scholarly journals Phenotypic and transcriptomic analyses reveal major differences between apple and pear scab nonhost resistance

2021 ◽  
Author(s):  
Emilie VERGNE ◽  
Elisabeth CHEVREAU ◽  
Elisa RAVON ◽  
Sylvain GAILLARD ◽  
Sandra PELLETIER ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Venturia Inaequalis ◽  
Stomatal Closure ◽  
Phenylpropanoid Pathway ◽  
Differentially Expressed ◽  
Scab Resistance ◽  
Nonhost Resistance ◽  
Type I ◽  
European Pear ◽  
Pear Scab

Background: Nonhost resistance is the outcome of most plant/pathogen interactions, but it has rarely been described in Rosaceous fruit species. Apple (Malus x domestica Borkh.) is a nonhost for Venturia pyrina, the scab species attacking European pear (Pyrus communis L.). Reciprocally, P. communis is a nonhost for Venturia inaequalis, the scab species attacking apple. The major objective of our study was to compare the scab nonhost resistance in apple and in European pear, at the phenotypic and transcriptomic levels. Results: Macro- and microscopic observations after reciprocal scab inoculations indicated that, after a similar germination step, nonhost apple/V. pyrina interaction remained nearly symptomless, whereas hypersensitive reactions were observed during nonhost pear/V. inaequalis interaction. Comparative transcriptomic analyses of apple and pear nonhost interactions with V. pyrina and V. inaequalis, respectively, revealed considerable differences. Very few differentially expressed genes were detected during apple/V. pyrina interaction, which is consistent with a symptomless type I nonhost resistance. On the contrary, numerous genes were differentially expressed during pear/V. inaequalis interaction, as expected in a type II nonhost resistance involving visible hypersensitive reaction. Pre-invasive defense, such as stomatal closure, was detected, as well as several post-invasive defense mechanisms (apoplastic reactive oxygen species accumulation, phytoalexin production and alterations of the epidermis composition). In addition, a comparative analysis between pear scab host and nonhost interactions indicated that, although specificities were observed, two major defense lines were shared in these resistances: cell wall and cuticle modifications and phenylpropanoid pathway induction. Conclusion: This first deciphering of the molecular mechanisms underlying a nonhost scab resistance in pear offers new possibilities for the genetic engineering of sustainable scab resistance in this species.

scholarly journals Successful intergeneric transfer of a major apple scab resistance gene (Rvi6) from apple to pear and precise comparison of the downstream molecular mechanisms of this resistance in both species

2021 ◽  
Author(s):  
Laure PERCHEPIED ◽  
Elisabeth CHEVREAU ◽  
Elisa RAVON ◽  
Sylvain GAILLARD ◽  
Sandra PELLETIER ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Molecular Mechanisms ◽  
Systemic Acquired Resistance ◽  
Venturia Inaequalis ◽  
Apple Scab ◽  
Defense Responses ◽  
Scab Resistance ◽  
European Pear ◽  
Intergeneric Transfer ◽  
Transgenic Apple

Background: Scab is the most important fungal disease of apple and pear. Apple (Malus x domestica Borkh.) and European pear (Pyrus communis L.) are genetically related but they are hosts of two different fungal species: Venturia inaequalis for apple and V. pyrina for European pear. The apple/V. inaequalis pathosystem is quite well known, whereas knowledge about the pear/V. pyrina pathosystem is still limited. The aim of our study was to analyse the mode of action of a major resistance gene of apple (Rvi6) in transgenic apple and pear plants interacting with the two scab species (V. inaequalis and V. pyrina), in order to determine the degree of functional transferability between the two pathosystems. Results: Transgenic pear clones constitutively expressing the Rvi6 gene from apple were compared to a scab transgenic apple clone carrying the same construct. After inoculation in greenhouse with V. pyrina, strong defense reactions and very limited sporulation were observed on all transgenic pear clones tested. Microscopic observations revealed frequent aborted conidiophores in the Rvi6 transgenic pear / V. pyrina interaction. The macro- and microscopic observations were very comparable to the Rvi6 apple / V. inaequalis interaction. However, this resistance in pear proved variable according to the strain of V. pyrina, and one of the strains tested overcame the resistance of most of the transgenic pear clones. Comparative transcriptomic analyses of apple and pear resistant interactions with V. inaequalis and V. pyrina, respectively, revealed different cascades of molecular mechanisms downstream of the pathogen recognition by Rvi6 in the two species. Signal transduction was triggered in both species with calcium (and G-proteins in pear) and interconnected hormonal signaling (jasmonic acid in pear, auxins in apple and brassinosteroids in both species), without involvement of salicylic acid. This led to the induction of defense responses such as a remodeling of primary and secondary cell wall, lipids biosynthesis (galactolipids in apple and cutin and cuticular waxes in pear), systemic acquired resistance signal generation (in apple) or perception in distal tissues (in pear), and the biosynthesis of phenylpropanoids (flavonoids in apple but also lignin in pear). Conclusion: This study is the first example of a successful intergeneric transfer of a resistance gene among Rosaceae, with a resistance gene functioning towards another species of pathogen.

