
Control Group ◽  
Q Value

Abstract Gestating cows have an increased nutrient demand to meet the needs of developing the fetus and the mid-gestation is a critical period for the fetal skeletal muscle development. The aim of this study was to evaluate the skeletal muscle transcriptome in the progeny as a function of the maternal protein nutrition during mid-gestation. Eleven Tabapuã cows and their male calves were used in this study. In the first third of gestation (0 to 100 days of gestation; dg), all cows were kept on pasture. From 100 to 200 dg, the control group (CTRL; 7 animals) received a basal diet achieving 5.5% crude protein (CP), whereas the supplemented group (SUPPL; 4 animals) received a basal diet plus protein supplementation (40% CP). After 200 dg, all animals received the same diet. Weaning was performed at 205 ± 7.5 days of age and animals were kept on pasture until reaching 240 days of age, when they were transferred to a feedlot. Muscle samples were collected at 260 days of age and RNA was extracted for RNA-seq analysis. Gene expression data was analyzed with a negative binomial model to identify (q-value ≤ 0.05) differentially expressed genes (DEG) between treatments. A total of 716 DEG were identified (289 DEG up-regulated and 427 down-regulated in SUPPL group; q-value ≤ 0.05). From the 10 most significant down-regulated DEG in the SUPPL group, two genes associated with apoptotic process were identified: MAPK8IP1 and GRINA, with log2 Fold-Changes (log2FC) of 1.04 and 0.49, respectively. From the 10 most significant up-regulated DEG in the SUPPL group, mTOR was identified, with log2FC=0.31. This is a well-known gene involved in muscle protein synthesis. In conclusion, maternal protein supplementation during mid-gestation affects the expression of genes related to energy metabolism and muscle development, which can lead to long-term impacts on production efficiency.

scholarly journals Profiling of BABA-induced differentially expressed genes of Zea mays using suppression subtractive hybridization

RSC Advances ◽  
2017 ◽  
Vol 7 (69) ◽  
pp. 43849-43865 ◽  
Author(s):  
Arun K. Shaw ◽  
Pardeep K. Bhardwaj ◽  
Supriya Ghosh ◽  
Ikbal Azahar ◽  
Sinchan Adhikari ◽  
...  
Keyword(s):  
Zea Mays ◽  
Differentially Expressed Genes ◽  
Suppression Subtractive Hybridization ◽  
Defense Mechanisms ◽  
Subtractive Hybridization ◽  
Differentially Expressed ◽  
Maize Leaves

This study aims to identify differentially expressed transcripts in BABA-primed maize leaves using suppression subtractive hybridization (SSH) strategy. Findings shed new light on the BABA potentiated defense mechanisms in plants.

scholarly journals Identification of Differentially Expressed Genes in Porcine Ovaries at Proestrus and Estrus Stages Using RNA-Seq Technique

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
Songbai Yang ◽  
Xiaolong Zhou ◽  
Yue Pei ◽  
Han Wang ◽  
Ke He ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Hormone Secretion ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
The Novel ◽  
Kegg Pathways ◽  
Go Enrichment ◽  
Single Organism

Estrus is an important factor for the fecundity of sows, and it is involved in ovulation and hormone secretion in ovaries. To better understand the molecular mechanisms of porcine estrus, the expression patterns of ovarian mRNA at proestrus and estrus stages were analyzed using RNA sequencing technology. A total of 2,167 differentially expressed genes (DEGs) were identified (P≤0.05, log2  Ratio≥1), of which 784 were upregulated and 1,383 were downregulated in the estrus compared with the proestrus group. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in the cellular process, single-organism process, cell and cell part, and binding and metabolic process. In addition, a pathway analysis showed that these DEGs were significantly enriched in 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including cell adhesion molecules, ECM-receptor interaction, and cytokine-cytokine receptor interaction. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) confirmed the differential expression of 10 selected DEGs. Many of the novel candidate genes identified in this study will be valuable for understanding the molecular mechanisms of the sow estrous cycle.

scholarly journals Identification and characterization of differentially expressed genes in Caenorhabditis elegans in response to pathogenic and nonpathogenic Stenotrophomonas maltophilia

2019 ◽  
Author(s):  
Leah J Radeke ◽  
Michael Herman
Keyword(s):  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Stenotrophomonas Maltophilia ◽  
Defense Mechanisms ◽  
Virulent Strain ◽  
Differentially Expressed ◽  
Transcriptional Responses ◽  
Transcriptomic Response ◽  
C Elegans ◽  
Realistic Interaction

