Stemphylium lycopersici strain:CIDEFI 212
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ABSTRACT:
PROVIDER: PRJNA451500 | ENA |
REPOSITORIES: ENA
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Project description:Draft genome sequence with gene annotation of Stemphylium lycopersici, strain CIDEFI 213
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Project description:Stemphylium lucomagnoense Transcriptome based proteome
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Project description:BACKGROUND:Gray leaf spot is a devastating disease caused by Stemphylium lycopersici that threatens tomato-growing areas worldwide. Typically, many pathogenesis-related and unrelated secreted proteins can be predicted in genomes using bioinformatics and computer-based prediction algorithms, which help to elucidate the molecular mechanisms of pathogen-plant interactions. RESULTS:S. lycopersici-secreted proteins were predicted from 8997 proteins using a set of internet-based programs, including SignalP v4.1 TMHMM v2.0, big-PI Fungal Predictor, ProtComp V9.0 and TargetP v1.1. Analysis showed that 511 proteins are predicted to be secreted. These proteins vary from 51 to 600 residues in length, with signal peptides ranging from 14 to 30 residues in length. Functional analysis of differentially expressed proteins was performed using Blast2GO. Gene ontology analysis of 305 proteins classified them into 8 groups in biological process (BP), 6 groups in molecular function (MF), and 10 groups in cellular component (CC). Pathogen-host interaction (PHI) partners were predicted by performing BLASTp analysis of the predicted secreted proteins against the PHI database. In total, 159 secreted proteins in S. lycopersici might be involved in pathogenicity and virulence pathways. Scanning S. lycopersici-secreted proteins for the presence of carbohydrate-active enzyme (CAZyme)-coding gene homologs resulted in the prediction of 259 proteins. In addition, 12 of the 511 proteins predicted to be secreted are small cysteine-rich proteins (SCRPs). CONCLUSIONS:S. lycopersici secretory proteins have not yet been studied. The study of S. lycopersici genes predicted to encode secreted proteins is highly significant for research aimed at understanding the hypothesized roles of these proteins in host penetration, tissue necrosis, immune subversion and the identification of new targets for fungicides.
| S-EPMC6247510 | biostudies-literature
Project description:Stemphylium eturmiunum Transcriptome or Gene expression
| PRJNA414265 | ENA
Project description:miR-132 and miR-212 are structurally-related microRNAs that have been found to exert powerful modulatory effects within the central nervous system (CNS). Notably, these microRNAs are tandomly processed from the same non-coding transcript, and share a common seed sequence: thus it has been difficult to assess the distinct contribution of each microRNA to gene expression within the CNS. Here, we employed a combination of conditional knockout and transgenic mouse models to examine the contribution of the miR-132/212 gene locus to learning and memory, and then to assess the distinct effects that each microRNA has on hippocampal gene expression. Using a conditional deletion approach, we show that miR-132/212 double knockout mice exhibit significant cognitive deficits in spatial memory, recognition memory, and in tests of novel object recognition. Next, we utilized transgenic miR-132 and miR-212 overexpression mouse lines and the miR-132/212 double knockout line explore the distinct effects of these two miRNAs on the transcriptional profile of the hippocampus. Illumina sequencing revealed that miR-132/212 deletion increased the expression of 1,138 genes; Venn analysis showed that 96 of these genes were also downregulated in mice overexpressing miR-132. Of the 58 genes that were decreased in animals overexpressing miR-212, only four of them were also increased in the knockout line. Functional gene ontology analysis of downregulated genes revealed significant enrichment of genes related to synaptic transmission, neuronal proliferation, and morphogenesis, processes known for their roles in learning, and memory formation. These data, coupled with previous studies, firmly establish a role for the miR-132/212 gene locus as a key regulator of cognitive capacity. Further, although miR-132 and miR-212 share a seed sequence, these data indicate that these miRNAs do not exhibit strongly overlapping mRNA targeting profiles, thus indicating that, these two genes may function in a complex, non-redundant manner to shape the transcriptional profile of the CNS. The dysregulation of miR-132/212 expression could contribute to signaling mechanisms that are involved in an array of cognitive disorders
2016-03-01 | GSE73413 | GEO
Project description:Pyrenochaeta lycopersici overview
| PRJNA202944 | ENA