scholarly journals Successful intergeneric transfer of a major apple scab resistance gene (Rvi6) from apple to pear and precise comparison of the downstream molecular mechanisms of this resistance in both species

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
L. Perchepied ◽  
E. Chevreau ◽  
E. Ravon ◽  
S. Gaillard ◽  
S. Pelletier ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Molecular Mechanisms ◽  
Systemic Acquired Resistance ◽  
Venturia Inaequalis ◽  
Apple Scab ◽  
Defense Responses ◽  
Scab Resistance ◽  
European Pear ◽  
Intergeneric Transfer ◽  
Transgenic Apple

Abstract Background Scab is the most important fungal disease of apple and pear. Apple (Malus x domestica Borkh.) and European pear (Pyrus communis L.) are genetically related but they are hosts of two different fungal species: Venturia inaequalis for apple and V. pyrina for European pear. The apple/V. inaequalis pathosystem is quite well known, whereas knowledge about the pear/V. pyrina pathosystem is still limited. The aim of our study was to analyse the mode of action of a major resistance gene of apple (Rvi6) in transgenic apple and pear plants interacting with the two scab species (V. inaequalis and V. pyrina), in order to determine the degree of functional transferability between the two pathosystems. Results Transgenic pear clones constitutively expressing the Rvi6 gene from apple were compared to a scab transgenic apple clone carrying the same construct. After inoculation in greenhouse with V. pyrina, strong defense reactions and very limited sporulation were observed on all transgenic pear clones tested. Microscopic observations revealed frequent aborted conidiophores in the Rvi6 transgenic pear / V. pyrina interaction. The macro- and microscopic observations were very comparable to the Rvi6 apple / V. inaequalis interaction. However, this resistance in pear proved variable according to the strain of V. pyrina, and one of the strains tested overcame the resistance of most of the transgenic pear clones. Comparative transcriptomic analyses of apple and pear resistant interactions with V. inaequalis and V. pyrina, respectively, revealed different cascades of molecular mechanisms downstream of the pathogen recognition by Rvi6 in the two species. Signal transduction was triggered in both species with calcium (and G-proteins in pear) and interconnected hormonal signaling (jasmonic acid in pear, auxins in apple and brassinosteroids in both species), without involvement of salicylic acid. This led to the induction of defense responses such as a remodeling of primary and secondary cell wall, lipids biosynthesis (galactolipids in apple and cutin and cuticular waxes in pear), systemic acquired resistance signal generation (in apple) or perception in distal tissues (in pear), and the biosynthesis of phenylpropanoids (flavonoids in apple but also lignin in pear). Conclusion This study is the first example of a successful intergeneric transfer of a resistance gene among Rosaceae, with a resistance gene functioning towards another species of pathogen.

scholarly journals Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species

2021 ◽  
Vol 22 (5) ◽  
pp. 2481
Author(s):  
Jodi Callwood ◽  
Kalpalatha Melmaiee ◽  
Krishnanand P. Kulkarni ◽  
Amaranatha R. Vennapusa ◽  
Diarra Aicha ◽  
...  
Keyword(s):  
Heat Stress ◽  
Molecular Mechanisms ◽  
Stomatal Closure ◽  
Enrichment Analysis ◽  
Leaf Size ◽  
Vaccinium Corymbosum ◽  
Climatic Conditions ◽  
Differentially Expressed ◽  
Transcriptomic Changes ◽  
Go Terms

