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778 results for “TOMATO”
A tomato fruit RNA extraction method that isolates mRNAs encoding secreted and endomembrane associated proteins
GEO Series GSE17222. Solanum lycopersicum. 3 samples. Type: Expression profiling by array.
Identification of JA/COI1-regulated genes in tomato reproductive tissue and JA-treated roots.
GEO Series GSE8284. Solanum tuberosum; Solanum lycopersicum. 26 samples. Type: Expression profiling by array.
BSc project data repository, In silico analysis of microRNA regulation of tomato trichome-based specialized metabolism
<p>Data repository of the bachelor project of Sjors Huizinga (April - June, 2020).</p> <p>The following files are present:</p> <p>README.txt</p> <p>NDA_SjorsHuizinga.pdf<br> Contains the non-disclosure agreement signed before the start of the project.</p> <p>Scripts_Github_Repository.txt<br> Contains the URL of the github repostory in which all custom scripts created<br> and used during the project are stored.</p> <p>The following subfolders are present:</p> <p>ProjectPlan<br> Contains the research proposal.</p> <p>RawData<br> Contains raw data that is considered read-only; degradome data, metabolite<br> data, miRNA data, and trichome count data.</p> <p>Results<br> Contains figures, tables, and data generated during the project; annotation<br> target prediction, degradome analysis, etc.</p>
Small RNA-seq data from leaf, stem trichomes, bald stems and leaf primordiums from different tomato genetic backgrounds
<p><strong>Description</strong></p> <p>Various tissues of cultivated and wild tomato genotypes were harvested.</p> <p>Trichomes are stem trichomes (isolated from the stem of tomatoes).</p> <p><strong>RNA isolation</strong></p> <p>To isolate RNA, plant tissues were flash frozen in liquid nitrogen immediately after harvesting and stored at −80°C prior to RNA extraction. Frozen pellets were grounded by using a mortar and pestle before immersion in QIAzol Lysis Reagent (Qiagen). RNA was isolated and purified into two separate fractions (>200 nt and <200 nt) using the miRNeasy Mini kit (Qiagen). For the >200 nt RNA an on-column treatment was included using the RNase-free DNase set (Qiagen).</p> <p><strong>Small RNA-Seq</strong></p> <p>Small RNA-Seq libraries were generated from the <200 nt RNA fraction according to the manufacturers’ protocols using the Small RNA-Seq Library Prep Kit (Lexogen). The size distribution of the libraries with indexed adapters was assessed using a 2200 TapeStation System with Agilent D1000 ScreenTapes (Agilent Technologies). The libraries were quantified on a QuantStudio 3 Real-Time PCR System (Thermo Fisher Scientific) using the NEBNext Library Quant Kit for Illumina (New England BioLabs) according to the instructions of the manufacturer. The libraries were clustered and sequenced (75 bp) on a NextSeq 550 Sequencing System (Illumina) using a NextSeq 500/550 High Output Kit v2.5 (75 Cycles) (Illumina).</p> <p> </p> <p><strong>The list of samples</strong> is available in the <a href="https://zenodo.org/api/files/195143fa-2210-4b7f-bfe2-a649e124b7b0/sample_list.csv">sample_list.csv</a> file.</p> <ul> <li>Myc-1 stands for a knock-out mutant of the MYC1 gene (Solyc08g005050). The line full name is MS5-4.</li> <li>Pik is an introgression line containing a fragment of chromosome 1 from <em>S. habrochaites</em> PI127826 into a MicroTom genetic background. </li> </ul> <p> </p> <p><strong>Pooled samples</strong></p> <p>Some samples corresponding to the same tomato genotype and tissue were pooled altogether and are also available in fastq format.</p> <pre><code class="language-markdown">| species | genotype | pool_of | tissue | file | reads | |--------------|------------|---------------|----------------|----------|----------| | habrochaites | PI127826 | S01, S02, S03 | trichomes | PI127826.fastq.gz | 16,539,495 | | lycopersicum | Moneymaker | S04, S05, S06 | trichomes | Moneymaker.fastq.gz | 11,539,748 | | habrochaites | LYC4 | S07, S08, S25 | trichomes | LYC4.fastq.gz | 15,980,718 | | lycopersicum | LA4024 | S10, S11, S12 | trichomes | LA4024.fastq.gz | 13,888,953 | | habrochaites | LA1777 | S13, S14, S15 | trichomes | LA1777.fastq.gz | 14,136,265 | | pennellii | LA0716 | S19, S20, S21 | trichomes | LA0716.fastq.gz | 14,045,182 |</code></pre> <p> </p>
