scholarly journals Transcriptional profiling of Impatiens walleriana genes through different stages of downy mildew infection reveals novel genes involved in disease susceptibility

2019 ◽  
Author(s):  
Stephanie Suarez ◽  
Zunaira Afzal Naveed ◽  
Gul Shad Ali
Keyword(s):  
Downy Mildew ◽  
Disease Susceptibility ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Transcriptional Profiling ◽  
Differential Expression Analysis ◽  
Plant Stress ◽  
Differentially Expressed ◽  
Mildew Resistance ◽  
Impatiens Walleriana

AbstractImpatiens downy mildew is a highly destructive disease of Impatiens walleriana, and economically important bedding ornamental crop. This disease is caused by a recently emerged pathogen Plasmopara obducens. Since both the host and pathogen are relatively less studied, there are only a few genomic resources available for both I. walleriana and P. obducens. In this study, we have analyzed transcriptional changes in I. walleriana in response to P. obducens infection during different stages of disease development. Our main goal was to identify candidate genes that may be involved in I. walleriana susceptibility to P. obducens. Since the genome of I. walleriana is not available publicly, we constructed and optimized a de novo transcriptome assembly consisting of 73,022 transcripts. Differential expression analysis based on this optimized de novo transcriptome assembly revealed 3,000 to 4,500 differentially expressed transcripts (DETs) at 0 hr, 12 hr, 48 hr, 120 hr, and 240 hr time points after infection. Functional annotation of these DETs revealed that numerous plant stress responsive genes are activated and deactivated throughout the infection cycle. Genes in the calcium signaling pathways, receptor-like kinases (RLKs) including 10 disease resistance associated RLK transcripts, powdery mildew resistance genes (MLO), and many other plant stress related genes were predominantly differentially expressed in I. walleriana in response to P. obducens. Analyses reported here provides molecular insights into the disease susceptibility mechanism of the Impatiens downy mildew, and lays out a strong foundation for future studies aimed at improving downy mildew resistance in I. walleriana.

scholarly journals De novo assembly of the Brown trout (Salmo trutta m. fario) brain and muscle transcriptome: transcript annotation, tissue differential expression profile and SNP discovery

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
J. Fibla ◽  
N. Oromi ◽  
M. Pascual-Pons ◽  
J. L. Royo ◽  
A. Palau ◽  
...  
Keyword(s):  
Differential Expression ◽  
Brown Trout ◽  
Salmo Trutta ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Differential Expression Analysis ◽  
Cdna Libraries ◽  
Significant Differential Expression ◽  
Reference Transcriptome ◽  
Salmonid Species

Abstract Objectives The Brown trout is a salmonid species with a high commercial value in Europe. Life history and spawning behaviour include resident (Salmo trutta m. fario) and migratory (Salmo trutta m. trutta) ecotypes. The main objective is to apply RNA-seq technology in order to obtain a reference transcriptome of two key tissues, brain and muscle, of the riverine trout Salmo trutta m. fario. Having a reference transcriptome of the resident form will complement genomic resources of salmonid species. Data description We generate two cDNA libraries from pooled RNA samples, isolated from muscle and brain tissues of adult individuals of Salmo trutta m. fario, which were sequenced by Illumina technology. Raw reads were subjected to de-novo transcriptome assembly using Trinity, and coding regions were predicted by TransDecoder. A final set of 35,049 non-redundant ORF unigenes were annotated. Tissue differential expression analysis was evaluated by Cuffdiff. A False Discovery Rate (FDR) ≤ 0.01 was considered for significant differential expression, allowing to identify key differentially expressed unigenes. Finally, we have identified SNP variants that will be useful tools for population genomic studies.

scholarly journals RNA-Seq and differential gene expression analysis in Temora stylifera copepod females with contrasting non-feeding nauplii survival rates: an environmental transcriptomics study