Blueberries (Vaccinium spp.) are highly vulnerable to changing climatic conditions, especially increasing temperatures. To gain insight into mechanisms underpinning the response to heat stress, two blueberry species were subjected to heat stress for 6 and 9 h at 45 °C, and leaf samples were used to study the morpho-physiological and transcriptomic changes. As compared with Vaccinium corymbosum, Vaccinium darrowii exhibited thermal stress adaptation features such as small leaf size, parallel leaf orientation, waxy leaf coating, increased stomatal surface area, and stomatal closure. RNAseq analysis yielded ~135 million reads and identified 8305 differentially expressed genes (DEGs) during heat stress against the control samples. In V. corymbosum, 2861 and 4565 genes were differentially expressed at 6 and 9 h of heat stress, whereas in V. darrowii, 2516 and 3072 DEGs were differentially expressed at 6 and 9 h, respectively. Among the pathways, the protein processing in the endoplasmic reticulum (ER) was the highly enriched pathway in both the species: however, certain metabolic, fatty acid, photosynthesis-related, peroxisomal, and circadian rhythm pathways were enriched differently among the species. KEGG enrichment analysis of the DEGs revealed important biosynthesis and metabolic pathways crucial in response to heat stress. The GO terms enriched in both the species under heat stress were similar, but more DEGs were enriched for GO terms in V. darrowii than the V. corymbosum. Together, these results elucidate the differential response of morpho-physiological and molecular mechanisms used by both the blueberry species under heat stress, and help in understanding the complex mechanisms involved in heat stress tolerance.

Pear scab resistance QTLs via a European pear (Pyrus communis) linkage map

2006 ◽  
Vol 3 (4) ◽  
pp. 311-317 ◽  
Author(s):  
L. Pierantoni ◽  
L. Dondini ◽  
K.-H. Cho ◽  
I.-S. Shin ◽  
F. Gennari ◽  
...  
Keyword(s):  
Linkage Map ◽  
Pyrus Communis ◽  
Scab Resistance ◽  
Resistance Qtls ◽  
European Pear ◽  
Pear Scab

scholarly journals Molecular background of impairments in skeletal muscle of heart failure patients

2021 ◽  
Vol 42 (Supplement_1) ◽  
Author(s):  
O Ivanova ◽  
M Y Komarova ◽  
E V Ignatieva ◽  
T A Lelyavina ◽  
V L Galenko ◽  
...  
Keyword(s):  
Heart Failure ◽  
Skeletal Muscle ◽  
Differentially Expressed Genes ◽  
Skeletal Muscles ◽  
Molecular Mechanisms ◽  
Class Ii ◽  
Differentially Expressed ◽  
Exercise Intolerance ◽  
Type I ◽  
Molecular Abnormalities

Abstract Background Heart failure (HF) is characterised by systematic inflammation and chronic metabolic dysregulation. HF enhances the release of pro-inflammatory cytokines, induces activation of the complement system, production of autoantibodies, and over-expression of the major histocompatibility (MHC) complex class II molecules. It is known that skeletal muscles are exposed to the immunologic injury in disease; and muscle tissue appeared to be affected by HF leading to the muscle weakness and exercise intolerance development. However, molecular abnormalities occurring in HF patients' muscles and the mechanisms underlying its development are not clarified. Purpose To understand the molecular mechanisms underlying skeletal muscle immune and non-immune impairments in HF. Methods 8 health donors and 5 HF patients with reduced ejection fraction (NYHA Class II and III) were enrolled in this study in accordance with the principles under the Declaration of Helsinki (1989). mRNA of skeletal muscle biopsies of gastrocnemius lateralis were sequenced on Illumina HiSeq. RNA-seq analysis was performed using STAR with reference genome GRCh38 and featureCounts program; differentially expressed genes (DEGs) were assessed using R package DESeq2 with FDR=0.01 and log2 fold change (l2fc) >1.5 filter; pathway analysis was performed using clusterProfiler in R (FDR=0.01). Results 1404 differentially expressed genes distinguish muscles of HF patients and controls. Among upregulated genes there are different classical MHC molecules and specific one HLA-G (l2fc=2) that has been previously shown appeared in muscles under autoimmune myopathies, and potentially protect them. Unregulated DEGs were responsible for the activation of many molecular immunological pathways: type I interferon signaling pathway (16 DEGs out of total 89), regulation of T cell proliferation (14/153), neutrophil degranulation (31/485), granulocyte differentiation (7/32), negative regulation of viral process (11/53), that indicates about specific inflammatory response in HF muscles. Response to hypoxia (22/314) and gluconeogenesis pathways (12/87) were also activated. Downregulated genes include SLC5A1 (l2fc=−4) sodium glucose cotransporter; NRP3 (l2fc=−4) that plays a role in modulating intravascular volume and vascular tone; MMP1 (l2fc=−13) involved in the breakdown of extracellular matrix; the expression of many genes responsible for DNA-repair (44/534) and cilium assembly (34/366) was also suppressed. Conclusion Transcriptome analysis shows immunological and non-immunological alterations in HF skeletal muscles and provides the information about molecular mechanisms of its development. FUNDunding Acknowledgement Type of funding sources: Foundation. Main funding source(s): Russian Science Foundation grant

