scholarly journals Lignin Synthesis Related Genes with Potential Significance in the Response of Upland Cotton to Fusarium Wilt Identified by Transcriptome Profiling

2021 ◽  
Author(s):  
Jianan Hou ◽  
Fu’an Zhao ◽  
Xiaojie Yang ◽  
Wu Li ◽  
Deyi Xie ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fusarium Wilt ◽  
Gene Expression Pattern ◽  
Transcriptome Profiling ◽  
Global Gene Expression ◽  
Resistant Cultivar ◽  
Susceptible Cultivar ◽  
Single Organism ◽  
Before And After ◽  
Phenylpropanoid Biosynthesis

AbstractFusarium wilt, caused by the fungus Fusarium oxysporum Schlecht. f. sp. vasinfectum (Fov) is a destructive soil-borne cotton disease. To profile the genes and pathways responding to Fov infection, we compared transcriptomic responses before and after F. oxysporum inoculation in a highly resistant cotton cultivar, Yumian21, and a highly susceptible cultivar, Jimian11. Although the overall gene expression pattern was downregulated in both cultivars, the global gene expression in the resistant cultivar was stronger than that in the susceptible cultivar. In addition, the expressed genes of two cultivars mostly differed in “cellular process,” “single-organism process,” “metabolic process,” and “response to stimulus” functional groups in the biological process Gene Ontology category: the upregulated differentially expressed genes (DEG) were largely enriched in the resistant cultivar, while the downregulated DEGs were largely enriched in the susceptible cultivar. Phenylpropanoid biosynthesis and phenylalanine metabolism are the key metabolic pathways in cotton in response to Fov. We found that lignin plays a potential role in cotton resistance to Fov. Two coding genes, caffeic acid 3-O-methyltransferase and peroxidase2, as well as the two transcription factors MYB46 and MYB86, are possibly involved in the accumulation and synthesis of lignin. Furthermore, the result showed that the quantification of lignin could be potentially used as a selection tool to identify Fusarium wilt resistant cotton.

scholarly journals Proteomic and Transcriptomic Analyses Provide Novel Insights into the Crucial Roles of Host-Induced Carbohydrate Metabolism Enzymes in Xanthomonas oryzae pv. oryzae Virulence and Rice-Xoo Interaction

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Guichun Wu ◽  
Yuqiang Zhang ◽  
Bo Wang ◽  
Kaihuai Li ◽  
Yuanlai Lou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Amino Acids ◽  
Secondary Metabolites ◽  
Carbohydrate Metabolism ◽  
Virulence Factors ◽  
Global Gene Expression ◽  
Xanthomonas Oryzae ◽  
Oxidation Reduction ◽  
Phenylpropanoid Biosynthesis

Abstract Background Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial leaf blight, a devastating rice disease. The Xoo-rice interaction, wherein wide ranging host- and pathogen-derived proteins and genes wage molecular arms race, is a research hotspot. Hence, the identification of novel rice-induced Xoo virulence factors and characterization of their roles affecting rice global gene expression profiles will provide an integrated and better understanding of Xoo-rice interactions from the molecular perspective. Results Using comparative proteomics and an in vitro interaction system, we revealed that 5 protein spots from Xoo exhibited significantly different expression patterns (|fold change| > 1.5) at 3, 6, 12 h after susceptible rice leaf extract (RLX) treatment. MALDI-TOF MS analysis and pathogenicity tests showed that 4 host-induced proteins, including phosphohexose mutase, inositol monophosphatase, arginase and septum site-determining protein, affected Xoo virulence. Among them, mutants of two host-induced carbohydrate metabolism enzyme-encoding genes, ΔxanA and Δimp, elicited enhanced defense responses and nearly abolished Xoo virulence in rice. To decipher rice differentially expressed genes (DEGs) associated with xanA and imp, transcriptomic responses of ΔxanA-treated and Δimp-treated susceptible rice were compared to those in rice treated with PXO99A at 1 and 3 dpi. A total of 1521 and 227 DEGs were identified for PXO99A vs Δimp at 1 and 3 dpi, while for PXO99A vs ΔxanA, there were 131 and 106 DEGs, respectively. GO, KEGG and MapMan analyses revealed that the DEGs for PXO99A vs Δimp were mainly involved in photosynthesis, signal transduction, transcription, oxidation-reduction, hydrogen peroxide catabolism, ion transport, phenylpropanoid biosynthesis and metabolism of carbohydrates, lipids, amino acids, secondary metabolites, hormones, and nucleotides, while the DEGs from PXO99A vs ΔxanA were predominantly associated with photosynthesis, signal transduction, oxidation-reduction, phenylpropanoid biosynthesis, cytochrome P450 and metabolism of carbohydrates, lipids, amino acids, secondary metabolites and hormones. Although most pathways were associated with both the Δimp and ΔxanA treatments, the underlying genes were not the same. Conclusion Our study identified two novel host-induced virulence factors XanA and Imp in Xoo, and revealed their roles in global gene expression in susceptible rice. These results provide valuable insights into the molecular mechanisms of pathogen infection strategies and plant immunity.

