Transcriptome datasets of big-fruit tomato MM, cherry tomato CC and wild tomato PP
Ontology highlight
ABSTRACT:
ORGANISM(S): Solanum lycopersicum Solanum lycopersicum var. cerasiforme Solanum pimpinellifolium
PROVIDER: GSE74828 | GEO | 2018/01/01
SECONDARY ACCESSION(S): PRJNA301611
REPOSITORIES: GEO
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Project description:Transcriptome analysis of 7 tissues of commercial tomato (S. lycopersicum cv MoneyMaker) and its wild red-fruited ancestor (S. pimpinellifolium LA0722) genotypes performed to assess expression level of tomato transcriptome and to aid whole genome annotation. Sequencing of fruit at 3 different developmental stages will help to assess gene regulation through ripening.
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Project description:Wild halophytic tomato has long been considered as an ideal gene donor for improving salt tolerance in tomato cultivars. Here, a wild tomato genotype, Solanum pimpinellifolium ‘PI365967’ is significantly more salt-tolerant than a cultivar, Solanum lycopersicom ‘moneymaker’. Affymetrix Tomato Genome Arrays was used to compare the transcriptome change of PI365967 and Moneymaker by salt treatment.After treatment with 200 mM NaCl for 5 h, PI365967 showed relatively fewer responsive genes compared to Moneymaker. Salt Overly Sensitive (SOS) pathway was found to be more active in PI365967 than in Moneymaker, coinciding with relatively less accumulation of Na+ in shoots of PI365967. A gene encoding salicylic acid-binding protein 2 (SABP2) was induced by salinity only in PI365967, suggesting a possible role of salicylic acid signaling in salt response of PI365967. The fact that two genes encoding lactoylglutathione lyase were salt-inducible only in PI365967, together with much higher basal expression of several glutathione S-transferase genes, suggested a more effective detoxification system in PI365967. Key words: salt tolerance, transcriptomic profiling, wild tomato, ion homeostasis, SABP2.
2010-06-01 | GSE16401 | GEO
Project description:Wild halophytic tomato has long been considered as an ideal gene donor for improving salt tolerance in tomato cultivars. Here, a wild tomato genotype, Solanum pimpinellifolium M-bM-^@M-^XPI365967M-bM-^@M-^Y is significantly more salt-tolerant than a cultivar, Solanum lycopersicom M-bM-^@M-^XmoneymakerM-bM-^@M-^Y. Affymetrix Tomato Genome Arrays was used to compare the transcriptome change of PI365967 and Moneymaker by salt treatment.After treatment with 200 mM NaCl for 5 h, PI365967 showed relatively fewer responsive genes compared to Moneymaker. Salt Overly Sensitive (SOS) pathway was found to be more active in PI365967 than in Moneymaker, coinciding with relatively less accumulation of Na+ in shoots of PI365967. A gene encoding salicylic acid-binding protein 2 (SABP2) was induced by salinity only in PI365967, suggesting a possible role of salicylic acid signaling in salt response of PI365967. The fact that two genes encoding lactoylglutathione lyase were salt-inducible only in PI365967, together with much higher basal expression of several glutathione S-transferase genes, suggested a more effective detoxification system in PI365967. Key words: salt tolerance, transcriptomic profiling, wild tomato, ion homeostasis, SABP2. In one treatment, 9 six-leaf-old plants of one tomato genotype (PI365967 or Moneymaker) were divided into three biological replicates and treated hydroponically under sterile condition with (or without) 200 mM NaCl for 5 h. RNA isolated from pooled three individual plants was used in hybridization to one chip, resulting in 12 chips in total.