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Ennio Russo ◽  
Chiara Lauritano ◽  
Giuliana d’Ippolito ◽  
Angelo Fontana ◽  
Diana Sarno ◽  
...  
Keyword(s):  
Differential Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Survival Rates ◽  
Natural Populations ◽  
Zooplankton Community ◽  
Differentially Expressed ◽  
Diatom Cell ◽  
Functional Interpretation ◽  
Protein Ubiquitination

Abstract Background Copepods are fundamental components of pelagic food webs, but reports on how molecular responses link to reproductive success in natural populations are still scarce. We present a de novo transcriptome assembly and differential expression (DE) analysis in Temora stylifera females collected in the Gulf of Naples, Mediterranean Sea, where this copepod dominates the zooplankton community. High-Throughput RNA-Sequencing and DE analysis were performed from adult females collected on consecutive weeks (May 23rd and 30th 2017), because opposite naupliar survival rates were observed. We aimed at detecting key genes that may have influenced copepod reproductive potential in natural populations and whose expression was potentially affected by phytoplankton-derived oxylipins, lipoxygenase-derived products strongly impacting copepod naupliar survival. Results On the two sampling dates, temperature, salinity, pH and oxygen remained stable, while variations in phytoplankton cell concentration, oxylipin concentration and oxylipin-per-diatom-cell production were observed. T. stylifera naupliar survival was 25% on May 23rd and 93% on May 30th. De novo assembly generated 268,665 transcripts (isoforms) and 120,749 unique ‘Trinity predicted genes’ (unigenes), of which 50% were functionally annotated. Out of the 331 transcript isoforms differentially expressed between the two sampling dates, 119 sequences were functionally annotated (58 up- and 61 down-regulated). Among predicted genes (unigenes), 144 sequences were differentially expressed and 31 (6 up-regulated and 25 down-regulated) were functionally annotated. Most of the significantly down-regulated unigenes and isoforms were A5 Putative Odorant Binding Protein (Obp). Other differentially expressed sequences (isoforms and unigenes) related to developmental metabolic processes, protein ubiquitination, response to stress, oxidation-reduction reactions and hydrolase activities. DE analysis was validated through Real Time-quantitative PCR of 9 unigenes and 3 isoforms. Conclusions Differential expression of sequences involved in signal detection and transduction, cell differentiation and development offered a functional interpretation to the maternally-mediated low naupliar survival rates observed in samples collected on May 23rd. Down-regulation of A5 Obp along with higher quantities of oxylipins-per-litre and oxylipins-per-diatom-cell observed on May 23rd could suggest oxylipin-mediated impairment of naupliar survival in natural populations of T. stylifera. Our results may help identify biomarker genes explaining variations in copepod reproductive responses at a molecular level.

scholarly journals Identification of cordycepin biosynthesis-related genes through de novo transcriptome assembly and analysis in Cordyceps cicadae

2018 ◽  
Vol 5 (12) ◽  
pp. 181247 ◽  
Author(s):  
Tengfei Liu ◽  
Ziyao Liu ◽  
Xueyan Yao ◽  
Ying Huang ◽  
Qingsong Qu ◽  
...  
Keyword(s):  
Fruiting Body ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Quantitative Polymerase Chain Reaction ◽  
Nucleotide Metabolism ◽  
Differentially Expressed ◽  
Parasitic Fungus ◽  
Active Constituent ◽  
Illumina Hiseq ◽  
Cordyceps Cicadae