scholarly journals Transcriptome profiling in blood before and after hepatitis B vaccination shows significant differences in gene expression between responders and non-responders

Vaccine ◽  
2018 ◽  
Vol 36 (42) ◽  
pp. 6282-6289 ◽  
Author(s):  
Esther Bartholomeus ◽  
Nicolas De Neuter ◽  
Pieter Meysman ◽  
Arvid Suls ◽  
Nina Keersmaekers ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatitis B ◽  
Transcriptome Profiling ◽  
Hepatitis B Vaccination ◽  
Before And After

Identification of differential gene expression related to epirubicin-induced cardiomyopathy in breast cancer patients

2019 ◽  
Vol 39 (4) ◽  
pp. 393-401 ◽  
Author(s):  
J Peng ◽  
Z Wang ◽  
Y Li ◽  
D Lv ◽  
X Zhao ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Cancer Patients ◽  
Enrichment Analysis ◽  
Global Gene Expression ◽  
Pathway Enrichment Analysis ◽  
Breast Cancer Patients ◽  
Chlorophyll Metabolism ◽  
Pathway Enrichment ◽  
Before And After

Background: Epirubicin is a potent chemotherapeutic agent for the treatment of breast cancer. However, it may lead to cardiotoxicity and cardiomyopathy, and no reliable biomarker was available for the early prediction of epirubicin-induced cardiomyopathy. Methods: Global gene expression changes of peripheral blood cells were studied using high-throughput RNA sequencing in three pair-matched breast cancer patients (patients who developed symptomatic cardiomyopathy paired with patients who did not) before and after the full session of epirubicin-based chemotherapy. Functional analysis was conducted using gene ontology and pathway enrichment analysis. Results: We identified 13 significantly differentially expressed genes between patients who developed symptomatic epirubicin-induced cardiomyopathy and their paired control who did not. Among them, the upregulated Bcl-associated X protein was related to “apoptosis,” while the downregulated 5′-aminolevulinate synthase 2 (ALAS2) was related to both “glycine, serine, and threonine metabolism” and “porphyrin and chlorophyll metabolism” in pathway enrichment analysis. Conclusions: ALAS2 and the metabolic pathways which were involved may play an important role in the development of epirubicin-induced cardiomyopathy. ALAS2 may be useful as an early biomarker for epirubicin-induced cardiotoxicity detection.

scholarly journals Transcriptome Profiling across Five Tissues of Giant Panda

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Feng Li ◽  
Chengdong Wang ◽  
Zhongxian Xu ◽  
Mingzhou Li ◽  
Linhua Deng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Giant Panda ◽  
Expression Patterns ◽  
Genetic Research ◽  
Gene Expression Pattern ◽  
Transcriptome Profiling ◽  
Ailuropoda Melanoleuca ◽  
Ppi Network ◽  
Illumina Hiseq ◽  
Lung And Kidney