Messenger RNA-seq data from leaves, stem trichomes, bald stems and leaf primordia from different tomato genetic backgrounds
<p><strong>RNA isolation</strong></p> <p>To isolate RNA, plant tissues were flash frozen in liquid nitrogen immediately after harvesting and stored at −80°C prior to RNA extraction. Frozen pellets were grounded by using a mortar and pestle before immersion in QIAzol Lysis Reagent (Qiagen). RNA was isolated and purified into two separate fractions (>200 nt and <200 nt) using the miRNeasy Mini kit (Qiagen). For the >200 nt RNA an on-column treatment was included using the RNase-free DNase set (Qiagen).</p> <p><strong>mRNA sequencing protocol</strong></p> <p>A poly-A enrichment was performed on the >200 nt RNA fraction using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). RNA-Seq libraries were generated according to the manufacturers’ protocols using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (Unique Dual Index Primer Pairs) (New England BioLabs). The size distribution of the libraries with indexed adapters was assessed using a 2200 TapeStation System with Agilent D1000 ScreenTapes (Agilent Technologies). The libraries were quantified on a QuantStudio 3 Real-Time PCR System (Thermo Fisher Scientific) using the NEBNext Library Quant Kit for Illumina (New England BioLabs) according to the instructions of the manufacturer. The libraries were clustered and sequenced (75 bp) on a NextSeq 550 Sequencing System (Illumina) using a NextSeq 500/550 High Output Kit v2.5 (75 Cycles) (Illumina).</p> <p><strong>List of samples is available in the <a href="https://zenodo.org/api/files/168d9731-fc3e-4baa-8053-1656862769ee/mrna_sample_list.csv?versionId=de4bd2de-7ddc-4d03-9ac6-545f98896874">mrna_sample_list.csv</a> file.</strong></p> <ul> <li>Myc-1 stands for a knock-out mutant of the MYC1 gene (Solyc08g005050). The line full name is MS5-4.</li> </ul> <p> </p> <p><strong>Processed data</strong></p> <ul> <li><strong>Samples S28 to S48 </strong> <ul> <li>Provenance: run from the snakemake_rnaseq pipeline v0.3.1 available from <a href="https://github.com/BleekerLab/snakemake_rnaseq/releases/tag/v0.3.1">GitHub</a> and <a href="http:// https://zenodo.org/record/4034215">Zenodo</a>:</li> <li><strong>Scaled counts:</strong> `S28_to_S48_scaled_counts.tsv<strong>`. </strong>A file with DESeq2 normalised counts wiith tab-separated values. Useful for visualisations (heatmaps, PCA) <em>NOT</em> for differential expression analysis. </li> <li><strong>Raw counts:</strong> `S28_to_S48_raw_counts.tsv<strong>`. </strong>A file with the raw counts that can be used for differential expression analysis with DESeq2. </li> </ul> </li> </ul> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Small RNA-seq and messenger RNA-seq of F1 cross between different species of tomato (lycopersicum, habrochaites)
<p>Small RNA and messenger RNA data from stem trichomes of various crosses (S. lycopersicum x S. habrochaites or S. habrochaites with itself). </p> <p>There are now also R2 reads for the samples. Reason for this is that the Mid Output flow cell doesn’t have the 1x75 option.</p> <p>The sample list is available in F1_samples.csv</p>
Atlas of phenotypic, genotypic and geographical diversity present in the European traditional tomato: Datasets 6 and 7
<p><a href="#_Toc87944988">Dataset 6. Complete set of imputed SNPs located on chromosomes and accessions.</a></p> <p><a href="#_Toc87944989">Dataset 7. Complete set of SNPs located on chromosomes and accessions that have passed all filters.</a></p>
