scholarly journals Differential Gene Expression Analysis of Wheat Breeding Lines Reveal Molecular Insights in Yellow Rust Resistance under Field Conditions

Agronomy ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1888
Author(s):  
Sandeep Kumar Kushwaha ◽  
Ramesh R. Vetukuri ◽  
Firuz Odilbekov ◽  
Nidhi Pareek ◽  
Tina Henriksson ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
De Novo ◽  
Puccinia Striiformis ◽  
Specific Resistance ◽  
Expression Profiles ◽  
Yellow Rust ◽  
Differentially Expressed ◽  
Wheat Production ◽  
Rust Infection

The evolution of pathogens in the changing climate raises new challenges for wheat production. Yellow rust is one of the major wheat diseases worldwide, leading to an increased use of fungicides to prevent significant yield losses. The enhancement of the resistance potential of wheat cultivars is a necessary and environmentally friendly solution for sustainable wheat production. In this study, we aimed to identify the differentially expressed genes induced upon yellow rust infection in the field. Reference and de novo based transcriptome analysis was performed among the resistant and susceptible lines of a bi-parental population to study the global transcriptome changes in contrasting wheat genotypes. Based on the analysis, the de novo transcriptome analysis approach was found to be more supportive for field studies. Expression profiles, gene ontology, KEGG pathway analysis and enrichment studies indicated the relation between differentially expressed genes of wheat and yellow rust infection. The h0igh expression of genes related to non-race specific resistance along with pathogen-specific resistance might be a reason for the better resistance ability of a resistant wheat genotype in the field. The targeted metagenomic analysis of wheat samples revealed that Puccinia striiformis tritici was the most dominant pathogen along with other pathogens on the collected leaf material and validating the disease scoring carried out in the field and transcriptomics analyses.

Transcript profiling of neuroendocrine tumors (NETs) to identify new targets and mechanism of progression.

2019 ◽  
Vol 37 (4_suppl) ◽  
pp. 292-292
Author(s):  
Emily Walzer ◽  
Suraj Peri ◽  
Karthik Devarajan ◽  
Jianming Pei ◽  
Kathy Q. Cai ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Count Data ◽  
Transcriptional Repression ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Future Research ◽  
Linear Modeling ◽  
M Cell ◽  
Therapeutic Implications

292 Background: Few studies have characterized the molecular drivers of NET growth and mechanisms differentiating poorly differentiated (PD) and well differentiated (WD) NETs. We explored the role of dysregulated transcriptome as the principal molecular mechanism of NETs with the goal to identify novel targets and biomarkers of differentiation. Methods: With IRB approval, de-identified, formalin fixed NET samples were used to extract total RNA for transcriptome analysis. All pathology specimens were centrally reviewed. Gene expression profiles of 774 genes were obtained using nCounter platform (PanCancer pathway panel, Nanostring TechnologiesTM). The resulting count data was voom normalized and differentially expressed genes between PD and WD NETs were identified using linear modeling methods available in R-Bioconductor LIMMA package. Candidate genes with potential therapeutic implications were validated in tissue microarrays by immunohistochemistry (IHC). Results: Analysis of gene count data between 16 PD and 23 WD NETs resulted in 154 differentially expressed genes on the 774 gene panel (FDR < 10% and 2 fold change (FC) up- or down-regulated), some of which may be potential drug targets (Figure 1). E.g. Enhancer of zeste homolog 2 (EZH2), a histone methyltransferase responsible for transcriptional repression, and CHK1, a G2/M cell cycle regulator, were upregulated in PD compared to WD NETs (2.7 and 3.1 FC, respectively) and serine/threonine-protein kinase PAK 3, involved in cytoskeleton reorganization, was upregulated in WD NETs (3.4 FC). IHC staining also suggested overexpression of EZH2 and its enzymatic substrate H3K27me in PD NETs (p < 0.001). PAK 3, another novel therapeutic candidate overexpressed in WD NETs (p < 0.001) was confirmed using IHC, validating the transcriptome analysis at protein level. Conclusions: These findings, combined with previously reported pathway analysis (Vijayvergia et.al 2017)], highlight biological differences between PD and WD NETs and serve as a platform for future research. They also support investigation of novel drugs that inhibit activity of EZH2 (e.g. EPZ6438) in PD NETs and PAK3 (e.g FRAX597) in WD NETs.

scholarly journals In-depth secretome analysis of Puccinia striiformis f. sp. tritici in infected wheat uncovers effector functions

