scholarly journals Transcriptome profiling of pepper leaves by RNA-Seq during an incompatible and a compatible pepper-tobamovirus interaction

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Balázs Kalapos ◽  
Csilla Juhász ◽  
Eszter Balogh ◽  
Gábor Kocsy ◽  
István Tóbiás ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Carbon Fixation ◽  
Systemic Infection ◽  
Transcriptome Profiling ◽  
Hypersensitive Reaction ◽  
Post Inoculation ◽  
Rna Seq ◽  
Virus Infections ◽  
Transcriptional Reprogramming ◽  
Pepper Leaves

AbstractUpon virus infections, the rapid and comprehensive transcriptional reprogramming in host plant cells is critical to ward off virus attack. To uncover genes and defense pathways that are associated with virus resistance, we carried out the transcriptome-wide Illumina RNA-Seq analysis of pepper leaves harboring the L3 resistance gene at 4, 8, 24 and 48 h post-inoculation (hpi) with two tobamoviruses. Obuda pepper virus (ObPV) inoculation led to hypersensitive reaction (incompatible interaction), while Pepper mild mottle virus (PMMoV) inoculation resulted in a systemic infection without visible symptoms (compatible interaction). ObPV induced robust changes in the pepper transcriptome, whereas PMMoV showed much weaker effects. ObPV markedly suppressed genes related to photosynthesis, carbon fixation and photorespiration. On the other hand, genes associated with energy producing pathways, immune receptors, signaling cascades, transcription factors, pathogenesis-related proteins, enzymes of terpenoid biosynthesis and ethylene metabolism as well as glutathione S-transferases were markedly activated by ObPV. Genes related to photosynthesis and carbon fixation were slightly suppressed also by PMMoV. However, PMMoV did not influence significantly the disease signaling and defense pathways. RNA-Seq results were validated by real-time qPCR for ten pepper genes. Our findings provide a deeper insight into defense mechanisms underlying tobamovirus resistance in pepper.

scholarly journals Dual RNA-Seq Analysis of the Interaction Between Edible Fungus Morchella sextelata and Its Pathogenic Fungus Paecilomyces penicillatus Uncovers the Candidate Defense and Pathogenic Factors

2021 ◽  
Vol 12 ◽  
Author(s):  
Yang Yu ◽  
Hao Tan ◽  
Tianhai Liu ◽  
Lixu Liu ◽  
Jie Tang ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Expression Profiles ◽  
Pathogenic Fungus ◽  
Post Inoculation ◽  
Rna Seq ◽  
Edible Fungus ◽  
Pathogenic Factors ◽  
Recognition Protein ◽  
Genetic Mechanisms ◽  
Prevalent Species

Morels (Morchella spp.) are economically important mushrooms cultivated in many countries. However, their production and quality are hindered by white mold disease because of Paecilomyces penicillatus infection. In this study, we aimed to understand the genetic mechanisms of interactions between P. penicillatus and Morchella. M. sextelata, the most prevalent species of Morchella in China, was inoculated with P. penicillatus; then, the expression profiles of both fungi were determined simultaneously at 3 and 6 days post-inoculation (dpi) using a dual RNA-Seq approach. A total of 460 and 313 differentially expressed genes (DEGs) were identified in P. penicillatus and M. sextelata, respectively. The CAZymes of β-glucanases and mannanases, as well as subtilase family, were upregulated in P. penicillatus, which might be involved in the degradation of M. sextelata cell walls. Chitin recognition protein, caffeine-induced death protein, and putative apoptosis-inducing protein were upregulated, while cyclin was downregulated in infected M. sextelata. This indicates that P. penicillatus could trigger programmed cell death in M. sextelata after infection. Laccase-2, tyrosinases, and cytochrome P450s were also upregulated in M. sextelata. The increased expression levels of these genes suggest that M. sextelata could detoxify the P. penicillatus toxins and also form a melanin barrier against P. penicillatus invasion. The potential pathogenic mechanisms of P. penicillatus on M. sextelata and the defense mechanisms of M. sextelata against P. penicillatus were well described.

scholarly journals Comparative Transcriptome Analysis of Two Aegilops tauschii with Contrasting Drought Tolerance by RNA-Seq

2020 ◽  
Vol 21 (10) ◽  
pp. 3595
Author(s):  
Xinpeng Zhao ◽  
Shenglong Bai ◽  
Lechen Li ◽  
Xue Han ◽  
Jiahui Li ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Common Wheat ◽  
Carbon Fixation ◽  
Aegilops Tauschii ◽  
Transcriptome Profiling ◽  
Mapk Signaling ◽  
Mitogen Activated Protein Kinase ◽  
Rna Seq ◽  
Alpha Linolenic Acid