Solanum section Lycopersicon (cultivated and wild tomato genotypes) trichome pictures
<p><strong>Stem trichome pictures of various genotypes from the <em>Solanum</em> section Lycopersicon:</strong></p> <pre><code class="language-markdown">| accession | species | accession nr | synonym | origin | |------------|--------------------------------|--------------|---------|-------------| | LA2172 | S. arcanum | TR0009 | - | Peru | | LA1401 | S. cheesmaniae f. minor | EA00652 | - | Ecuador | | LA1840 | S. chmielewskii | - | - | unknown | | LA2695 | S. chmielewskii | EA00759 | - | Peru | | LA0407 | S. habrochaites f. glabratum | EA00558 | - | Ecuador | | LA1777 | S. habrochaites f. hirsutum | EA00703 | - | Peru | | PI134418 | S. habrochaites f. glabratum | TR00015 | LYC38 | unknown | | LYC4 | S. habrochaites f. hirsutum | TR00017 | - | unknown | | LA1718 | S. habrochaites f. glabratum | EA00699 | LYC4934 | Peru | | PI127826 | S. habrochaites f. hirsutum | - | - | Peru | | LA1364 | S. huaylasense | TR00030 | - | Peru | | Moneymaker | S. lycopersicum | - | C32 | Netherlands | | LA4024 | S. lycopersicum | TA209 | - | unknown | | LA2133 | S. neorickii/L. parviflorum | EA00729 | - | Peru | | LA0735 | S. neorickii | TR00025 | LYC140 | unknown | | LA0716 | S. pennellii | EA00585 | - | Peru | | LA1278 | S. peruvianum/pimpinellifolium | TR00005 | - | unknown | | LA1954 | S. peruvianum | EA00713 | - | Peru | | LA1578 | S. pimpinellifolium | EA00674 | - | Peru |</code></pre> <p><strong>Pictures were taken in March 2018 following this two-step protocol:</strong></p> <pre><code class="language-markdown"># Making high-quality pictures of tomato trichomes This protocol is to take high-quality pictures of trichomes and stack them into one unique final picture. The stem from the 4th leaf from the top will be used to make a picture. This protocol is composed of two parts: - Firstly: take a series of pictures (15 to 30 pictures) using a stereomicroscope - Secondly: photo stacking using Photoshop # First part: taking pictures using the Leica MZFLII 1. Turn on the microscope zoom mechanism 2. Turn on the ebq 100 lamp and the Olympus Highlight 2000 lamp 3. Make sure no filter (e.g. dsRed) is applied 4. Open the Nikon NIS-Elements program. 5. Take a piece of stem and place it horizontally (---) under the microscope. . 6. Zoom out completely. 7. Zoom in at 10,000x on the side of the branch ("labeled 10.0 on the microscope). 8. Focus on a few trichomes. Get them as much as possible in focus. This is going to be your first picture (foreground). 9. Zoom in about a few trichome layers away. There should not be too much overlap between the different trichomes (otherwise they get merged together during the stacking phase). This will be your background. 10. Zoom out to go back to the foreground (= your first picture). 11. Depending on the number of trichomes in-between your foreground and background, you need to take a variable number of pictures. - If trichome density is high, then trichomes will overlap during the stacking meaning that you need to take more pictures (~30) and reduce the distance between your foreground and background. - If trichome density is low, then trichomes won't overlap and you need less pictures (~10) # Second part: alignment of pictures using Photoshop See the trichome layer photography protocol (PDF file)made by Maurice Heilijgers (August 2018).</code></pre> <p> </p>
A NOVEL AND INTEGRATED APPROACH TO INCREASE MULTIPLE AND COMBINED STRESS TOLERANCE IN PLANTS USING TOMATO AS A MODEL
<p>This will be a screening experiment aiming a first evaluation of the five PGPR that have been isolated in AUA, Laboratory go General & Agricultural Microbiology in a previous research project. To minimize interference of the treatments with soil fertility and soil heterogeneity, this first experiment will be conducted in a soilless cultivation system</p>