2020 ◽  
Author(s):  
Ahmet Caglar Ozketen ◽  
Ayse Andac-Ozketen ◽  
Bayantes Dagvadorj ◽  
Burak Demiralay ◽  
Mahinur S. Akkaya
Keyword(s):  
De Novo ◽  
Puccinia Striiformis ◽  
Yellow Rust ◽  
Expression System ◽  
Differentially Expressed ◽  
Secreted Proteins ◽  
Central Anatolia ◽  
Human Populations ◽  
Post Inoculation ◽  
Small Secreted Proteins

ABSTRACTThe importance of wheat yellow rust disease, caused by Puccinia striiformis f. sp. tritici (Pst), has increased substantially due to the emergence of aggressive new Pst races in the last couple of decades. In an era of escalating human populations and climate change, it is vital to understand the infection mechanism of Pst in order to develop better strategies to combat wheat yellow disease. This study focuses on the identification of small secreted proteins (SSPs) and candidate-secreted effector proteins (CSEPs) that are used by the pathogen to support infection and control disease development. We generated de novo assembled transcriptomes of Pst collected from wheat fields in central Anatolia. We inoculated both susceptible and resistant seedlings with Pst and analyzed haustoria formation. At 10 days post-inoculation (dpi), we analyzed the transcriptomes and identified 10,550 Differentially Expressed Unigenes (DEGs), of which 6,220 were Pst-related. Among those Pst-related genes, 230 were predicted as PstSSPs. In silico characterization was performed using an approach combining the transcriptomic data and data mining results to provide a reliable list to narrow down the ever-expanding repertoire of predicted effectorome. The comprehensive analysis detected 14 Differentially Expressed Small-Secreted Proteins (DESSPs) that overlapped with the genes in available literature data to serve as the best CSEPs for experimental validation. One of the CSEPs was cloned and studied to test the reliability of the presented data. Biological assays show that the randomly selected CSEP, Unigene17495 (PSTG_10917), localizes in the chloroplast and is able to suppress cell death induced by INF1 in a Nicotiana benthamiana heterologous expression system.

Haploinsufficiency of RPS14 and Deregulation of Ribosomal- and Translation-Related Genes in MDS Patients with Del(5q)

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 3641-3641
Author(s):  
Andrea Pellagatti ◽  
Eva Hellström-Lindberg ◽  
Aristoteles Giagounidis ◽  
Janet Perry ◽  
Luca Malcovati ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Hierarchical Clustering ◽  
Ribosome Biogenesis ◽  
De Novo ◽  
Bone Marrow Cells ◽  
Expression Profiles ◽  
Ribosomal Subunit ◽  
Differentially Expressed ◽  
Expression Levels ◽  
Lower Expression

Abstract The del(5q) is the most commonly reported deletion in de novo MDS and is found in 10–15% of all patients. Our group demonstrated haploinsufficiency for the ribosomal gene RPS14, which is required for the maturation of 40S ribosomal subunits and maps to the commonly deleted region in patients with the 5q- syndrome (Boultwood et al, Br J Haematol2007, 139:578–89). Haploinsufficiency of RPS14 has been shown to be the mechanism underlying the erythroid defect in this disorder (Ebert et al, Nature2008, 451:335–9). We have recently shown that haploinsufficiency of RPS14 in patients with the 5q- syndrome is associated with deregulated expression of ribosomal- and translation-related genes, suggesting that the 5q- syndrome represents a disorder of aberrant ribosome biogenesis (Pellagatti et al, Br J Haematol2008, 142:57–64). The del(5q) in the 5q-syndrome is cytogenetically indistinguishable from the del(5q) found in other MDS and in the vast majority of these patients the CDR of the 5q- syndrome will be deleted (and therefore one allele of RPS14 will be lost). We are investigating the hypothesis that haploinsufficiency of RPS14 and consequent deregulated ribosome biogenesis may also play a role in the pathogenesis of non-5q- syndrome MDS patients with del(5q). Using Affymetrix U133 Plus2.0 arrays, we have studied the expression profiles of a group of 579 ribosomal- and translation-related genes in the CD34+ cells of 21 non-5q- syndrome MDS patients with del(5q) and 95 MDS patients without del(5q). 168 of 579 ribosomal-and translation-related probe sets were found to be significantly differentially expressed between these two groups, with approximately 90% of these showing lower expression levels in patients with del(5q). Hierarchical clustering using this set of 168 genes gave a good separation between patients with and without the del(5q). RPS14 was one of the most significant differentially expressed genes, with lower expression levels in patients with del(5q) confirming its haploinsufficient status in these patients. Other significant differentially expressed genes include the ribosomal protein RPL22L1, and the translation initiation factors EIF4EBP3 and EIF4B. Interestingly, when samples from 16 patients with 5q- syndrome were included in the analysis, hierarchical clustering using significantly differentially expressed ribosomal- and translation-related genes showed that most patients with 5q- syndrome and most patients with del(5q) clustered together. We are currently using polysome profile analysis on bone marrow cells to examine the levels of the 40S ribosomal subunit in patients with del(5q) and without del(5q). Our results support the hypothesis that haploinsufficiency of RPS14 and deregulation of ribosomal- and translation-related genes contribute to disease pathogenesis in MDS patients with del(5q). An exciting possibility is that other MDS with the del(5q) and the 5q- syndrome share a related molecular basis in that they are all disorders of defective ribosomal biogenesis.