Cordyceps cicadae (Chanhua) is a parasitic fungus that grows on Cicada flammata larvae and is used to relieve exhaustion and treat numerous diseases, in part through its active constituent, cordycepin. We used de novo Illumina HiSeq 4000 sequencing to obtain transcriptomes of C. cicadae mycelium, fruiting body, and sclerotium, and identify differentially expressed genes. In the mycelium versus sclerotium libraries, 1576 upregulated and 2300 downregulated genes were identified. In the mycelium versus fruiting body and fruiting body versus sclerotium body libraries, 1604 and 1474 upregulated and 1365 and 1320 downregulated genes, respectively, were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses identified 19 genes differentially expressed in mycelium versus fruiting body as related to the purine pathway, along with 28 and 16 genes differentially expressed in the mycelium versus sclerotium and fruiting body versus sclerotium groups, respectively. Gene expression of six key enzymes was validated by quantitative polymerase chain reaction. Specifically, 5′-nucleotidase (c62060g1) and adenosine deaminase (c35629g1) in purine nucleotide metabolism, which are involved in cordycepin biosynthesis, were significantly upregulated in the sclerotium group. These findings improved our understanding of genes involved in the biosynthesis of cordycepin and other characteristic secondary metabolites in C. cicadae .

scholarly journals Identification of defense related gene families and their response against powdery and downy mildew infections in Vitis vinifera

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Neetu Goyal ◽  
Garima Bhatia ◽  
Naina Garewal ◽  
Anuradha Upadhyay ◽  
Kashmir Singh
Keyword(s):  
Vitis Vinifera ◽  
Downy Mildew ◽  
Defense Mechanisms ◽  
Molecular Mechanisms ◽  
Differential Expression Analysis ◽  
Gene Families ◽  
Pathogen Resistance ◽  
Differentially Expressed ◽  
Phylogenetic Study ◽  
In Planta

Abstract Background Grapevine (Vitis vinifera) productivity has been severely affected by various bacterial, viral and fungal diseases worldwide. When a plant is infected with the pathogen, various defense mechanisms are subsequently activated in plants at various molecular levels. Thus, for substantiating the disease control in an eco-friendly way, it is essential to understand the molecular mechanisms governing pathogen resistance in grapes. Results In our study, we performed genome-wide identification of various defensive genes expressed during powdery mildew (PM) and downy mildew (DM) infections in grapevine. Consequently, we identified 6, 21, 2, 5, 3 and 48 genes of Enhanced Disease Susceptibility 1 (EDS1), Non-Race-specific Disease Resistance (NDR1), Phytoalexin deficient 4 (PAD4), Nonexpressor of PR Gene (NPR), Required for Mla-specified resistance (RAR) and Pathogenesis Related (PR), respectively, in the grapevine genome. The phylogenetic study revealed that V. vinifera defensive genes are evolutionarily related to Arabidopsis thaliana. Differential expression analysis resulted in identification of 2, 4, 7, 2, 4, 1 and 7 differentially expressed Nucleotide-binding leucine rich repeat receptor (NLR), EDS1, NDR1, PAD4, NPR, RAR1 and PR respectively against PM infections and 28, 2, 5, 4, 1 and 19 differentially expressed NLR, EDS1, NDR1, NPR, RAR1 and PR respectively against DM infections in V. vinifera. The co-expression study showed the occurrence of closely correlated defensive genes that were expressed during PM and DM stress conditions. Conclusion The PM and DM responsive defensive genes found in this study can be characterized in future for impelling studies relaying fungal and oomycete resistance in plants, and the functionally validated genes would then be available for conducting in-planta transgenic gene expression studies for grapes.

scholarly journals De novo Transcriptome Assembly of Senna occidentalis Sheds Light on the Anthraquinone Biosynthesis Pathway

2022 ◽  
Vol 12 ◽  
Author(s):  
Sang-Ho Kang ◽  
Woo-Haeng Lee ◽  
Joon-Soo Sim ◽  
Niha Thaku ◽  
Saemin Chang ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Differential Expression Analysis ◽  
Biosynthesis Pathway ◽  
Rna Seq ◽  
Pharmacological Activities ◽  
Secondary Metabolite Biosynthesis ◽  
Long Read ◽  
Gene Expression Levels