scholarly journals Whole Genome Sequence Resource of the Asian Pear Scab Pathogen Venturia nashicola

2019 ◽  
Vol 32 (11) ◽  
pp. 1463-1467 ◽  
Author(s):  
Shakira Johnson ◽  
Dan Jones ◽  
Amali H. Thrimawithana ◽  
Cecilia H. Deng ◽  
Joanna K. Bowen ◽  
...  
Keyword(s):  
Host Specificity ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Nonhost Resistance ◽  
Whole Genome ◽  
European Pear ◽  
Asian Pear ◽  
Pear Scab ◽  
Venturia Nashicola ◽  
Biotrophic Fungus

Venturia nashicola, the cause of scab disease of Asian pears, is a host-specific, biotrophic fungus. It is restricted to Asia and is regarded as a quarantine threat outside this region. European pear displays nonhost resistance (NHR) to V. nashicola and Asian pears are nonhosts of V. pyrina (the cause of European pear scab disease). The host specificity of these two fungi is likely governed by differences in their effector arsenals, with a subset hypothesized to activate NHR. The Pyrus-Venturia pathosystem provides an opportunity to dissect the underlying genetics of nonhost interactions in this potentially more durable form of resistance. The V. nashicola genome will enable comparisons to other Venturia spp. genomes to identify effectors that potentially activate NHR in the pear scab pathosystem.

scholarly journals Identification of Differentially Expressed Genes in COVID-19 and Integrated Bioinformatics Analysis of Signaling Pathways

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Linjie Fang ◽  
Tingyu Tang ◽  
Mengqi Hu
Keyword(s):  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Cellular Response ◽  
Molecular Mechanisms ◽  
Interaction Network ◽  
Differentially Expressed ◽  
Type I ◽  
Hub Genes ◽  
Gene Set ◽  
Go Terms

Coronavirus disease 2019 (COVID-19) is acutely infectious pneumonia. Currently, the specific causes and treatment targets of COVID-19 are still unclear. Herein, comprehensive bioinformatics methods were employed to analyze the hub genes in COVID-19 and tried to reveal its potential mechanisms. First of all, 34 groups of COVID-19 lung tissues and 17 other diseases’ lung tissues were selected from the GSE151764 gene expression profile for research. According to the analysis of the DEGs (differentially expressed genes) in the samples using the limma software package, 84 upregulated DEGs and 46 downregulated DEGs were obtained. Later, by the Database for Annotation, Visualization, and Integrated Discovery (DAVID), they were enriched in the Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. It was found that the upregulated DEGs were enriched in the type I interferon signaling pathway, AGE-RAGE signaling pathway in diabetic complications, coronavirus disease, etc. Downregulated DEGs were in cellular response to cytokine stimulus, IL-17 signaling pathway, FoxO signaling pathway, etc. Then, based on GSEA, the enrichment of the gene set in the sample was analyzed in the GO terms, and the gene set was enriched in the positive regulation of myeloid leukocyte cytokine production involved in immune response, programmed necrotic cell death, translesion synthesis, necroptotic process, and condensed nuclear chromosome. Finally, with the help of STRING tools, the PPI (protein-protein interaction) network diagrams of DEGs were constructed. With degree ≥13 as the cutoff degree, 3 upregulated hub genes (ISG15, FN1, and HLA-G) and 4 downregulated hub genes (FOXP3, CXCR4, MMP9, and CD69) were screened out for high degree. All these findings will help us to understand the potential molecular mechanisms of COVID-19, which is also of great significance for its diagnosis and prevention.

