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Genome assembly of 12 Nigrospora species Assembly

ABSTRACT: To ascertain which genes were influenced in deletion mutants, we newly generated transcriptome data for deletion mutant vs control for each of three convergent genes (ΔNrURED, ΔNrGMF1, and ΔNrGLA) in N. rubi, respectively. After comparing the differentially expressed genes between all three mutants and controls, we found that 868 genes were identified as co-upregulated and 350 genes as co-downregulated (Figs. S7A and S7B). Gene Ontology (GO) enrichment analysis and KEGG pathway analysis revealed that these differentially expressed genes also are mainly involved in the secretory protein synthesis pathway, such as transmembrane transport, hydrolase activity, and protein processing within the endoplasmic reticulum (Figs. S7C and S7D). These results suggest that deletion of the convergent genes affected secretory protein synthesis, modification, and export.

ORGANISM(S): Nigrospora rubi

PROVIDER: GSE270150 | GEO | 2025/06/16

REPOSITORIES: GEO

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Project description:Thiele2005 - Genome-scale metabolic network of Helicobacter pylori (iIT341) This model is described in the article: Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. Thiele I, Vo TD, Price ND, Palsson BØ. J. Bacteriol. 2005 Aug; 187(16): 5818-5830 Abstract: Helicobacter pylori is a human gastric pathogen infecting almost half of the world population. Herein, we present an updated version of the metabolic reconstruction of H. pylori strain 26695 based on the revised genome annotation and new experimental data. This reconstruction, iIT341 GSM/GPR, represents a detailed review of the current literature about H. pylori as it integrates biochemical and genomic data in a comprehensive framework. In total, it accounts for 341 metabolic genes, 476 intracellular reactions, 78 exchange reactions, and 485 metabolites. Novel features of iIT341 GSM/GPR include (i) gene-protein-reaction associations, (ii) elementally and charge-balanced reactions, (iii) more accurate descriptions of isoprenoid and lipopolysaccharide metabolism, and (iv) quantitative assessments of the supporting data for each reaction. This metabolic reconstruction was used to carry out in silico deletion studies to identify essential and conditionally essential genes in H. pylori. A total of 128 essential and 75 conditionally essential metabolic genes were identified. Predicted growth phenotypes of single knockouts were validated using published experimental data. In addition, in silico double-deletion studies identified a total of 47 synthetic lethal mutants involving 67 different metabolic genes in rich medium. This model is hosted on BioModels Database and identified by: MODEL1507180007. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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Genome assembly of 12 Nigrospora species Assembly

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