NGS of sRNA reads in plants
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ABSTRACT:
PROVIDER: PRJNA559551 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Previous works had found correlation between the association of small RNAs (sRNAs) to Potyvirus HCPro variants in infected plants, and their abilities to suppress silencing. Moreover, we had shown a preference by HCPro for sRNAs of 21-22 nt with 5´-end adenines, and of viral sequence. Conformational properties can explain preferences for sRNAs by size and/or 5´-ends, but preference for sRNAs of viral over plant sequence would require their having different accessibilities to the suppressor, or chemical properties. To investigate this, we expressed suppressor-competent and –deficient HCPro variants by agro-infiltration or from potex- and potyviral vectors and characterized the sRNAs in infiltrated tissues and associated to the purified proteins. In input infiltrated or virus-infected tissues, methylation levels in selected sRNAs of either T-DNA or plant sequence were assessed, and the former were found significantly less methylated in the presence of suppression-competent HCPro. In purified preparations of suppression-competent HCPro, sRNAs of non-plant sequence of 21 ntwere selectively enriched in those having 5´-end adenines. Our data indicate that the ratio of sRNAs of plant vs. non-plant sequence associated to HCPro is influenced by the context in its expression, and suggest that also by a concurrent interference by HCPro on the methylation of newly generated sRNAs of non-plant sequence.
2020-12-31 | GSE135651 | GEO
Project description:Potato yellow vein virus (PYVV) was detected by RT-PCR in potatoes grown in the Central Colombian highlands, north of Bogotá (~3000 mt height). At this altitude viral whitefly vectors are largely absent, but infection persists because of the use of uncertified tubers. Plants with typical PYVV-induced yellowing symptoms, as well as with atypical yellowing or non-symptomatic were sampled at three separate geographical locations. And five of them were subjected to Next Generation Sequencing (NGS) of their small RNA (sRNA) populations. Contigs to any virus were assembled, and complete or almost complete sequences of four PYVV isolates were thus re-constructed, all from symptomatic plants. Three viral isolates infected plants singly, while the fourth one co-infected the plant together with a potyvirus (potato virus Y, PVY). Relative proportions of sRNAs to each of the three viral genomic RNAs were assessed and found to remain comparable between the four infections. Genomic regions were identified as hotspots to sRNA formation, or as regions that induced poorly sRNAs. Furthermore, PYVV titers in the mixed vs. the single infections were found to be remained comparable, indicating absence of synergistic/antagonistic effect of the potyvirus on the accumulation of PYVV.
2021-03-03 | GSE157752 | GEO
Project description:sRNA-seq datasets of OsRDR3 transgenic plants.
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Project description:In order to analyze the production of small RNA (sRNA) by Potato spindle tuber viroid- RG1 strain (PSTVd-RG1) upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the PSTVd-RG1. After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina MiSeq platform. The primers were trimmed and the 21- to 24-nt long small RNA species were filtered after quality check of the raw data.
2017-09-20 | GSE70166 | GEO
Project description:In order to analyze the production of small RNA (sRNA) by Potato spindle tuber viroid-intermediate strain (PSTVd-I) upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the PSTVd-I. After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina MiSeq platform. The primers were trimmed and the 21- to 24-nt long small RNA species were filtered after quality check of the raw data.
2017-09-20 | GSE70096 | GEO
Project description:NGS of small RNA reads in sampled potato plants from the highlands of Colombia
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Project description:In order to identify microRNAs involved in response to nitrogen excess stress we performed deep sequencing of sRNA libraries constructed form RNA isolated from roots and shoots of two week old barley plants that have been grown under nitrogen excess stress and control conditions.
2022-02-24 | GSE145799 | GEO
Project description:We sequenced mRNA and small RNA (sRNA) profiles in the interaction between Brachypodium distachyon (Bd) and Serendipita indica (Si; syn. Piriformospora indica), at four (4) days post inoculation (DPI). sRNA sequencing reads of Si-colonized and non-colonized roots, as well as axenic fungal cultures were generated. Three biological samples of each were sequenced, with two technical replicates per sample (SE). Raw reads from sRNA sequencing were submitted to technical adapter trimming (Cutadapt) before upload.
2021-07-15 | E-MTAB-10650 | biostudies-arrayexpress
Project description:In order to increase our understanding on the epigenetic regulation in response to abiotic stresses in plants, sRNA regulation in sugarcane plants submitted to drought stress was analyzed. Deep sequencing analysis was carried out to identify the sRNA regulated in leaves and roots of sugarcane cultivars with different drought sensitivities. An enrichment of 22-nt sRNA species was observed in leaf libraries. The pool of sRNA selected allowed the analysis of different sRNA classes (miRNA and siRNA). Twenty eight and 36 families of conserved miRNA were identified in leaf and root libraries, respectively. Dynamic regulation of miRNA was observed and the expression profile of eight miRNA was verified in leaf samples by stem-loop qRT-PCR assay. Altered miRNA regulation was correlated with changes in mRNA levels of specific targets. 22-nt miRNA triggered siRNA-candidates production by cleavage of their targets in response to drought stress. Some genes of sRNA biogenesis were down-regulated in tolerant genotypes and up-regulated in sensitive in response to drought stress. Our analysis contributes to increase the knowledge on the roles of sRNA in epigenetic-regulatory pathways in sugarcane submitted to drought stress.
2012-11-24 | GSE42483 | GEO
Project description:We describe a series of computational pipelines for the in silico analysis of small RNAs (sRNA) produced in response to viral infections in plants. Our workflow is primarily focused on the analysis of sRNA populations derived from known or previously undescribed viruses infecting host plants. Furthermore, we provide an additional pipeline to examine host-specific endogenous sRNAs activated or specifically expressed during viral infections in plants. We present some key points for a successful and cost-efficient processing of next generation sequencing sRNA libraries, from purification of high quality RNA to guidance for library preparation and sequencing strategies. We report a series of free available tools and programs as well as in-house Perl scripts to perform in-house sRNA-seq data mining. A multi-step analysis pipeline is extensively detailed so previous bioinformatic background is not required, but experience with basic Unix commands is desirable.
2017-10-12 | GSE104799 | GEO