Identification of Differentially Expressed Genes Associated with Papillary Thyroid Carcinoma

2020 ◽  
Vol 23 (6) ◽  
pp. 546-553
Author(s):  
Hongyuan Cui ◽  
Mingwei Zhu ◽  
Junhua Zhang ◽  
Wenqin Li ◽  
Lihui Zou ◽  
...  
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Cellular Proliferation ◽  
Mrna Level ◽  
Thyroid Tissue ◽  
Differentially Expressed ◽  
Thyroid Tumors ◽  
Papillary Thyroid

Objective: Next-generation sequencing (NGS) was performed to identify genes that were differentially expressed between normal thyroid tissue and papillary thyroid carcinoma (PTC). Materials & Methods: Six candidate genes were selected and further confirmed with quantitative real-time polymerase chain reaction (qRT-PCR), and immunohistochemistry in samples from 24 fresh thyroid tumors and adjacent normal tissues. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was used to investigate signal transduction pathways of the differentially expressed genes. Results: In total, 1690 genes were differentially expressed between samples from patients with PTC and the adjacent normal tissue. Among these, SFRP4, ZNF90, and DCN were the top three upregulated genes, whereas KIRREL3, TRIM36, and GABBR2 were downregulated with the smallest p values. Several pathways were associated with the differentially expressed genes and involved in cellular proliferation, cell migration, and endocrine system tumor progression, which may contribute to the pathogenesis of PTC. Upregulation of SFRP4, ZNF90, and DCN at the mRNA level was further validated with RT-PCR, and DCN expression was further confirmed with immunostaining of PTC samples. Conclusion: These results provide new insights into the molecular mechanisms of PTC. Identification of differentially expressed genes should not only improve the tumor signature for thyroid tumors as a diagnostic biomarker but also reveal potential targets for thyroid tumor treatment.

Systems Biology Approaches Reveal a Multi-stress Responsive WRKY Transcription Factor and Stress Associated Gene Co-expression Networks in Chickpea

2019 ◽  
Vol 14 (7) ◽  
pp. 591-601 ◽  
Author(s):  
Aravind K. Konda ◽  
Parasappa R. Sabale ◽  
Khela R. Soren ◽  
Shanmugavadivel P. Subramaniam ◽  
Pallavi Singh ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Wrky Transcription Factor ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Callose Deposition ◽  
Significant Probability

Background: Chickpea is a nutritional rich premier pulse crop but its production encounters setbacks due to various stresses and understanding of molecular mechanisms can be ascribed foremost importance. Objective: The investigation was carried out to identify the differentially expressed WRKY TFs in chickpea in response to herbicide stress and decipher their interacting partners. Methods: For this purpose, transcriptome wide identification of WRKY TFs in chickpea was done. Behavior of the differentially expressed TFs was compared between other stress conditions. Orthology based cofunctional gene networks were derived from Arabidopsis. Gene ontology and functional enrichment analysis was performed using Blast2GO and STRING software. Gene Coexpression Network (GCN) was constructed in chickpea using publicly available transcriptome data. Expression pattern of the identified gene network was studied in chickpea-Fusarium interactions. Results: A unique WRKY TF (Ca_08086) was found to be significantly (q value = 0.02) upregulated not only under herbicide stress but also in other stresses. Co-functional network of 14 genes, namely Ca_08086, Ca_19657, Ca_01317, Ca_20172, Ca_12226, Ca_15326, Ca_04218, Ca_07256, Ca_14620, Ca_12474, Ca_11595, Ca_15291, Ca_11762 and Ca_03543 were identified. GCN revealed 95 hub genes based on the significant probability scores. Functional annotation indicated role in callose deposition and response to chitin. Interestingly, contrasting expression pattern of the 14 network genes was observed in wilt resistant and susceptible chickpea genotypes, infected with Fusarium. Conclusion: This is the first report of identification of a multi-stress responsive WRKY TF and its associated GCN in chickpea.

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