Senna occidentalis is an annual leguminous herb that is rich in anthraquinones, which have various pharmacological activities. However, little is known about the genetics of S. occidentalis, particularly its anthraquinone biosynthesis pathway. To broaden our understanding of the key genes and regulatory mechanisms involved in the anthraquinone biosynthesis pathway, we used short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) to perform a spatial and temporal transcriptomic analysis of S. occidentalis. This generated 121,592 RNA-Seq unigenes and 38,440 Iso-Seq unigenes. Comprehensive functional annotation and classification of these datasets using public databases identified unigene sequences related to major secondary metabolite biosynthesis pathways and critical transcription factor families (bHLH, WRKY, MYB, and bZIP). A tissue-specific differential expression analysis of S. occidentalis and measurement of the amount of anthraquinones revealed that anthraquinone accumulation was related to the gene expression levels in the different tissues. In addition, the amounts and types of anthraquinones produced differ between S. occidentalis and S. tora. In conclusion, these results provide a broader understanding of the anthraquinone metabolic pathway in S. occidentalis.

scholarly journals Investigating Resistance to Emamectin Benzoate in the Tomato Borer Tuta Absoluta

2021 ◽  
Author(s):  
Emmanouil Roditakis ◽  
Marianna Stavrakaki ◽  
Aris Ilias ◽  
Panagiotis Ioannidis ◽  
John Vontas
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Differential Expression Analysis ◽  
Tuta Absoluta ◽  
Emamectin Benzoate ◽  
Metabolic Resistance ◽  
Resistance Level ◽  
Specific Chemical ◽  
Potential Implication ◽  
Tomato Borer

Abstract The tomato borer Tuta absoluta is a major pest of tomato mainly controlled by chemical insecticides. However, development of resistance to specific chemical classes has made control of the pest extremely difficult. Emamectin benzoate belongs to the avermectin mode of action and to date, low or no resistance levels against this insecticide have been documented. Recently, reduced efficacy of emamectin benzoate was documented, in a field population from Crete (9-fold resistant ratio (RR)). Subsequent laboratory selections with emamectin benzoate for eight sequential generations, resulted in an increase of the RR to 60-fold, the highest resistance level reported to the particular insecticide. Hereby, we are presenting the characterization of emamectin benzoate resistance in T. absoluta. Sequencing of the GluCl and GABA receptor (rdl) genes, the molecular targets of emamectin benzoate, indicted absence of non-synonymous SNPs. The use of known enzyme inhibitors (PBO, DEF and DEM) revealed that P450s partially synergized emamectin benzoate resistance, suggesting potential implication of metabolic resistance. RNA-seq approach was used to identify differentially expressed genes, from emamectin benzoate resistant and susceptible T. absoluta populations. Twelve libraries were sequenced using the Illumina platform, which generated 81 Gbp, thus substantially increasing the number of publicly available genomic resources for this species. The de novo transcriptome assembly consisted of 549,601 contigs, grouped in 233,453 unigenes. Differential expression analysis and qPCR validation revealed over-expression of one unigene similar to cytochrome P450 (Clan 4) potentially implicated in emamectin benzoate resistance, supporting further the involvement of P450s in the observed resistance phenotype.

scholarly journals Integrative Transcriptome and Proteome Analysis Identifies Major Molecular Regulation Pathways Involved in Ramie (Boehmeria nivea (L.) Gaudich) under Nitrogen and Water Co-Limitation

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1267
Author(s):  
Jikang Chen ◽  
Gang Gao ◽  
Ping Chen ◽  
Kunmei Chen ◽  
Xiaofei Wang ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Proteome Analysis ◽  
Differentially Expressed ◽  
Poor Correlation ◽  
Factors Affecting ◽  
Protein Levels ◽  
Boehmeria Nivea ◽  
N Efficiency ◽  
New Information