scholarly journals In-depth secretome analysis of Puccinia striiformis f. sp. tritici in infected wheat uncovers effector functions

2020 ◽  
Vol 40 (12) ◽  
Author(s):  
Ahmet Caglar Ozketen ◽  
Ayse Andac-Ozketen ◽  
Bayantes Dagvadorj ◽  
Burak Demiralay ◽  
Mahinur S. Akkaya
Keyword(s):  
De Novo ◽  
Puccinia Striiformis ◽  
Yellow Rust ◽  
Expression System ◽  
Differentially Expressed ◽  
Secreted Proteins ◽  
Central Anatolia ◽  
Human Populations ◽  
Post Inoculation ◽  
Small Secreted Proteins

Abstract The importance of wheat yellow rust disease, caused by Puccinia striiformis f. sp. tritici (Pst), has increased substantially due to the emergence of aggressive new Pst races in the last couple of decades. In an era of escalating human populations and climate change, it is vital to understand the infection mechanism of Pst in order to develop better strategies to combat wheat yellow disease. The present study focuses on the identification of small secreted proteins (SSPs) and candidate-secreted effector proteins (CSEPs) that are used by the pathogen to support infection and control disease development. We generated de novo assembled transcriptomes of Pst collected from wheat fields in central Anatolia. We inoculated both susceptible and resistant seedlings with Pst and analyzed haustoria formation. At 10 days post-inoculation (dpi), we analyzed the transcriptomes and identified 10550 Differentially Expressed Unigenes (DEGs), of which 6072 were Pst-mapped. Among those Pst-related genes, 227 were predicted as PstSSPs. In silico characterization was performed using an approach combining the transcriptomic data and data mining results to provide a reliable list to narrow down the ever-expanding repertoire of predicted effectorome. The comprehensive analysis detected 14 Differentially Expressed Small-Secreted Proteins (DESSPs) that overlapped with the genes in available literature data to serve as the best CSEPs for experimental validation. One of the CSEPs was cloned and studied to test the reliability of the presented data. Biological assays show that the randomly selected CSEP, Unigene17495 (PSTG_10917), localizes in the chloroplast and is able to suppress cell death induced by INF1 in a Nicotiana benthamiana heterologous expression system.

scholarly journals Comparative analysis of the transcriptional responses of five Leishmania species to trivalent antimony

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Julián Medina ◽  
Lissa Cruz-Saavedra ◽  
Luz Helena Patiño ◽  
Marina Muñoz ◽  
Juan David Ramírez
Keyword(s):  
Comparative Analysis ◽  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Rna Binding ◽  
De Novo ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Orthologous Genes ◽  
Transcriptional Responses ◽  
Species Specific

Abstract Background Leishmaniasis is a neglected tropical disease caused by several species of Leishmania. The resistance phenotype of these parasites depends on the characteristics of each species, which contributes to increased therapeutic failures. Understanding the mechanism used by the parasite to survive under treatment pressure in order to identify potential common and specific therapeutic targets is essential for the control of leishmaniasis. The aim of this study was to investigate the expression profiles and potential shared and specific resistance markers of the main Leishmania species of medical importance [subgenus L. (Leishmania): L. donovani, L. infantum and L. amazonensis; subgenus L. (Viannia): L. panamensis and L. braziliensis)] resistant and sensitive to trivalent stibogluconate (SbIII). Methods We conducted comparative analysis of the transcriptomic profiles (only coding sequences) of lines with experimentally induced resistance to SbIII from biological replicates of five Leishmania species available in the databases of four articles based on ortholog attribution. Simultaneously, we carried out functional analysis of ontology and reconstruction of metabolic pathways of the resulting differentially expressed genes (DEGs). Results Resistant lines for each species had differential responses in metabolic processes, compound binding, and membrane components concerning their sensitive counterpart. One hundred and thirty-nine metabolic pathways were found, with the three main pathways comprising cysteine and methionine metabolism, glycolysis, and the ribosome. Differentially expressed orthologous genes assigned to species-specific responses predominated, with 899 self-genes. No differentially expressed genes were found in common among the five species. Two common upregulated orthologous genes were found among four species (L. donovani, L. braziliensis, L. amazonensis, and L. panamensis) related to an RNA-binding protein and the NAD(P)H cytochrome-B5-oxidoreductase complex, associated with transcriptional control and de novo synthesis of linoleic acid, critical mechanisms in resistance to antimonials. Conclusion Herein, we identified potential species-specific genes related to resistance to SbIII. Therefore, we suggest that future studies consider a treatment scheme that is species-specific. Despite the limitations of our study, this is the first approach toward unraveling the pan-genus genetic mechanisms of resistance in leishmaniasis. Graphical Abstract