Gene differential expression studies can serve to explore and understand the laws and characteristics of animal life activities, and the difference in gene expression between different animal tissues has been well demonstrated and studied. However, for the world-famous rare and protected species giant panda (Ailuropoda melanoleuca), only the transcriptome of the blood and spleen has been reported separately. Here, in order to explore the transcriptome differences between the different tissues of the giant panda, transcriptome profiles of the heart, liver, spleen, lung, and kidney from five captive giant pandas were constructed with Illumina HiSeq 2500 platform. The comparative analysis of the intertissue gene expression patterns was carried out based on the generated RNA sequencing datasets. Analyses of Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network were performed according to the identified differentially expressed genes (DEGs). We generated 194.52 GB clean base data from twenty-five sequencing libraries and identified 18,701 genes, including 3492 novel genes. With corrected p value <0.05 and |log2FoldChange| >2, we finally obtained 921, 553, 574, 457, and 638 tissue-specific DEGs in the heart, liver, spleen, lung, and kidney, respectively. In addition, we identified TTN, CAV3, LDB3, TRDN, and ACTN2 in the heart; FGA, AHSG, and SERPINC1 in the liver; CD19, CD79B, and IL21R in the spleen; NKX2-4 and SFTPB in the lung; GC and HRG in the kidney as hub genes in the PPI network. The results of the analyses showed a similar gene expression pattern between the spleen and lung. This study provided for the first time the heart, liver, lung, and kidney’s transcriptome resources of the giant panda, and it provided a valuable resource for further genetic research or other potential research.

scholarly journals Multitarget Effects of Danqi Pill on Global Gene Expression Changes in Myocardial Ischemia

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Qiyan Wang ◽  
Hui Meng ◽  
Qian Zhang ◽  
Tianjiao Shi ◽  
Xuefeng Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Myocardial Ischemia ◽  
Differentially Expressed Genes ◽  
Sham Group ◽  
Gene Expression Pattern ◽  
Enrichment Analysis ◽  
Global Gene Expression ◽  
Differentially Expressed ◽  
Group Model ◽  
Model Group

Danqi pill (DQP) is a widely prescribed traditional Chinese medicine (TCM) in the treatment of cardiovascular diseases. The objective of this study is to systematically characterize altered gene expression pattern induced by myocardial ischemia (MI) in a rat model and to investigate the effects of DQP on global gene expression. Global mRNA expression was measured. Differentially expressed genes among the sham group, model group, and DQP group were analyzed. The gene ontology enrichment analysis and pathway analysis of differentially expressed genes were carried out. We quantified 10,813 genes. Compared with the sham group, expressions of 339 genes were upregulated and 177 genes were downregulated in the model group. The upregulated genes were enriched in extracellular matrix organization, response to wounding, and defense response pathways. Downregulated genes were enriched in fatty acid metabolism, pyruvate metabolism, PPAR signaling pathways, and so forth. This indicated that energy metabolic disorders occurred in rats with MI. In the DQP group, expressions of genes in the altered pathways were regulated back towards normal levels. DQP reversed expression of 313 of the 516 differentially expressed genes in the model group. This study provides insight into the multitarget mechanism of TCM in the treatment of complex diseases.

48 GLOBAL GENE EXPRESSION PATTERN OF BOS INDICUS AND BOS TAURUS VITRIFIED EMBRYOS

2015 ◽  
Vol 27 (1) ◽  
pp. 117
Author(s):  
R. Cancian ◽  
M. Macelai ◽  
G. Tavares ◽  
R. S. Valente ◽  
E. S. Caixeta ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Cellular Response ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Gene Expression Pattern ◽  
Global Gene Expression ◽  
Differentially Expressed ◽  
Canonical Pathways

