scholarly journals RNA-seq Profiling Reveals Defense Responses in a Tolerant Potato Cultivar to Stem Infection by Pectobacterium carotovorum ssp. brasiliense

2016 ◽  
Vol 7 ◽  
Author(s):  
Stanford Kwenda ◽  
Tshepiso V. Motlolometsi ◽  
Paul R. J. Birch ◽  
Lucy N. Moleleki
Keyword(s):  
Potato Cultivar ◽  
Defense Responses ◽  
Pectobacterium Carotovorum ◽  
Rna Seq ◽  
Stem Infection

scholarly journals Dual Analysis of Virus-Host Interactions: The Case of Ostreid herpesvirus 1 and the Cupped Oyster Crassostrea gigas

2019 ◽  
Vol 15 ◽  
pp. 117693431983130
Author(s):  
Umberto Rosani ◽  
Tim Young ◽  
Chang-Ming Bai ◽  
Andrea C. Alfaro ◽  
Paola Venier
Keyword(s):  
Crassostrea Gigas ◽  
Current Knowledge ◽  
Expression Profiles ◽  
Defense Responses ◽  
Viral Disease ◽  
Complex Case ◽  
Rna Seq ◽  
Omics Technologies ◽  
Herpesvirus 1 ◽  
Ostreid Herpesvirus 1

Dual analyses of the interactions between Ostreid herpesvirus 1 (OsHV-1) and the bivalve Crassostrea gigas during infection can unveil events critical to the onset and progression of this viral disease and can provide novel strategies for mitigating and preventing oyster mortality. Among the currently used “omics” technologies, dual transcriptomics (dual RNA-seq) coupled with the analysis of viral DNA in the host tissues has greatly advanced the knowledge of genes and pathways mostly contributing to host defense responses, expression profiles of annotated and unknown OsHV-1 open reading frames (ORFs), and viral genome variability. In addition to dual RNA-seq, proteomics and metabolomics analyses have the potential to add complementary information, needed to understand how a malacoherpesvirus can redirect and exploit the vital processes of its host. This review explores our current knowledge of “omics” technologies in the study of host-pathogen interactions and highlights relevant applications of these fields of expertise to the complex case of C gigas infections by OsHV-1, which currently threaten the mollusk production sector worldwide.

scholarly journals RNA-seq reveals few differences in resistant and susceptible responses of barley to infection by the spot blotch pathogenBipolaris sorokiniana

2018 ◽  
Author(s):  
Matthew Haas ◽  
Martin Mascher ◽  
Claudia Castell-Miller ◽  
Brian J. Steffenson
Keyword(s):  
Expression Profiles ◽  
Durable Resistance ◽  
Defense Responses ◽  
Spot Blotch ◽  
Seedling Stage ◽  
Differentially Expressed ◽  
Adult Plant ◽  
Rna Seq ◽  
Adult Plant Stage ◽  
Plant Stage

AbstractSpot blotch, caused byBipolaris sorokiniana(Sacc.) Shoem., is an economically important disease affecting barley (Hordeum vulgareL.). The disease has largely been controlled in the Upper Midwest region of the USA through a suite of quantitative trait loci (QTL) termed the Midwest Six-rowed Durable Resistance Haplotype (MSDRH). These QTL have been bred into all six-rowed Midwest barley cultivars, including the widely used cultivar Morex. We identified a gamma ray- induced Morex mutant (MUT) that exhibits spot blotch susceptibility at the seedling stage. This mutant also spontaneously develops extremely large necrotic lesions in the absence of the pathogen at the adult plant stage. Spot blotch susceptibility at the seedling stage and necrotic lesion formation at the adult plant stage are highly correlated. To start dissecting the molecular responses underlying the observed symptoms at the seedling stage, we conducted a time course RNA-seq experiment comparing the wild type (WT) and the mutant (MUT) Morex at 12, 24 and 36 h afterB. sorokinianainoculation. Mock-inoculated controls were also included. A total of 10,772 and 11,530 genes were differentially expressed between treatments for WT and MUT genotypes, respectively, while 277 and 195 genes were differentially expressed between fungal and mock-inoculated genotypes, respectively. The transcript expression profiles of WT and MUT Morex samples were similar for most treatments. Two genes whose expression was putatively knocked out in the MUT were identified: HORVU3Hr1G019920 (glycine-rich protein) and HORVU5Hr1G120850 (Long- chain-fatty-acid—CoA ligase 1). The latter appears to be genetically intact, but not expressed. Collectively, these data suggest that MUT susceptibility toB. sorokinianais a result of minor, rather than major, differences in the defense responses.

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.