Abstract Background: Stenotrophomonas maltophilia is an emerging nosocomial pathogen that causes infection in immunocompromised patients. S. maltophilia isolates are genetically diverse, contain diverse virulence factors, and are variably pathogenic within several host species. Members of the Stenotrophomonas genus are part of the native microbiome of C. elegans , being found in greater relative abundance within the worm than its environment, suggesting that these bacteria accumulate within C. elegans . Thus, study of the C. elegans-Stenotrophomonas interaction is of both medical and ecological significance. To identify host defense mechanisms, we analyzed the C. elegans transcriptomic response to S. maltophilia strains of varying pathogenicity: K279a, an avirulent clinical isolate, JCMS, a virulent strain isolated in association with soil nematodes near Manhattan, KS, and JV3, an even more virulent environmental isolate. Results: Overall, we found 145 genes that are commonly differentially expressed in response to pathogenic S. maltophilia strains, 89% of which are upregulated, with many even further upregulated in response to JV3 as compared to JCMS. There are many more JV3-specific differentially expressed genes (225, 11% upregulated) than JCMS-specific differentially expressed genes (14, 86% upregulated), suggesting JV3 has unique pathogenic mechanisms that could explain its increased virulence. We used connectivity within a gene network model to choose pathogen-specific and strain-specific differentially expressed candidate genes for functional analysis. Mutations in 13 of 22 candidate genes caused significant differences in C. elegans survival in response to at least one S. maltophilia strain, although not always the strain that induced differential expression, suggesting a dynamic response to varying levels of pathogenicity. Conclusions: Variation in observed pathogenicity and differences in host transcriptional responses to S. maltophilia strains reveal that strain-specific mechanisms play important roles in S. maltophilia pathogenesis. Furthermore, utilizing bacteria closely related to strains found in C. elegans natural environment provides a more realistic interaction for understanding host-pathogen response.

scholarly journals RNA-Seq Analysis of Prickled and Prickle-Free Epidermis Provides Insight into the Genetics of Prickle Development in Red Raspberry (Rubus ideaus L.)

Agronomy ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1904 ◽  
Author(s):  
Archana Khadgi ◽  
Courtney A. Weber
Keyword(s):  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Rubus Idaeus ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Sequencing Analysis ◽  
Red Raspberry ◽  
Specialty Crop ◽  
Rubus Species ◽  
R2r3 Myb

Red raspberry (Rubus idaeus L.) is a globally commercialized specialty crop with growing demand worldwide. The presence of prickles on the stems, petioles and undersides of the leaves complicates both the field management and harvesting of raspberries. An RNA sequencing analysis was used to identify differentially expressed genes in the epidermal tissue of prickled “Caroline” and prickle-free “Joan J.” and their segregating progeny. Expression patterns of differentially expressed genes (DEGs) in prickle-free plants revealed the downregulation of some vital development-related transcription factors (TFs), including a MIXTA-like R2R3-MYB family member; MADS-box; APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) and NAM, ATAF1/2 and CUC2 (NAC) in prickle-free epidermis tissue. The downregulation of these TFs was confirmed by qRT-PCR analysis, indicating a key regulatory role in prickle development. This study adds to the understanding of prickle development mechanisms in red raspberries needed for utilizing genetic engineering strategies for developing prickle-free raspberry cultivars and, possibly, other Rubus species, such as blackberry (Rubus sp.) and black raspberry (R. occidentalis L.).

Identification of Differentially Expressed and Spliced Genes with RNA Sequencing Analysis of CLL Specimens

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 4582-4582
Author(s):  
Wei Liao ◽  
Gwen Jordaan ◽  
Artur Jaroszewicz ◽  
Matteo Pellegrini ◽  
Sanjai Sharma
Keyword(s):  
B Cells ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Fold Change ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Mrna Isoforms ◽  
Core Set

Abstract Abstract 4582 High throughput sequencing of cellular mRNA provides a comprehensive analysis of the transcriptome. Besides identifying differentially expressed genes in different cell types, it also provides information of mRNA isoforms and splicing alterations. We have analyzed two CLL specimens and a normal peripheral blood B cells mRNA by this approach and performed data analysis to identify differentially expressed and spliced genes. The result showed CLLs specimens express approximately 40% more transcripts compared to normal B cells. The FPKM data (fragment per kilobase of exon per million) revealed a higher transcript expression on chromosome 12 in CLL#1 indicating the presence of trisomy 12, which was confirmed by fluorescent in-situ hybridization assay. With a two-fold change in FPKM as a cutoff and a p value cutoff of 0.05 as compared to the normal B cell control, 415 genes and 174 genes in CLL#1 and 676 and 235 genes in CLL#2 were up and downregulated or differentially expressed. In these two CLL specimens, 45% to 75% of differentially expressed genes are common to both the CLL specimens indicating that genetically disparate CLL specimens have a high percentage of a core set of genes that are potentially important for CLL biology. Selected differentially expressed genes with increased expression (selectin P ligand, SELPLG, and adhesion molecule interacts with CXADR antigen 1, AMICA) and decreased (Fos, Jun, CD69 and Rhob) expression based on the FPKM from RNA-sequencing data were also analyzed in additional CLL specimens by real time PCR analysis. The expression data from RNA-seq closely matches the fold-change in expression as measured by RT-PCR analysis and confirms the validity of the RNA-seq analysis. Interestingly, Fos was identified as one of the most downregulated gene in CLL. Using the Cufflinks and Cuffdiff software, the splicing patterns of genes in CLL specimens and normal B cells were analyzed. Approximately, 1100 to 1250 genes in the two CLL specimens were significantly differentially spliced as compared to normal B cells. In this analysis as well, there is a core set of 800 common genes which are differentially spliced in the two CLL specimens. The RNA-sequencing analysis accurately identifies differentially expressed novel genes and splicing variations that will help us understand the biology of CLL. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Pathway Analysis of Differentially Expressed Genes in Patients with Acute Aortic Dissection