2010-05-31 | E-GEOD-16401 | biostudies-arrayexpress
Project description:Transcriptome datasets of big-fruit tomato MM, cherry tomato CC and wild tomato PP
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Project description:Proteomics and transcriptomics data of tomato fruits (Solanum lycopersicum L. var. Moneymaker) at 9 developmental stages were used to calculate with a mathematical model the rate constants of synthesis and degradation for over 1,000 proteins. Proteome and transcriptome were extracted from the pericarp tissue and analyzed using label-free LC-MS/MS (Orbitrap Q-Exactive) and RNA Sequencing (Illumina), respectively. Absolute quantification of transcriptome has been obtained by spiking-in internal standard before total-RNA extraction. Absolute quantification of the proteome has been approximated using the "Total Protein" approach. An OD equation defining the changes of protein content has been used to determine the synthesis and degradation rate constants (day -1). Almost 2,400 transcript-protein pairs were identified and the translation and degradation rate constants were determined for more than a thousand proteins. The model predicted median values of about 2 min for the translation and a lifetime of approximately 11 days. Proteins involved in protein synthesis had higher ks and kd values, indicating that the protein machinery is particularly flexible. None sequenced-based features were found that could be used to predict these rate constants.
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Project description:In this study the F8 population of 100 Recombinant Inbred Lines (RILs) obtained from a cross between Solanum lycopersicum X Solanum pimpinellifolium were intelligently allocated to two sub-populations optimized for the distribution of parental alleles using the R-procedure DesignGG (Li et al., 2009; Joosen et al., 2013); hence 50 RIL lines were used for dry seeds and 50 lines for 6h imbibed seeds
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Project description:Understanding the genetic basis of plants’ response to environmental stresses such as drought and salinity is vital for improving the future crop productivity and for deciphering the evolutionary mechanisms of adaptation and speciation. Here, we screened for genes and functional groups that are potentially involved in drought tolerance in tomato by comparing genome-wide transcriptome profiles of drought-sensitive S. lycopersicum and drought-tolerant S. pimpinellifolium populations under control and water deficit conditions. We also compared the transcriptome profiles from this study and a previous salt treatment study to investigate expression similarities and differences in gene expression patterns between water and salt stress responses, which are physiologically and biochemically similar. Stress-induced genes such as dehydration responsive element binding (DREB) protein, ABA-response element binding factor (AREB)-like protein, heat shock proteins, and chaperones were commonly up-regulated in S. lycopersicum and S. pimpinellifolium. Genes such as WRKY transcription factors and 1-aminocyclopropane-1-carboxylate (ACC) synthase exhibited striking differences in both the baseline expression under the control condition as well as expression changes in response to water deficit, suggesting that the two species have accumulated heritable differences in gene expression patterns. At the genome scale, there was a tendency that down-regulated genes in S. lycopersicum are more neutral or even up-regulated in S. pimpinellifolium, suggesting that S. pimpinellifolium may be able to maintain cellular activities during prolonged droughts. In comparison of water and salt stress responses, known stress-induced genes such as DREB protein, AREB-like protein, and nine-cis-epoxycarotenoid dioxygenase (NCED) were commonly up-regulated in response to these stresses. However, we also found fundamental differences between these stress responses in terms of genome-wide expression patterns, partly attributable to the difference in how these stresses were applied during the experiments. We compared Affymetrix microarray transcriptome profiles of root tissues from three natural populations each of S. lycopersicum and S. pimpinellifolium (3-4 individuals in each population as biological replicates under control (well-watered) and water deficit treatments.
2013-12-01 | E-GEOD-39894 | biostudies-arrayexpress
Project description:Fruit pericarp at two stages, cell expasion and orange red. From Solaunm Lycopersicum and Solaunm Lycopersicum var cerasiforme genotypes. Two Dimensional Polyacrylamide Gel Electrophoresis (Coomasie staining, Band excision, Enzyme digestion) LC/MS (Thermo Finnigan LTQ XL) Software processing (X! Tandem, CYCLONE (2010.12.01.1)) Databases (Contaminants database is a home-made database. It is a set of 25 proteic sequences corresponding to proteins that could be present in the samples, 21 correspond with keratins, 2 with trypsin and 2 with bovin serum albumins. 17 sequences come from SwissProt and 8 from TrEMBL. ITAG2.3 database is the set of proteic sequences predicted in the version 2.3 of the annotation of the tomate genome published by the ITAG group (ftp.solgenomics.net))
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