Use of alfalfa pellets as an alternative greenhouse tomato fertilization method
<p>A tomato experiment was established on February 20th 2019 and was terminated in July 25th 2019. In this experiment the commercial tomato hybrid ‘Nissos F1’ grafted onto the commercial rootstock ‘Maxifort F1’ was planted, at a density of 2.13 plants m-2.<br> In treatment 1, which was considered as control, no other source of N was applied except for farmyard manure (FYM) at a rate of 170 kg ha-1 which had been incorporated to the soil on August 7th, 2018 before the establishment of the preceding tomato crop (GE1E3). In treatments 2 and 3, alfalfa pellets (2.72 % N, 10% moisture) were applied at a rate of 330 g m-2 and 660 g m-2 respectively. Finally, in treatment 4, faba bean grown outside the greenhouse was applied as a natural organic fertilizer contributing biologically-fixed N, at a rate of 4 kg m-2 fresh biomass.</p>
Strigolactones influence on tomato water use efficiency under drought
<p>The present work aims to analyse the influence of strigolactones on yield and agronomic WUE under drought. In order to investigate this issue, these parameters are being evaluated under well-watered and drought stress conditions, in self-grafted wild-type (M82) and strigolactone-depleted tomato plants (CCD7-silenced). Additionally, hetero-grafted plants (wild-type scions on strigolactone-depleted rootstocks, which leads to higher strigolactones in leaves) and self-grafted, strigolactone-treated wild-type plants are used to investigate the potentially positive effects of a moderate excess of hormone in the shoot on agronomic WUE and yield.</p>
Impact of green manure and intercropping in organic greenhouse tomato
<p>Test the impact of green manure and intercropping with legumes inoculated or non-inoculated with rhizobia and endophytic bacteria on nitrogen, phosphorus and potassium nutrition in organic greenhouse tomato.<br> The first experiment (GE1E1) started on May 23rd 2017 and was terminated on January 19th 2018; the second experiment (GE1E2) started on February 8th and was terminated on June 11th 2018; the third experiment (GE1E3) started on June 12th 2018 and was terminated on January 30th 2019. In 1st experiment (GE1E1), self-rooted plants of the commercial tomato hybrid ‘Elpida F1’ were cultivated, while in 2nd and 3nd experiment (GE1E2 and GE1E3, respectively), the commercial tomato hybrids ‘Ekstasis F1’ and ‘Elpida F1’, respectively, grafted onto the commercial rootstock ‘Maxifort F1’ were cultivated. The plant density was 2.13 plants/m2 in all experiments of GE1.<br> In GE1E1 and GE1E3 (tomato crops established in August and terminated in January), summer-grown cowpea was applied as green manure before establishment of the tomato crop, in order to be tested as a source of nitrogen in addition to farmyard manure (FYM). The treatments were identical in both GE1E1 and GE1E3. More specifically, in treatment 1 (CON), which was considered as control, no other source of N was applied except for FYM. In treatments 2 (GM-C), 3 (GM-C+BV) and 4 (GM-C+BV+EB), additional N was provided through green manure, by sowing cowpea (<em>Vigna unguiculata </em>(L) Walp.) and incorporating the plants at anthesis into the soil, shortly before planting the tomato crop. However, in GM-C the seeds of cowpea were not inoculated with any rhizobia, while in GM-C+BV the cowpea seeds were inoculated with<em> Bradyrhizobium sp</em>. VULI11 (BV) (Tampakaki et al. 2017), and in GM-C+BV+EB the seeds of cowpea were inoculated with a mix of BV and endophytic bacteria.</p>
Comparison of compost or green manure with farmyard manure for fertilizing organic greenhouse tomato
