The 100 tomato genome project
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 601.vcf.gz | Vcf | |||
| ERZ020636.md5 | Other | |||
| 603.vcf.gz | Vcf | |||
| ERZ020637.md5 | Other | |||
| 608.vcf.gz | Vcf |
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Project description:Lycopersicon esculentum cv. Moneymaker tomato plants were grown for 4 weeks in greenhouse conditions (16h/8h light/darkness, 27 °C). L. esculentum was randomly sorted into two groups of 16 plants each and a third reference group of 6 plants. All plants were contained individually in mesh bags. One group of 16 plants was infested with 25 female adult tomato psyllids that were 2-3 days old per plant. The other two groups of 16 and 6 plants were not infested (healthy control, and reference pool). After 3 days, the adults were removed from the infested plants to allow for egg eclosion and eventually nymphal development. In this study, leaves infested and healthy plants were harvested for RNA extraction at 0, 3, 11, and 17 days after infestation with tomato psyllids. The reference pool was harvested on day 0. Tissue (all-leaflets) from at least three plants per group was collected, flash frozen in liquid nitrogen and pooled for each time point (0, 3, 11 and 17 days after infestation) to represent treatments for before feeding (0 d), adult feeding and egg deposition (3 d), 1st and 2nd instar feeding (11 d) and 3rd to 5th instar feeding (17 d ), respectively. The whole experiment was repeated three times (three biological replicates). Plant tissues were ground using a cold mortar and pestle. Total tomato leaf RNA was extracted using the hot-phenol protocol. The RNA was precipitated, pooled, cleaned with a kit and stored at –80C. Two populations of single-stranded cDNAs will be generated from the aliquots and labeled with the cyanine Cy3 and Cy5 fluorophores. RNA isolated from the reference pool (0 d) will be pooled from each replicate and will be labeled with Cy5; this is the reference sample for each hybridization. RNA isolated from leaves infested with tomato psyllids and healthy uninfested plants from each time point will be query samples labeled with Cy3. The two samples of labeled cDNA will be simultaneously hybridized to the same microarray. Keywords: Reference design
2008-02-21 | GSE10550 | GEO
Project description:An intriguing new paradigm in plant biology is that systemically-mobile mRNAs play a role in coordinating development. In this process, specific mRNAs are loaded into the phloem transport stream for translocation to distant tissues, where they may impact developmental processes. However, despite its potential significance for plant growth regulation, mRNA trafficking remains poorly understood and challenging to study. Here we show that phloem-mobile mRNAs can also traffic between widely divergent species from a host to the plant parasite, lespedeza dodder (Cuscuta pentagona Engelm.). Reverse transcriptase PCR (RT-PCR) and microarray analysis were used to detect specific tomato transcripts in dodder grown on tomato (Lycopersicon esculentum Mill.) that were not present in control dodder grown on other host species. The foreign transcripts included LeGAI, which has been previously shown to be translocated in the phloem, as well as nine other transcripts not reported to be mobile. Dodders are parasitic plants that obtain resources by drawing from the phloem of a host plant, and have joint plasmodesmata with host cortical cells. Although viruses are known to move between dodder and its hosts, translocation of endogenous plant mRNA has not been reported. These results point to a potentially new level of interspecies communication, and raise questions about the ability of parasites to recognize, use, and respond to transcripts acquired from their hosts. Experiment Overall Design: In order to identify potential tomato transcripts in dodder, microarray analysis was performed on RNA from dodder and hosts. Total RNA was extracted from the tomato host and from dodder grown on tomato, Arabidopsis, tobacco, or pumpkin. The host tomato RNA was included to verify that any transcripts detected in the parasite were in fact expressed in the host. The dodder samples grown on tobacco, Arabidopsis, and pumpkin served as controls for dodder genes that may cross-hybridize with tomato array probes, with three different host species used to minimize any host-specific effects on dodder gene expression. Samples were analyzed using the Affymetrix GeneChip Tomato Array and transcripts scored for presence or absence in each sample. Considering that host transcripts present in dodder would be at low levels and diluted with dodder transcripts, a P-value of 0.06 in at least two of three biological replicates was used as the threshold for scoring a transcript as being present.
2008-06-15 | E-GEOD-6736 | biostudies-arrayexpress
Project description:The occurrence of Tomato chlorosis virus (ToCV) disease seriously damages tomato growth and yield, and there is no effective way to control ToCV transmission. So far, no studies have reported exploring the interaction between ToCV and tomato at the single cellular level. In this study, single cell RNA sequence was performed on a total of 26720 individual cells from healthy and ToCV-infected tomato leaves. We through identifying cell types, the first tomato leaf cell atlas was successfully constructed. In situ hybridization experiments identified specific marker genes that can be used to identify tomato cell types. Moreover, we have characterized transcription factors that may play a key role in tomato response to ToCV infection, and described the trichome differentiation trajectory during ToCV infection through pseudotime analysis. In conclusion, we proved the feasibility of single-cell sequencing to study the response of plants to biotic stress, and put forward new insights into the interaction between ToCV and tomato from the cellular level. Our data will lay the foundation for following studies between ToCV and plants, and will also provide a valuable reference for future research on non-model plant single cells.
2024-05-01 | GSE201931 | GEO