Water and N are the most important factors affecting ramie (Boehmeria nivea (L.) Gaudich) growth. In this study, de novo transcriptome assembly and Tandem Mass Tags (TMT) based quantitative proteome analysis of ramie under nitrogen and water co-limitation conditions were performed, and exposed to treatments, including drought and N-deficit (WdNd), proper water but N-deficit (WNd), proper N but drought (WdN), and proper N and water (CK), respectively. A total of 64,848 unigenes (41.92% of total unigenes) were annotated in at least one database, including NCBI non-redundant protein sequences (Nr), Swiss-Prot, Protein family (Pfam), Gene Ontology (GO) and KEGG Orthology (KO), and 4268 protein groups were identified. Most significant changes in transcript levels happened under water-limited conditions, but most significant changes in protein level happened under water-limited conditions only with proper N. Poor correlation between differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) was observed in ramie responding to the treatments. DEG/DEP regulation patterns related to major metabolic processes responding to water and N deficiency were analyzed, including photosynthesis, ethylene responding, glycolysis, and nitrogen metabolism. Moreover, 41 DEGs and 61 DEPs involved in regulating adaptation of ramie under water and N stresses were provided in the study, including DEGs/DEPs related to UDP—glucuronosyhransferase (UGT), ATP synthase, and carbonate dehydratase. The strong dependency of N-response of ramie on water conditions at the gene and protein levels was highlighted. Advices for simultaneously improving water and N efficiency in ramie were also provided, especially in breeding N efficient varieties with drought resistance. This study provided extensive new information on the transcriptome, proteome, their correlation, and diversification in ramie responding to water and N co-limitation.

scholarly journals Physiological Characterization and Transcriptome Analysis of Camellia oleifera Abel. during Leaf Senescence

Forests ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 812
Author(s):  
Shiwen Yang ◽  
Kehao Liang ◽  
Aibin Wang ◽  
Ming Zhang ◽  
Jiangming Qiu ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Leaf Senescence ◽  
Transcriptome Analysis ◽  
Unsaturated Fatty Acids ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Economic Value ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Rna Seq

Camellia (C.) oleifera Abel. is an evergreen small arbor with high economic value for producing edible oil that is well known for its high level of unsaturated fatty acids. The yield formation of tea oil extracted from fruit originates from the leaves, so leaf senescence, the final stage of leaf development, is an important agronomic trait affecting the production and quality of tea oil. However, the physiological characteristics and molecular mechanism underlying leaf senescence of C. oleifera are poorly understood. In this study, we performed physiological observation and de novo transcriptome assembly for annual leaves and biennial leaves of C. oleifera. The physiological assays showed that the content of chlorophyll (Chl), soluble protein, and antioxidant enzymes including superoxide dismutase, peroxide dismutase, and catalase in senescing leaves decreased significantly, while the proline and malondialdehyde concentration increased. By analyzing RNA-Seq data, we identified 4645 significantly differentially expressed unigenes (DEGs) in biennial leaves with most associated with flavonoid and phenylpropanoid biosynthesis and phenylalanine metabolism pathways. Among these DEGs, 77 senescence-associated genes (SAGs) including NOL, ATAF1, MDAR, and SAG12 were classified to be related to Chl degradation, plant hormone, and oxidation pathways. The further analysis of the 77 SAGs based on the Spearman correlation algorithm showed that there was a significant expression correlation between these SAGs, suggesting the potential connections between SAGs in jointly regulating leaf senescence. A total of 162 differentially expressed transcription factors (TFs) identified during leaf senescence were mostly distributed in MYB (myeloblastosis), ERF (Ethylene-responsive factor), WRKY, and NAC (NAM, ATAF1/2 and CUCU2) families. In addition, qRT-PCR analysis of 19 putative SAGs were in accordance with the RNA-Seq data, further confirming the reliability and accuracy of the RNA-Seq. Collectively, we provide the first report of the transcriptome analysis of C. oleifera leaves of two kinds of age and a basis for understanding the molecular mechanism of leaf senescence.

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