<p>The 2nd group of experiments (GE2) included two successive tomato experiments. The first experiment (GE2E1) started on May 23rd 2017 and was terminated on January 19th 2018; the second experiment (GE2E2) started on February 8th and was terminated in on June 11th 2018. In the 1st experiment (GE2E1) the commercial tomato hybrid ‘Elpida F1’ grafted onto the commercial rootstock ‘Arazi F1’ was cultivated, while in the 2nd experiment (GE2E2) the commercial tomato hybrid ‘Ekstasis F1’ grafted onto the commercial rootstock ‘Maxifort F1’ was cultivated. The plant density was 1.07 plants m-2 in GE2E1 and 2.13 plants m-2 in GE2E2 but the plants in the GE2E1 were pruned into two stems and thus the stem density was identical in both experiments (2.13 plants m-2).<br> The GE2 was designed to assess the efficiency of compost, or green manure using legume crops inoculated with rhizobia, as sole sources of nitrogen in organic greenhouse crops of tomato in comparison with FYM. Therefore, in GE2, FYM (the same source and amount as in GE1) was applied only in treatment 1 (T1) which was considered the control treatment.</p>
Analysis of M82 tomato inoculated with Gigaspora margarita containing or not endobacteria under combined drought
<p>In this experiment we tested if the tripartite interaction between tomato, AMF and endobacteria they host is able to improve plant resilience to water/nutrient stress. To this aim we used the Gigaspora margarita-CaGg (<em>Candidatus Glomeribacter gigasporarum</em>) biological system. Tomato M82 plants were inoculated with <em>G. margarita </em>spores containing its endobacterium (B+), cured spores without endobacterium (B-) or not inoculated (control) and grown under combined stress or not. Mycorrhizal colonization and plant traits were measured considering two time points, 60 days and 90 days after the experiment start. At the last sampling plant WUE/NUE and expression profiles of AM marker genes were measured. Results showed that <em>Gigaspora </em>is not a good symbiont for tomato since mycorrhizal frequency was rather low. Plant growth was not influenced by presence/absence of endobacteria while moderate water stress had the strongest impact. Interestingly we found that, irrespective of combined stress, B+ inoculated plants were more responsive to the AM symbiosis since they showed a higher activation of the 3 AM marker genes compared to the B- or not inoculated plants. These results indicate that the presence/absence of endobacteria could finely modulate plant metabolism at molecular level although a clear growth response was not detected.</p>
Tobacco and Tomato Dataset 2 - Experience II - 03.07.2020
<p>Tomato leaves photos (healthy and diseased) from different dates taken in different locations (different light and environmental conditions).</p> <p>Cv. Cherry</p> <p>Bacteria: Pst and Xeu</p> <p> </p> <p>Tobacco leaves (healthy and disease) </p>
Tobacco and Tomato Dataset 1 - Experience II - 02.07.2020
<p>Tomato leaves photos (healthy and diseased) from different dates taken in different locations (different light and environmental conditions).</p> <p>Cv. Cherry</p> <p>Bacteria: Pst and Xeu</p>
Tomato Dataset 6 - 12.10.2020
<p>Tomato leaves photos (healthy and diseased) from different dates taken in different locations (different light and environmental conditions).</p> <p>Cv. Cherry</p> <p>Bacteria: Pst and Xeu</p>
Tomato Dataset 5 - 07.10.2020
<p>Tomato leaves photos (healthy and diseased) from different dates taken in different locations (different light and environmental conditions).</p> <p>Cv. Cherry</p> <p>Bacteria: Pst and Xeu</p>
Tomato Dataset 4 - 06.10.2020
<p>Tomato leaves photos (healthy and diseased) from different dates taken in different locations (different light and environmental conditions).</p> <p>Cv. Cherry</p> <p>Bacteria: Pst and Xeu</p>
Tomato Dataset 3 - 01.10.2020
<p>Tomato leaves photos (healthy and diseased) from different dates taken in different locations (different light and environmental conditions).</p> <p>Cv. Cherry</p> <p>Bacteria: Pst and Xeu</p>
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