De novo assembly, differential gene expression and pathway analyses for anthracnose resistance in chilli (Capsicum annuum L.)

2021 ◽  
Author(s):  
Rajesh Kumar ◽  
Ashutosh Rai ◽  
Avinash Chandra Rai ◽  
Vinay Kumar Singh ◽  
Major Singh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Capsicum Annuum ◽  
Differential Gene Expression ◽  
De Novo Assembly ◽  
De Novo ◽  
Anthracnose Resistance ◽  
Capsicum Annuum L ◽  
Differential Gene ◽  
Pathway Analyses

scholarly journals De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech

PLoS ONE ◽  
2017 ◽  
Vol 12 (9) ◽  
pp. e0184167 ◽  
Author(s):  
Markus Müller ◽  
Sarah Seifert ◽  
Torben Lübbe ◽  
Christoph Leuschner ◽  
Reiner Finkeldey
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
European Beech ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Differential Gene

scholarly journals Transcriptome Sequencing of Trichoderma Koningiopsis Strain Tk1 to Identify and Analyze Differential Gene Expression Patterns

2020 ◽  
Author(s):  
Mei Luo ◽  
Zhangyong Dong ◽  
Yongxin Shu ◽  
Mobing Chen
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Differential Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Antimicrobial Effect ◽  
Carbohydrate Active Enzymes ◽  
Differential Gene

Abstract Background: Trichoderma koningiopsis strain Tk1 shows good biocontrol potential. However, its biocontrol function may differ under different conditions. The objective of this study is to elucidate the biological and transcriptome differences of T. koningiopsis Tk1 under different media. Results: In this study, the mycelium weight and sporulation of T. koningiopsis Tk1 was found to differ in various media. Further, the Tk1 strain inhibited the growth of the pathogen Fusarium oxysporum in the three media tested. Fries3, PD, and PS were collected for RNA sequencing of Tk1 mycelia to identify the genes that are differentially expressed genes (DEGs) between Tk1 grown on different media. De novo transcriptome assembly resulted in identification of 14,208 unigenes. The differential gene expression pattern was more similar between the Fries3 and PS samples, whereas PD samples showed a different expression pattern. The DEGs were enriched in some metabolic and biosynthetic pathways. Additional analysis of the DEGs identified a set of carbohydrate-active enzymes that are upregulated or downregulated under different conditions.Conclusions: These results indicate that the Tk1 strain cultured in Fires3 and PS mediums can produce specific metabolic and carbohydrate-active enzymes to enhance their antimicrobial effect, providing a foundation for the subsequent mining of specific genes.

Bovine hepatic differential gene expression in response to perennial ryegrass staggers

2015 ◽  
Vol 8 (3) ◽  
pp. 351-360 ◽  
Author(s):  
L. Li ◽  
D.D. Tanaree ◽  
Y. Di ◽  
C.T. Estill ◽  
J.M. Duringer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Perennial Ryegrass ◽  
Extended Period ◽  
Double Blind Study ◽  
Double Blind ◽  
Oxidation Reduction ◽  
Differential Gene ◽  
Lolitrem B ◽  
Pathway Analyses

>‘Perennial ryegrass staggers’ is a neurological condition characterised by muscular tremors and ataxia in livestock that ingest the indole diterpene lolitrem B from endophyte-infected perennial ryegrass. While the neurotoxic mechanism of action of ryegrass staggers has been defined, little is known about metabolic and other molecular processes that lolitrem B may affect in livestock. The objective of this study was to characterise differential gene expression in the liver of animals fed lolitrem B-containing feed over an extended period of time. Eighteen steers were fed one of three rations (n=6/group) containing lolitrem B (247, 1,554 or 2,256 μg/kg (dry matter basis)) over 64 days in a double-blind study. Microarray and confirmatory qPCR were performed to evaluate the hepatic gene expression profile from biopsies taken on days 0 and 64. Widespread perturbation of gene expression was observed in all groups receiving lolitrem B, with a total of 152 differential genes identified (false discovery rate ≤0.05). This suggests that chronic exposure to lolitrem B, even at levels below the current threshold of toxicity (2,000 μg/kg lolitrem B), can perturb many genes, biological processes and pathways. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that many of these genes were categorised under lipid/steroid biosynthesis/metabolism and oxidation-reduction. Specifically, genes involved in the biosynthesis pathway of ceramide, a sphingolipid molecule (ACSS2, LASS6 and SCD) and changes in neurosignaling through alteration of nitric oxide synthase activity (ARG1 and GPX4) were up-regulated. Future work should focus on the overall balance between ceramide and its metabolites and antioxidants/oxidants in a variety of body matrices in animals with perennial ryegrass staggers, to determine how these compounds contribute to the overall etiology of this disease.

scholarly journals Differential Gene Expression Between Polymorphic Zooids of the Marine Bryozoan Bugulina stolonifera

2020 ◽  
Vol 10 (10) ◽  
pp. 3843-3857
Author(s):  
Kira A. Treibergs ◽  
Gonzalo Giribet
Keyword(s):  
Gene Expression ◽  
Division Of Labor ◽  
Differential Gene Expression ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Cdna Libraries ◽  
Living Species ◽  
Differential Gene

Bryozoans are a diverse phylum of marine and freshwater colonial invertebrates containing approximately 6,300 described living species. Bryozoans grow by budding new physiologically connected colony members (zooids) from a founding individual that forms from a metamorphosed larva. In some species these zooids come in different shapes and sizes and are specialized to serve different tasks within the colony. A complex interaction of genotype, environment, and developmental pathway shapes zooid fate, however, the specific mechanisms underlying the establishment of this division of labor remain unknown. Here, the first characterization of differential gene expression between polymorphic zooids of a bryozoan colony is presented. The development of different zooid types of lab-cultured Bugulina stolonifera colonies including feeding autozooids, avicularia (derived non-feeding zooids that are homologous to feeding autozooids but shaped like a bird’s beak), and rhizoids (a branching network of non-feeding anchoring zooids) was explored using RNA sequencing, de novo transcriptome assembly, and differential gene expression analyses. High throughput sequencing of cDNA libraries yielded an average of 14.9 ± 1.3 (SE) million high-quality paired-end reads per sample. Data for the first de novo transcriptome assemblies of B. stolonifera and the first characterization of genes involved in the formation and maintenance of zooid types within a bryozoan colony are presented. In a comparison between autozooid and avicularium tissues, 1,097 significant differentially expressed genes were uncovered. This work provides a much-needed foundation for understanding the mechanisms involved in the development of polymorphic zooids and the establishment of division of labor in bryozoans.

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