As the diploid progenitor of common wheat, Aegilops tauschii is considered to be a valuable resistance source to various biotic and abiotic stresses. However, little has been reported concerning the molecular mechanism of drought tolerance in Ae. tauschii. In this work, the drought tolerance of 155 Ae. tauschii accessions was firstly screened on the basis of their coleoptile lengths under simulated drought stress. Subsequently, two accessions (XJ002 and XJ098) with contrasting coleoptile lengths were selected and intensively analyzed on rate of water loss (RWL) as well as physiological characters, confirming the difference in drought tolerance at the seedling stage. Further, RNA-seq was utilized for global transcriptome profiling of the two accessions seedling leaves under drought stress conditions. A total of 6969 differentially expressed genes (DEGs) associated with drought tolerance were identified, and their functional annotations demonstrated that the stress response was mediated by pathways involving alpha-linolenic acid metabolism, starch and sucrose metabolism, peroxisome, mitogen-activated protein kinase (MAPK) signaling, carbon fixation in photosynthetic organisms, and glycerophospholipid metabolism. In addition, DEGs with obvious differences between the two accessions were intensively analyzed, indicating that the expression level of DEGs was basically in alignment with the physiological changes of Ae. tauschii under drought stress. The results not only shed fundamental light on the regulatory process of drought tolerance in Ae. tauschii, but also provide a new gene resource for improving the drought tolerance of common wheat.

scholarly journals Reactive oxygen and nitrogen species and hormone signalling in systemic infection of pea by Pea enation mosaic virus

2013 ◽  
Vol 49 (No. 3) ◽  
pp. 105-119 ◽  
Author(s):  
H. Kyseláková ◽  
M. Sedlářová ◽  
M. Kubala ◽  
V. Nožková ◽  
J. Piterková ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Reactive Oxygen ◽  
Systemic Infection ◽  
Hypersensitive Reaction ◽  
Simultaneous Increase ◽  
Post Inoculation ◽  
Oxygen Species ◽  
Pea Enation Mosaic Virus ◽  
Local Accumulation ◽  
Hormone Signalling

The physiological responses of pea plants during 40 days of compatible interaction with Pea enation mosaic virus (PEMV) were evaluated. PEMV induces systemic changes in the concentration of phytohormones. At 5 days post inoculation (dpi), a simultaneous increase in abscisic acid (ABA) level and a decrease in salicylic acid (SA) level was observed, which is known to be involved in the suppression of hypersensitive reaction. In our pathosystem it preceded the virus presence in the systemic leaves. PEMV induces the accumulation of ABA, SA and Hsp70 and enhances peroxidase (POX) activity at 15 dpi, when it is already transmitted throughout the plant. The formation of enations was preceded by a local accumulation of nitric oxide, which was followed by the appearance of reactive oxygen species, mostly in the vicinity of leaf veins. Such heterogeneity suggests involvement of these molecules in the control of hyperplasia and tissue differentiation.  

scholarly journals Transcriptome profile of Carrizo citrange roots in response toPhytophthora parasiticainfection

2019 ◽  
Author(s):  
Zunaira Afzal Naveed ◽  
Jose C. Huguet-Tapia ◽  
Gul Shad Ali
Keyword(s):  
Plant Immunity ◽  
Brown Rot ◽  
Differentially Expressed ◽  
Post Inoculation ◽  
Rna Seq ◽  
Transcriptome Profile ◽  
Cellular Processes ◽  
Carrizo Citrange ◽  
Transcriptional Reprogramming ◽  
Citrus Rootstock

AbstractPhytophthora parasiticais one of the most widespreadPhytophthoraspecies, which is known to cause root rot, foot rot/gummosis and brown rot of fruits in citrus. In this study, we have analyzed the transcriptome of a commonly used citrus rootstock Carrizo citrange in response toP. parasiticainfection using the RNA-seq technology. In total, we have identified 6692 differentially expressed transcripts (DETs) amongP. parasitica-inoculated and mock-treated roots. Of these, 3960 genes were differentially expressed at 24 hours post inoculation and 5521 genes were differentially expressed at 48 hours post inoculation. Gene ontology analysis of DETs suggested substantial transcriptional reprogramming of diverse cellular processes particularly the biotic stress response pathways in Carrizo citrange roots. ManyRgenes, transcription factors, and several other genes putatively involved in plant immunity were differentially modulated in citrus roots in response toP. parasiticainfection. Analysis reported here lays out a strong foundation for future studies aimed at improving resistance of citrus rootstocks toP. parasitica.

scholarly journals Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids

2020 ◽  
Vol 21 (3) ◽  
pp. 1080
Author(s):  
Jawahar Lal Katara ◽  
Ram Lakhan Verma ◽  
Madhuchhanda Parida ◽  
Umakanta Ngangkham ◽  
Kutubuddin Ali Molla ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Carbon Fixation ◽  
Reference Genome ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Grain Filling ◽  
Rna Seq ◽  
Kegg Pathway Analysis ◽  
Expression Of Genes ◽  
Differential Expression Of Genes

