Genome-wide identification of Argonautes in Solanaceae with emphasis on potato
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ABSTRACT:
PROVIDER: PRJNA667351 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Regulatory small RNAs (sRNAs) play important roles in many fundamental processes in plant biology such as development, fertilization and stress responses. The AGO protein family has here a central importance in gene regulation based on their capacity to associate with sRNAs followed by mRNA targeting in a sequence-complementary manner. The present study explored Argonautes (AGOs) in the Solanaceae family, with emphasis on potato, Solanum tuberosum (St). A genome-wide monitoring was performed to provide a deeper insight into gene families, genomic localization, gene structure and expression profile against the potato late blight pathogen Phytophthora infestans. Among 15 species in the Solanaceae family we found a variation from ten AGOs in Nicotiana obtusifolia to 17 in N. tabacum. Comprehensive analyses of AGO phylogeny revealed duplication of AGO1, AGO10 and AGO4 paralogs during early radiation of Solanaceae. Fourteen AGOs were identified in potato. Orthologs of AGO8 and AGO9 were missing in the potato genome. However, AGO15 earlier annotated in tomato was identified. StAGO15 differs from the other paralogs having residues of different physico-chemical properties at functionally important amino acid positions. Upon pathogen challenge StAGO15 was significantly activated and hence may play a prominent role in sRNA-based regulation of potato defense.
2020-12-01 | GSE159015 | GEO
Project description:Six different Solanaceae species, Potato (Solanum tubersosum), Tomato (Lycopersicum esculentum), Pepper (Capsicum annuum), Tobacco (Nicotiana tabaccum), Petunia and Nicotiana benthiamana were grown at 25C, 16h light and 8h darkness. Mature leaves were harvested after 4-6 weeks. RNA was isolated using Qiagen RNeasy. Tomato, pepper, petunia, tobacco and N. benthamiana samples were hybridized against potato samples. Keywords: Solanaceae comparative gene expression profiling
2005-10-03 | GSE3380 | GEO
Project description:Six different Solanaceae species, Potato (Solanum tuberosum), Tomato (Lycopersicum esculentum), Pepper (Capsicum annuum), Tobacco (Nicotiana tabacum), Petunia and Nicotiana benthamiana were grown at 25C, 16h light and 8h darkness. Mature leaves were harvested after 4-6 weeks. RNA was isolated using Qiagen RNeasy. Tomato, pepper, petunia tobacco and N. benthamiana samples were hybridized against potato samples. Keywords: Direct comaprison
2007-09-01 | GSE8234 | GEO
Project description:Background: MicroRNAs (miRNAs) play roles in various biological processes including growth, development, and defense in plants. Recent studies revealed that some plant miRNAs could produce secondary small interfering RNAs (siRNAs) such as phased, secondary siRNAs (phasiRNAs) and they regulate cascade of gene expression. Results: We performed genome-wide comparative analysis of miRNAs and their targets in Solanaceae plants in an evolutionary perspective. miRNAs were mapped onto 12 chromosomes and microsynteny analysis, based on miRNAs and their flanking genes, revealed about 86% of conserved miRNAs in pepper maintained synteny with those of tomato or potato. Degradome analysis revealed that many of genes related to transcription or defense response are regulated by miRNAs in Solanaceae plants. We found several miRNAs in pepper targeting a number of genes encoding nucleotide-binding and leucine rich repeat (NLR) or receptor-like protein (RLP), known as major players in defense responses. In addition, resistance-related miRNAs trigger phasiRNA production indicating amplification of regulation of the disease-resistant gene families. Among them, specifically evolved miRNAs in pepper, can-miR-n033a and can-miR-n026, targets many NLRs and RLPs in an expanded subgroup in pepper, respectively. Conclusions: Taken together, miRNAs might be generated and evolved to regulate diverse genes involved in plant immunity in Solanaceae. This study provides an insight into possible co-evolution between resistance-related miRNAs and defense genes in pepper.
2018-07-18 | GSE102781 | GEO
Project description: Not available
| S-EPMC7689493 | biostudies-literature
Project description:Seven different Solanaceae species, Potato (Solanum tubersosum), Tomato (Solanum lycopersicum), Eggplant (Solanum melangena), Pepper (Capsicum annuum), Tobacco (Nicotiana tabaccum), Petunia and Nicotiana benthiamana were subjected to salt stress. The stress applied was 150mM NaCl and control plants were watered without the additional salt. Samples were collected at 0, 6, 12, 24, 48 and 96 hours after the first application of the salt. RNA was isolated using Qiagen RNeasy. Keywords: Direct comparison
2008-02-13 | GSE8158 | GEO
Project description:Seven different Solanaceae species, Potato (Solanum tubersosum), Tomato (Solanum lycopersicum), Eggplant (Solanum melongena), Pepper (Capsicum annuum), Tobacco (Nicotiana tabaccum), Petunia and Nicotiana benthiamana were subjected to drought stress. Drought stress was applied by stopping watering of the plants, control plants were normally watered with nutrient solution. Samples were collected at 0, 1, 3, 5, 7 and 10 days after the first application of the drought stress. RNA was isolated using Qiagen RNeasy. Keywords: Direct comparison
2007-09-01 | GSE8161 | GEO
Project description:Seven different Solanaceae species, Potato (Solanum tubersosum), Tomato (Lycopersicum esculentum), Eggplant (Solanum melangena), Pepper (Capsicum annuum), Tobacco (Nicotiana tabacum), Petunia and Nicotiana benthamiana were subjected to cold stress. Plants were grown at 25 C for 4-6 weeks after wich cold stress was initiated by exposing the plants to 4 C for 4, 8, 12, 24 and 48 hours. Control samples were isolated from plants just before the cold stress was initated. RNA was isolated using Qiagen RNeasy. Keywords: Direct comparison
2007-09-01 | GSE8203 | GEO
Project description:Seven different Solanaceae species, Potato (Solanum tuberosum), Tomato (Solanum lycopersicum), Eggplant (Solanum melongena), Pepper (Capsicum annuum), Tobacco (Nicotiana tabacum), Petunia and Nicotiana benthamiana were subjected to heat stress. Plants were grown for 4-6 weeks at 25 C after which heat stress was initiated by exposing the plants to 35 C for 6, 12, 24, 48 and 96 hours. Control samples were isolated from plants just before initiating the heat stress. RNA was isolated using Qiagen RNeasy. Keywords: Direct comparison
2007-09-01 | GSE8202 | GEO