Dual RNA-Seq of Lysobacter capsici AZ78 - Phytophthora infestans interaction shows the implementation of attack strategies by the bacterium and unsuccessful oomycete defense responses

2017 ◽  
Vol 19 (10) ◽  
pp. 4113-4125 ◽  
Author(s):  
Selena Tomada ◽  
Paolo Sonego ◽  
Marco Moretto ◽  
Kristof Engelen ◽  
Ilaria Pertot ◽  
...  
Keyword(s):  
Phytophthora Infestans ◽  
Defense Responses ◽  
Rna Seq

scholarly journals RNA-seq analysis reveals different drought tolerance mechanisms in two broadly adapted wheat cultivars ‘TAM 111’ and ‘TAM 112’

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chenggen Chu ◽  
Shichen Wang ◽  
Li Paetzold ◽  
Zhen Wang ◽  
Kele Hui ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Stress Responses ◽  
Expression Patterns ◽  
Defense Responses ◽  
Wheat Cultivars ◽  
Rna Seq ◽  
Tolerance Mechanisms ◽  
Novel Genes ◽  
Altered Expression ◽  
Cellular Components

AbstractWheat cultivars ‘TAM 111’ and ‘TAM 112’ have been dominantly grown in the Southern U.S. Great Plains for many years due to their high yield and drought tolerance. To identify the molecular basis and genetic control of drought tolerance in these two landmark cultivars, RNA-seq analysis was conducted to compare gene expression difference in flag leaves under fully irrigated (wet) and water deficient (dry) conditions. A total of 2254 genes showed significantly altered expression patterns under dry and wet conditions in the two cultivars. TAM 111 had 593 and 1532 dry–wet differentially expressed genes (DEGs), and TAM 112 had 777 and 1670 at heading and grain-filling stages, respectively. The two cultivars have 1214 (53.9%) dry–wet DEGs in common, which agreed with their excellent adaption to drought, but 438 and 602 dry–wet DEGs were respectively shown only in TAM 111 and TAM 112 suggested that each has a specific mechanism to cope with drought. Annotations of all 2254 genes showed 1855 have functions related to biosynthesis, stress responses, defense responses, transcription factors and cellular components related to ion or protein transportation and signal transduction. Comparing hierarchical structure of biological processes, molecule functions and cellular components revealed the significant regulation differences between TAM 111 and TAM 112, particularly for genes of phosphorylation and adenyl ribonucleotide binding, and proteins located in nucleus and plasma membrane. TAM 112 showed more active than TAM 111 in response to drought and carried more specific genes with most of them were up-regulated in responses to stresses of water deprivation, heat and oxidative, ABA-induced signal pathway and transcription regulation. In addition, 258 genes encoding predicted uncharacterized proteins and 141 unannotated genes with no similar sequences identified in the databases may represent novel genes related to drought response in TAM 111 or TAM 112. This research thus revealed different drought-tolerance mechanisms in TAM 111 and TAM 112 and identified useful drought tolerance genes for wheat adaption. Data of gene sequence and expression regulation from this study also provided useful information of annotating novel genes associated with drought tolerance in the wheat genome.

scholarly journals RNA-Seq based exploration of differentially expressed genes (DEGs) in cotton(Gossypium hirsutum. L) upon infection with Aspergillus tubingensis

2021 ◽  
Author(s):  
Maria Khizar ◽  
Jianxin Shi ◽  
Urooj Haroon ◽  
Musrat Ali ◽  
Fiza Liaquat ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Differentially Expressed Genes ◽  
Defense Responses ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Ascorbate Oxidase ◽  
Resistant Variety ◽  
Potential Candidate ◽  
Aspergillus Tubingensis ◽  
Rna Seq

Abstract Differentially expressed genes help in exploring plant defense mechanism under variable stress conditions. In current investigation, RNA sequencing was executed to explore the differential gene expression in resistant and susceptible varieties of Cotton (Gossypium hirsutum), upon infection with Aspergillus tubingensis. Comparative RNA-Seq of control and infected plants was performed using Illumina HiSeq 2,500. Overall 79.84 G clean data was generated and 6,558 DEGs were identified in both varieties, in response to pathogen inoculation. Differentially expressed genes were found to be involved in defense, antifungal response, signaling pathways, oxidative burst and transcription. Genes involved in defense responses, MAPK signaling, cell wall fortification and signal transduction were highly induced in resistant variety. Real time PCR also revealed the up regulation of MAPKKK YODA like, L-ascorbate oxidase, late embryogenesis abundant protein (At1g64065) and flavonoid 3',5'-hydroxylase-like, in resistant variety. Elevated accumulation of such DEGs in resistant variety could function as the source for identifying biomarkers for breeding and these can be used as potential candidate genes for transgenic manipulation. Their study also helped in understanding complex plant-fungal interaction and advanced the understanding of plant-microbe interaction. Inclusively, our findings provide an indispensable foundation for advanced understanding of the plant resistance mechanisms of cotton.

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