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 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 Construction of miRNA-target networks using microRNA profiles of CVB3-infected HeLa cells

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hai Lan Yao ◽  
Mi Liu ◽  
Wen Jun Wang ◽  
Xin Ling Wang ◽  
Juan Song ◽  
...  
Keyword(s):  
Hela Cells ◽  
Regulatory Networks ◽  
Cellular Differentiation ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Mirna Regulation ◽  
Cvb3 Infection ◽  
Differentially Expressed Mirnas

AbstractMicroRNAs (miRNAs) play an important role in regulating gene expression in multiple biological processes and diseases. Thus, to understand changes in miRNA during CVB3 infection, specific miRNA expression profiles were investigated at 3 h, 6 h, and 9 h postinfection in HeLa cells by small-RNA high-throughput sequencing. Biological implications of 68 differentially expressed miRNAs were analyzed through GO and KEGG pathways. Interaction networks between 34 known highly differentially expressed miRNAs and targets were constructed by mirDIP and Navigator. The predicted targets showed that FAM135A, IKZF2, PLAG1, ZNF148, PHC3, LCOR and DYRK1A, which are associated with cellular differentiation and transcriptional regulation, were recognized by 8 miRNAs or 9 miRNAs through interactional regulatory networks. Seven target genes were confirmed by RT-qPCR. The results showed that the expression of DYRK1A, FAM135A, PLAG1, ZNF148, and PHC3 were obviously inhibited at 3 h, 6 h, and 9 h postinfection. The expression of LCOR did not show a significant change, and the expression of IKZF2 increased gradually with prolonged infection time. Our findings improve the understanding of the pathogenic mechanism of CVB3 infection on cellular differentiation and development through miRNA regulation, which has implications for interventional approaches to CVB3-infection therapy. Our results also provide a new method for screening target genes of microRNA regulation in virus-infected cells.

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 Deep RNA sequencing analysis of syncytialization-related genes during BeWo cell fusion

Reproduction ◽  
2017 ◽  
Vol 153 (1) ◽  
pp. 35-48 ◽  
Author(s):  
Ru Zheng ◽  
Yue Li ◽  
Huiying Sun ◽  
Xiaoyin Lu ◽  
Bao-Fa Sun ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Cell Fate ◽  
Cell Fusion ◽  
Mapk Pathway ◽  
Differentially Expressed ◽  
Cell Junction ◽  
Bewo Cell ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Bewo Cells

The syncytiotrophoblast (STB) plays a key role in maintaining the function of the placenta during human pregnancy. However, the molecular network that orchestrates STB development remains elusive. The aim of this study was to obtain broad and deep insight into human STB formation via transcriptomics. We adopted RNA sequencing (RNA-Seq) to investigate genes and isoforms involved in forskolin (FSK)-induced fusion of BeWo cells. BeWo cells were treated with 50 μM FSK or dimethyl sulfoxide (DMSO) as a vehicle control for 24 and 48 h, and the mRNAs at 0, 24 and 48 h were sequenced. We detected 28,633 expressed genes and identified 1902 differentially expressed genes (DEGs) after FSK treatment for 24 and 48 h. Among the 1902 DEGs, 461 were increased and 395 were decreased at 24 h, whereas 879 were upregulated and 763 were downregulated at 48 h. When the 856 DEGs identified at 24 h were traced individually at 48 h, they separated into 6 dynamic patterns via a K-means algorithm, and most were enriched in down–even and up–even patterns. Moreover, the gene ontology (GO) terms syncytium formation, cell junction assembly, cell fate commitment, calcium ion transport, regulation of epithelial cell differentiation and cell morphogenesis involved in differentiation were clustered, and the MAPK pathway was most significantly regulated. Analyses of alternative splicing isoforms detected 123,200 isoforms, of which 1376 were differentially expressed. The present deep analysis of the RNA-Seq data of BeWo cell fusion provides important clues for understanding the mechanisms underlying human STB formation.

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 Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in Salvia miltiorrhiza Bge. flowers

2020 ◽  
Author(s):  
Tao Jiang ◽  
Meide Zhang ◽  
Chunxiu Wen ◽  
Xiaoliang Xie ◽  
Wei Tian ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Regulatory Networks ◽  
Anthocyanin Biosynthesis ◽  
Salvia Miltiorrhiza ◽  
Flower Color ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Anthocyanin Content ◽  
Transcriptomics Data

Abstract Background: The study objectives were to reveal the anthocyanin biosynthesis metabolic pathway in white and purple flowers of Salvia miltiorrhiza using metabolomics and transcriptomics, to identify different anthocyanin metabolites, and to analyze the differentially expressed genes involved in anthocyanin biosynthesis . Results: We analyzed the metabolomics and transcriptomics data of Salvia miltiorrhiza flowers. A total of 1994 differentially expressed genes and 84 flavonoid metabolites were identified between the white and purple flowers of Salvia miltiorrhiza . Integrated analysis of transcriptomic and metabolomics showed that cyanidin 3,5-O-diglucoside, malvidin 3,5-diglucoside, and cyanidin 3-O-galactoside were mainly responsible for the purple flower color of Salvia miltiorrhiza. A total of 100 unigenes encoding 10 enzymes were identified as candidate genes involved in anthocyanin biosynthesis in Salvia miltiorrhiza flowers. The low expression of the ANS gene decreased the anthocyanin content but enhanced the accumulation of flavonoids in Salvia miltiorrhiza flowers. Conclusions: Our results provide valuable information on the anthocyanin metabolites and the candidate genes involved in the anthocyanin biosynthesis pathways in Salvia miltiorrhiza .

scholarly journals Analysis of BMP15-Induced Transcriptome in Human Granulosa Cells for the Identification of Novel Candidate Genes for Primary Ovarian Insufficiency

2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. A763-A764
Author(s):  
Raffaella Rossetti ◽  
Marco Fornili ◽  
Silvia Moleri ◽  
Ilaria Ferrari ◽  
Davide Gentilini ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Granulosa Cells ◽  
Transcriptome Analysis ◽  
Primary Ovarian Insufficiency ◽  
Differentially Expressed ◽  
Incomplete Penetrance ◽  
Sequencing Analysis ◽  
Ovarian Insufficiency ◽  
Human Granulosa Cells

Abstract Primary Ovarian Insufficiency (POI) is a female fertility disorder which affects 1% of women before 40 years of age and manifests with amenorrhea, elevation of serum gonadotrophins and low estrogens. POI has a strong genetic component with incomplete penetrance. Several candidate genes have been described so far, however, its etiopathogenesis is mostly unknown. In order to discover the POI-related causative mechanisms, microarray transcriptome analysis in human granulosa cells (hGCs) stimulated with recombinant human BMP15 (rhBMP15) and next generation sequencing analysis (NGS) on the identified differentially expressed genes in a selected group of patients with POI were conducted on NGS Illumina platform. In the present study, we obtained 19 differentially expressed genes upon rhBMP15 stimulation in hGCs. Results: showed that all identified genes were upregulated and associated to pluripotency, inhibition of apoptosis, cell proliferation, BMP signaling and apoptosis. Moreover, we identified nine POI patients bearing six rare variants in 5 of the BMP15-induced genes (SAMD11, SMAD6, ID1, USP35, GPCR137C). The BMP15-induced transcriptome analysis in hGCs contributed the understanding of BMP15 role as transcriptional regulator, through the activation of transcriptional repressors, by inducing pathways inhibiting the ovarian follicle maturation, thus possibly maintaining an undifferentiated state of hGCs. These findings lead to the identification of novel candidate genes for POI.

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