RNA-Seq technology was used to analyze the transcriptome of two rice hybrids, Ajay (based on wild-abortive (WA)-cytoplasm) and Rajalaxmi (based on Kalinga-cytoplasm), and their respective parents at the panicle initiation (PI) and grain filling (GF) stages. Around 293 and 302 million high quality paired-end reads of Ajay and Rajalaxmi, respectively, were generated and aligned against the Nipponbare reference genome. Transcriptome profiling of Ajay revealed 2814 and 4819 differentially expressed genes (DEGs) at the PI and GF stages, respectively, as compared to its parents. In the case of Rajalaxmi, 660 and 5264 DEGs were identified at PI and GF stages, respectively. Functionally relevant DEGs were selected for validation through qRT-PCR, which were found to be co-related with the expression patterns to RNA-seq. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated significant DEGs enriched for energy metabolism pathways, such as photosynthesis, oxidative phosphorylation, and carbon fixation, at the PI stage, while carbohydrate metabolism-related pathways, such as glycolysis and starch and sucrose metabolism, were significantly involved at the GF stage. Many genes involved in energy metabolism exhibited upregulation at the PI stage, whereas the genes involved in carbohydrate biosynthesis had higher expression at the GF stage. The majority of the DEGs were successfully mapped to know yield related rice quantitative trait loci (QTLs). A set of important transcription factors (TFs) was found to be encoded by the identified DEGs. Our results indicated that a complex interplay of several genes in different pathways contributes to higher yield and vigor in rice hybrids.

scholarly journals Characterization of full-length transcriptome in Saccharum officinarum and molecular insights into tiller development

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Haifeng Yan ◽  
Huiwen Zhou ◽  
Hanmin Luo ◽  
Yegeng Fan ◽  
Zhongfeng Zhou ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Developmental Stages ◽  
Genomic Data ◽  
Saccharum Officinarum ◽  
Full Length ◽  
Rna Seq ◽  
Pyruvate Phosphate Dikinase ◽  
Sugarcane Yield ◽  
Tiller Bud

Abstract Background Although extensive breeding efforts are ongoing in sugarcane (Saccharum officinarum L.), the average yield is far below the theoretical potential. Tillering is an important component of sugarcane yield, however, the molecular mechanism underlying tiller development is still elusive. The limited genomic data in sugarcane, particularly due to its complex and large genome, has hindered in-depth molecular studies. Results Herein, we generated full-length (FL) transcriptome from developing leaf and tiller bud samples based on PacBio Iso-Seq. In addition, we performed RNA-seq from tiller bud samples at three developmental stages (T0, T1 and T2) to uncover key genes and biological pathways involved in sugarcane tiller development. In total, 30,360 and 20,088 high-quality non-redundant isoforms were identified in leaf and tiller bud samples, respectively, representing 41,109 unique isoforms in sugarcane. Likewise, we identified 1063 and 1037 alternative splicing events identified in leaf and tiller bud samples, respectively. We predicted the presence of coding sequence for 40,343 isoforms, 98% of which was successfully annotated. Comparison with previous FL transcriptomes in sugarcane revealed 2963 unreported isoforms. In addition, we characterized 14,946 SSRs from 11,700 transcripts and 310 lncRNAs. By integrating RNA-seq with the FL transcriptome, 468 and 57 differentially expressed genes (DEG) were identified in T1vsT0 and T2vsT0, respectively. Strong up-regulation of several pyruvate phosphate dikinase and phosphoenolpyruvate carboxylase genes suggests enhanced carbon fixation and protein synthesis to facilitate tiller growth. Similarly, up-regulation of linoleate 9S-lipoxygenase and lipoxygenase genes in the linoleic acid metabolism pathway suggests high synthesis of key oxylipins involved in tiller growth and development. Conclusions Collectively, we have enriched the genomic data available in sugarcane and provided candidate genes for manipulating tiller formation and development, towards productivity enhancement in sugarcane.

scholarly journals Non-Coding RNA Signatures of B-Cell Acute Lymphoblastic Leukemia

2021 ◽  
Vol 22 (5) ◽  
pp. 2683
Author(s):  
Princess D. Rodriguez ◽  
Hana Paculova ◽  
Sophie Kogut ◽  
Jessica Heath ◽  
Hilde Schjerven ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
B Cell ◽  
Molecular Mechanisms ◽  
Lymphoblastic Leukemia ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Protein Coding ◽  
Non Coding Rna ◽  
Technological Developments ◽  
Cell Acute Lymphoblastic Leukemia

Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell acute lymphoblastic leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.

scholarly journals Erratum: Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

2014 ◽  
Vol 32 (11) ◽  
pp. 1166-1166 ◽  
Author(s):  
Sheng Li ◽  
Scott W Tighe ◽  
Charles M Nicolet ◽  
Deborah Grove ◽  
Shawn Levy ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Next Generation ◽  
Generation Sequencing
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