Metagenomic survey of pre-harvest agricultural water using long read sequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA751542 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15359750_1.fastq.gz | Fastqsanger.gz | |||
| SRR15359751_1.fastq.gz | Fastqsanger.gz | |||
| SRR15359752_1.fastq.gz | Fastqsanger.gz | |||
| SRR15359753_1.fastq.gz | Fastqsanger.gz | |||
| SRR15359754_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 7 |
Similar Datasets
Project description:Transcriptional profiling comparing control berries (sampled at Traditional harvest, TH) with berries sampled after the application of different post-harvest techniques (late-harvest LH; double reasoned maturation-A, DMR-A; double reasoned maturation-B, DMR-B)
2013-09-01 | GSE43385 | GEO
Project description:The spread of antibiotic resistance genes (ARG) into agricultural soils, products, and foods severely limits the use of organic fertilizers in agriculture. In this study, experimental land plots were fertilized, sown, and harvested for two consecutive agricultural cycles using either mineral or three types of organic fertilizers: sewage sludge, pig slurry, or composted organic fraction of municipal solid waste. The analysis of the relative abundances of more than 200,000 ASV (Amplicon Sequence Variants) allowed the identification of a small, but significant (<10%) overlap between soil and fertilizer microbiomes, particularly in soils sampled the same day of the harvest (post-harvest soils). Loads of clinically relevant ARG were significantly higher (up to 100 fold) in fertilized soils relative to the initial soil. The highest increases corresponded to post-harvest soils treated with organic fertilizers, and they correlated with the extend of the contribution of fertilizers to the soil microbiome. Edible products (lettuce and radish) showed low, but measurable loads of ARG (sul1 for lettuces and radish, tetM for lettuces). These loads were minimal in mineral fertilized soils, and strongly dependent on the type of fertilizer. We concluded that at least part of the observed increase on ARG loads in soils and foodstuffs were actual contributions from the fertilizer microbiomes. Thus, we propose that adequate waste management and good pharmacological and veterinarian practices may significantly reduce the potential health risk posed by the presence of ARG in agricultural soils and plant products.
2021-07-09 | GSE179685 | GEO
Project description:Hot Spring metagenomic survey Raw sequence reads
| PRJNA698245 | ENA
Project description:Transcriptional profiling comparing control berries (sampled at Traditional harvest, TH) with berries sampled after the application of different post-harvest techniques (late-harvest LH; double reasoned maturation-A, DMR-A; double reasoned maturation-B, DMR-B) Comparison of Grape berries subjected to three different post-harvest techniques (LH, DMR-A, DMR-B) versus Grape berries sampled at traditional harvest (TH). Comparisons were as follows: LH berries versus TH berries (2 biological replicates), DMR-A berries versus TH berries (2 biological replicates, only one dye-swapped), DMR-B berries versus TH berries (2 biological replicates, only one dye-swapped).
2013-09-01 | E-GEOD-43385 | biostudies-arrayexpress
Project description:Resistance to agricultural fungicides in the field has created a need for discovering fungicides with new modes of action. DNA microarrays, because they provide information on expression of many genes simultaneously, could help to identify the modes of action. To begin an expression pattern database for agricultural fungicides, transcriptional patterns of Saccharomyces cerevisiae strain S288C genes were analysed following 2-h treatments with I50 concentrations of ergosterol biosynthesis inhibitors commonly used against plant pathogenic fungi. Eight fungicides, representing three classes of ergosterol biosynthesis inhibitors, were tested. To compare gene expression in response to a fungicide with a completely different mode of action, a putative methionine biosynthesis inhibitor (MBI) was also tested. Expression patterns of ergosterol biosynthetic genes supported the roles of Class I and Class II inhibitors in affecting ergosterol biosynthesis, confirmed that the putative MBI did not affect ergosterol biosynthesis, and strongly suggested that in yeast, the Class III inhibitor did not affect ergosterol biosynthesis. The MBI affected transcription of three genes involved in methionine metabolism, whereas there were essentially no effects of ergosterol synthesis inhibitors on methionine metabolism genes. There were no consistent patterns in other up- or downregulated genes between fungicides. These results suggest that inspection of gene response patterns within a given pathway may serve as a useful first step in identifying possible modes of action of fungicides. agricultural sterol biosynthesis inhibitor fungicides. Keywords = agriculture Keywords = ergosterol Keywords = methionine Keywords = fungicide Keywords = Saccharomyces cerevisiae S288C Keywords = biosynthesis
2005-05-01 | GSE2412 | GEO
Project description:In this study, we used RNA-seq to obtain and compare transcriptomic profiles of a resistant genotype J11 in pre-harvest seeds, with A. flavus inoculation at the whole-genome level. The TMT method was also implemented to help further understand the molecular mechanism of peanut resistance to A. flavus invasion at proteome level. Meanwhile, we conducted a thorough research on a chitinase and a NBS-LRR gene, which were found in our data. This study is our first step towards a comprehensive genome-scale platform for developing Aspergillus resistant peanut cultivars through genetic engineering.
2020-08-17 | GSE102782 | GEO
Project description: Not available
| S-EPMC6198144 | biostudies-literature
Project description:Comparative transcriptome profiling in winter wheat grown under different agricultural practices
2012-11-30 | E-MTAB-903 | biostudies-arrayexpress
Project description:Resistance to agricultural fungicides in the field has created a need for discovering fungicides with new modes of action. DNA microarrays, because they provide information on expression of many genes simultaneously, could help to identify the modes of action. To begin an expression pattern database for agricultural fungicides, transcriptional patterns of Saccharomyces cerevisiae strain S288C genes were analysed following 2-h treatments with I50 concentrations of ergosterol biosynthesis inhibitors commonly used against plant pathogenic fungi. Eight fungicides, representing three classes of ergosterol biosynthesis inhibitors, were tested. To compare gene expression in response to a fungicide with a completely different mode of action, a putative methionine biosynthesis inhibitor (MBI) was also tested. Expression patterns of ergosterol biosynthetic genes supported the roles of Class I and Class II inhibitors in affecting ergosterol biosynthesis, confirmed that the putative MBI did not affect ergosterol biosynthesis, and strongly suggested that in yeast, the Class III inhibitor did not affect ergosterol biosynthesis. The MBI affected transcription of three genes involved in methionine metabolism, whereas there were essentially no effects of ergosterol synthesis inhibitors on methionine metabolism genes. There were no consistent patterns in other up- or downregulated genes between fungicides. These results suggest that inspection of gene response patterns within a given pathway may serve as a useful first step in identifying possible modes of action of fungicides. agricultural sterol biosynthesis inhibitor fungicides. Keywords = agriculture Keywords = ergosterol Keywords = methionine Keywords = fungicide Keywords = Saccharomyces cerevisiae S288C Keywords = biosynthesis
2010-06-10 | E-GEOD-2412 | biostudies-arrayexpress