scholarly journals Comparative Transcriptome Analysis Reveals Candidate Genes Involved in Isoquinoline Alkaloid Biosynthesis in Stephania tetrandra

Planta Medica ◽  
2020 ◽  
Vol 86 (17) ◽  
pp. 1258-1268
Author(s):  
Yangyang Zhang ◽  
Yun Kang ◽  
Hui Xie ◽  
Yaqin Wang ◽  
Yaoting Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Expression Profiles ◽  
Isoquinoline Alkaloid ◽  
Differentially Expressed ◽  
Comparative Transcriptome ◽  
Isoquinoline Alkaloids ◽  
Alkaloid Biosynthesis ◽  
Isoquinoline Alkaloid Biosynthesis

AbstractThe roots of Stephania tetrandra are used as a traditional Chinese medicine. Isoquinoline alkaloids are considered to be the most important and effective components in this herb, but little is known about the molecular mechanism underlying their biosynthesis. In this context, this study aimed to reveal candidate genes related to isoquinoline alkaloid biosynthesis in S. tetrandra. Determination of tetrandrine and fangchinoline in the roots and leaves of S. tetrandra by HPLC showed that the roots had much higher contents of the two isoquinoline alkaloids than the leaves. Thus, a comparative transcriptome analysis of the two tissues was performed to uncover candidate genes involved in isoquinoline alkaloid biosynthesis. A total of 71 674 unigenes was obtained and 31 994 of these were assigned putative functions based on BLAST searches against 6 annotation databases. Among the 79 isoquinoline alkaloid-related unigenes, 51 were differentially expressed, with 42 and 9 genes upregulated and downregulated, respectively, when the roots were compared with the leaves. The upregulated differentially expressed genes were consistent with isoquinoline alkaloid accumulation in roots and thus were deemed key candidate genes for isoquinoline alkaloid biosynthesis in the roots. Moreover, the expression profiles of 10 isoquinoline alkaloid-related differentially expressed genes between roots and leaves were validated by quantitative real-time polymerase chain reaction, which indicated that our transcriptome and gene expression profiles were reliable. This study not only provides a valuable genomic resource for S. tetrandra but also proposes candidate genes involved in isoquinoline alkaloid biosynthesis and transcription factors related to the regulation of isoquinoline alkaloid biosynthesis. The results lay a foundation for further studies on isoquinoline alkaloid biosynthesis in this medicinal plant.

scholarly journals Comparative Analysis of the Intermolt and Postmolt Hepatopancreas Transcriptomes Provides Insight into the Mechanisms of Procambarus clarkii Molting Process

Life ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 480
Author(s):  
Shengyan Su ◽  
Brian Pelekelo Munganga ◽  
Can Tian ◽  
JianLin Li ◽  
Fan Yu ◽  
...  
Keyword(s):  
Immune Response ◽  
Differentially Expressed Genes ◽  
Hormonal Regulation ◽  
De Novo ◽  
Procambarus Clarkii ◽  
Expression Profiles ◽  
R Package ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Molting Process

In the present study, we used RNA-Seq to investigate the expression changes in the transcriptomes of two molting stages (postmolt (M) and intermolt (NM)) of the red swamp crayfish and identified differentially expressed genes. The transcriptomes of the two molting stages were de novo assembled into 139,100 unigenes with a mean length of 675.59 bp. The results were searched against the NCBI, NR, KEGG, Swissprot, and KOG databases, to annotate gene descriptions, associate them with gene ontology terms, and assign them to pathways. Furthermore, using the DESeq R package, differentially expressed genes were evaluated. The analysis revealed that 2347 genes were significantly (p > 0.05) differentially expressed in the two molting stages. Several genes and other factors involved in several molecular events critical for the molting process, such as energy requirements, hormonal regulation, immune response, and exoskeleton formation were identified and evaluated by correlation and KEGG analysis. The expression profiles of transcripts detected via RNA-Seq were validated by real-time PCR assay of eight genes. The information presented here provides a transient view of the hepatopancreas transcripts available in the postmolt and intermolt stage of crayfish, hormonal regulation, immune response, and skeletal-related activities during the postmolt stage and the intermolt stage.

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