2009 ◽  
Vol 4 ◽  
pp. BMI.S2530 ◽  
Author(s):  
Salah A. Mohamed ◽  
Hans H. Sievers ◽  
Thorsten Hanke ◽  
Doreen Richardt ◽  
Claudia Schmidtke ◽  
...  
Keyword(s):  
Aortic Dissection ◽  
Differentially Expressed Genes ◽  
Pathway Analysis ◽  
Acute Aortic Dissection ◽  
Differentially Expressed ◽  
Control Group ◽  
Pathophysiological Mechanism ◽  
Qrt Pcr ◽  
Starting Point ◽  
Fibrillin 1

Background Acute aortic dissection (AAD) is a life-threatening condition with high mortality and a relatively unclarified pathophysiological mechanism. Although differentially expressed genes in AAD have been recognized, interactions between these genes remain poorly defined. This study was conducted to gain a better understanding of the molecular mechanisms underlying AAD and to support the future development of a clinical test for monitoring patients at high risk. Materials and Methods Aortic tissue was collected from 19 patients with AAD (mean age 61.7 ± 13.1 years), and from eight other patients (mean age 32.9 ± 12.2 years) who carried the mutated gene for Marfan syndrome (MS). Six patients (mean age 56.7 ± 12.3 years) served as the control group. The PIQOR™ Immunology microarray with 1076 probes in quadruplicates was utilized; the differentially expressed genes were analysed in a MedScan search using PathwayAssist software. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and protein analysis were performed. Results Interactions of MS fibrillin-1 (FBN1) in the MedScan pathway analysis showed four genes, fibulin-1 (FBLN1), fibulin-2 (FBLN2), decorin (DCN) and microfibrillar associated protein 5 (MFAP5), which were differentially expressed in all tissue from AAD. The validation of these genes by qRT-PCR revealed a minimum of three-fold downregulation of FBLN1 (0.5 ± 0.4 vs. 6.1 ± 2.3 fold, p = 0.003) and of DCN (2.5 ± 1.0 vs. 8.5 ± 4.7 fold, p = 0.04) in AAD compared to MS and control samples. Conclusions Downregulation of fibrillin-1 (FBN1) may weaken extracellular components in the aorta and/or interfer with the transmission of cellular signals and eventually cause AAD. Additional research on these four identified genes can be a starting point to develop a diagnostic tool.

scholarly journals Genomic profiling of cancerous patients identifies FPR2 as an alternative immunotherapeutic target in glioblastoma multiforme

2020 ◽  
Author(s):  
Yuqing Yang ◽  
Ting Sun ◽  
Chuchen Qiu ◽  
Dongjing Chen ◽  
You Wu
Keyword(s):  
Glioblastoma Multiforme ◽  
Tumor Progression ◽  
Differentially Expressed Genes ◽  
Primary Tumor ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Control Group ◽  
Western Blots ◽  
Potential Biomarker

ABSTRACTBackgroundGlioblastoma multiforme (GBM) is a type of high-grade brain tumor known for its proliferative, invasive property, and low survival rate. Recently, with the advancement in therapeutics for tumors such as targeted therapy, individual cancer-specific biomarkers could be recognized as targets for curative purposes. This study identified six differentially expressed genes that have shown significant implications in clinical field, including FPR2, VEGFA, SERPINA1, SOX2, PBK, and ITGB3. FPR2 was of the same protein family with FPR1, and the latter has been repeatedly reported to promote motility and invasiveness of multiple tumor forms.MethodsThe gene expression profiling of 40 GBM samples and five normal samples from the TCGA database were comprehensively analyzed. The differentially expressed genes (DEGs) were identified using R package and screened by enrichment analysis and examination of protein–protein interaction networks, in order to further explore the functions of DEGs with the highest association with clinical traits and to find hub genes. A qRT-PCR and Western blots were conducted to verify the results of this study.ResultsOur investigation showed that FPR2, VEGFA, SERPINA1, SOX2, PBK, and ITGB3 were significantly up-regulated in GBM primary tumor compared to the control group. Functional enrichment analysis of the DEGs demonstrated that biological functions related to immune systems, cell division and cell cycle were significantly increased, which were closely related to tumor progression and development. Downstream construction of PPI network analysis indicated that FPR2 was a hub gene involved in high level of interaction with CR3 and VEGFA, which played a key role in inflammatory pathways and cellular dysfunction.ConclusionFPR2, VEGFA, SERPINA1, SOX2, PBK, and ITGB3 were significantly over-expressed in primary tumor samples of GBM patients and were involved in cellular functions and pathways contributing to tumor progression. Out of these six pivotal genes, we intensively focused on FPR2, and our analysis and experimental data both suggested its efficacy as a potential biomarker, serving as an alternative immunotherapeutic target for glioblastoma multiforme.

Sign in / Sign up

Export Citation Format

Share Document