The cryopreservation of in vitro-produced (IVP) bovine embryos is one of the most challenging areas of the assisted reproductive biotechnologies. The aim of the present study was to evaluate the global gene expression pattern of Bos indicus (Nellore) and Bos taurus (Simmental) IVP embryos after vitrification. Follicular aspiration was performed on Nellore (n = 14) and Simmental (n = 14) cows, and oocytes (n = 840 and 450; respectively) were submitted to in vitro maturation and in vitro fertilization. Presumptive zygotes were denuded and cultured in SOFaa with 0.5% BSA and 2.5% FCS during 7 days under standard culture conditions. Blastocysts (grade 1 and 2) were vitrified, warmed, and cultured for an additional 12 h under the same conditions. Nellore (n = 8) and Simmental (n = 8) IVP blastocysts considered viable after vitrification, with re-expanded blastocoel, were submitted to total RNA extraction (PicoPure, Arcturus, Applied Biosystems®, Foster Dity, CA, USA), DNAse I treatment (Qiagen®, Valencia, CA, USA), and amplification (RiboAmp, Applied Biosystems®). Fragmented cRNA were obtained through 3′IVT Express Kit (Affymetrix®, Santa Clara, CA, USA) to perform the hybridization using GeneChip Bovine Genome Array (Affymetrix®). Microarray data analysis was performed using the FlexArray 1.6.1.1 software. Genes with at least a 1.5-fold change and a P-value of less than 0.05 were considered differentially expressed. Of the 1278 genes differentially expressed between Bos taurus and Bos indicus vitrified embryos, 1108 were annotated, with 1193 genes up-regulated and 85 genes down-regulated in Bos taurus compared with Bos indicus IVP vitrified embryos. Differentially expressed genes were associated with the functional networks of cell cycle, cellular movement and DNA replication, recombination and repair; RNA post-transcriptional modifications; gene expression, protein synthesis; RNA damage and repair; cellular function and maintenance; and cell death and survival. The top 6 canonical pathways generated by Ingenuity Pathway Analysis® with the differentially expressed genes were ELF2 signalling, oxidative phosphorylation, tricarboxylic acid cycle, protein ubiquitination pathway, mTOR signalling, and IGF-1 signalling. In conclusion, Bos taurus IVP embryos seem to trigger different cellular response mechanisms to the vitrification stress in comparison with Bos indicus IVP embryos. Differential response is mainly represented by different expression profiles of genes regulating important canonical pathways involved in cellular response to stress that could be related with the higher post-cryopreservation survival capacity observed in Bos taurus embryos.Research was supported by FAPESP, CNPq, FAPERGS, and LNBio – National Laboratory of Biosciences/MCT.

A Comprehensive Analysis of Wheat Resistance to Rhopalosiphum padi (Hemiptera: Aphididae) in Brazilian Wheat Cultivars

2020 ◽  
Vol 113 (3) ◽  
pp. 1493-1503 ◽  
Author(s):  
Leia de Jesus Correa ◽  
Orlando Vilas Boas Maciel ◽  
Lauro Bücker-Neto ◽  
Laura Pilati ◽  
Ana Maria Morozini ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rhopalosiphum Padi ◽  
Green Leaf Volatiles ◽  
Resistant Cultivar ◽  
Green Leaf ◽  
Molecular Response ◽  
Susceptible Cultivar ◽  
Wheat Cultivars ◽  
Leaf Volatiles ◽  
Encoding Gene

Abstract Rhopalosiphum padi L. is one of the predominant aphids affecting wheat crops worldwide. Therefore, the identification of resistant genotypes and the understanding of molecular response mechanisms involved in wheat resistance to this aphid may contribute to the development of new breeding strategies. In this study, we evaluated the resistance of 15 wheat cultivars to R. padi and performed morpho-histological and gene expression analyses of two wheat cultivars (BRS Timbaúva, resistant and Embrapa 16, susceptible) challenged and unchallenged by R. padi. The main findings of our work are as follows: 1) most Brazilian wheat cultivars recently released are resistant to R. padi; 2) Green leaf volatiles are probably involved in the resistance of the BRS Timbaúva cultivar to the aphid; 3) trichomes were more abundant and larger in the resistant cultivar; 4) the internal morphology did not show differences between cultivars; 5) the lipoxygenase-encoding gene was downregulated in the susceptible cultivar and basal expression remained level in the resistant cultivar; and 6) the expression of resistance-related proteins was induced in the resistant but not in the susceptible cultivar. Lipoxygenase is the first enzyme in the octadecanoic pathway, a well-known route for the synthesis of signaling molecules involved in the activation of plant defense. The overall analyses suggest that the key steps in BRS Timbaúva resistance to R. padi may be presence or absence of green leaf volatiles decreasing the aphid preference and the action of nonglandular trichome as a physical barrier, which allows continuous lipoxygenase-encoding gene expression.

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