scholarly journals Identification of Long Non-Coding RNAs Associated with Tomato Fruit Expansion and Ripening by Strand-Specific Paired-End RNA Sequencing

Horticulturae ◽  
2021 ◽  
Vol 7 (12) ◽  
pp. 522
Author(s):  
Jinyu Wang ◽  
Yan Feng ◽  
Xiaotao Ding ◽  
Jingtian Huo ◽  
Wen-Feng Nie
Keyword(s):  
Rna Sequencing ◽  
Fruits And Vegetables ◽  
Developmental Stages ◽  
Tomato Fruit ◽  
Expression Patterns ◽  
Fleshy Fruit ◽  
Tomato Fruits ◽  
Tomato Plants ◽  
Horticultural Crops ◽  
Non Coding Rnas

As emerging essential regulators in plant development, long non-coding RNAs (lncRNAs) have been extensively investigated in multiple horticultural crops, as well as in different tissues of plants. Tomato fruits are an indispensable part of people’s diet and are consumed as fruits and vegetables. Meanwhile, tomato is widely used as a model to study the ripening mechanism in fleshy fruit. Although increasing evidence shows that lncRNAs are involved in lots of biological processes in tomato plants, the comprehensive identification of lncRNAs in tomato fruit during its expansion and ripening and their functions are partially known. Here, we performed strand-specific paired-end RNA sequencing (ssRNA-seq) of tomato Heinz1706 fruits at five different developmental stages, as well as flowers and leaves. We identified 17,674 putative lncRNAs by referencing the recently released SL4.0 and annotation ITAG4.0 in tomato plants. Many lncRNAs show different expression patterns in fleshy fruit at different developmental stages compared with leaves or flowers. Our results indicate that lncRNAs play an important role in the regulation of tomato fruit expansion and ripening, providing informative lncRNA candidates for further studies in tomato fruits. In addition, we also summarize the recent advanced progress in lncRNAs mediated regulation on horticultural fruits. Hence, our study updates the understanding of lncRNAs in horticultural plants and provides resources for future studies relating to the expansion and ripening of tomato fruits.

scholarly journals Effectiveness of Chemical and Thermal Treatments on Control Rhizopus Stolonifer Fruit Infection Comparing Tomato Cultivars with Different Sensitivities to Cracking

2019 ◽  
Vol 16 (15) ◽  
pp. 2754 ◽  
Author(s):  
Alfaro-Sifuentes ◽  
Juan ◽  
Meca ◽  
Elorrieta ◽  
Valenzuela
Keyword(s):  
Hydrogen Peroxide ◽  
Tomato Fruit ◽  
Control Sample ◽  
Hot Water ◽  
Economic Losses ◽  
Rhizopus Stolonifer ◽  
Tomato Fruits ◽  
Horticultural Crops ◽  
Tomato Yield ◽  
Fruit Cracking

Tomatoes are among the most important horticultural crops; however, it is estimated that 30% of tomato yield is lost due to postharvest rot due to Rhizopus stolonifer, a fungus which requires lesions to initiate the infectious process. Tomato fruit cracking is a physiopathy which causes significant economic losses, since cracking is the door used by the fungus. In this experiment, 14 cultivars of tomato of different types were used. Fruit sampling was carried out in the middle of the crop cycle, coinciding with the peak of yield; then, the fruits were divided into two groups: one group was inoculated with Rhizopus in order to assess the effectiveness of washing, whilst the other was treated with sterile water. The fruits of each group were divided into lots to be treated with six washing treatments: dipping in hot water at 20, 40 and 60 °C for 20 s; the fruits were then sprayed with the following solutions: 0.6% of Hydrogen Peroxide 23% + Peracetic acid 15%; commercial bleach at 0.5% and 2% of Hydrogen Peroxide 50%. The control sample was not washed. The results show that there was an influence of cultivar on fruit cracking, which was strongly related with Rhizopus infection. Three cultivars were not susceptible to cracking, and therefore, were not sensitive to Rhizopus infection. The effectiveness of different washing treatments of tomato fruits depends on several factors; nonetheless, hot water treatment has been shown to be more effective than the use of chemical products such as commercial bleach or hydrogen peroxide. Another factor, the susceptibility of cultivars to cracking, determines the effectiveness of the washing treatment. The results provide an important basis for making decisions about the washing management of tomato fruits in packaging houses.

scholarly journals Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs

2020 ◽  
Vol 21 (10) ◽  
pp. 3711
Author(s):  
Melina J. Sedano ◽  
Alana L. Harrison ◽  
Mina Zilaie ◽  
Chandrima Das ◽  
Ramesh Choudhari ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Expression Patterns ◽  
Biological Significance ◽  
Rna Seq ◽  
Biological Functions ◽  
Protein Coding ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Non Coding Rnas

Genome-wide RNA sequencing has shown that only a small fraction of the human genome is transcribed into protein-coding mRNAs. While once thought to be “junk” DNA, recent findings indicate that the rest of the genome encodes many types of non-coding RNA molecules with a myriad of functions still being determined. Among the non-coding RNAs, long non-coding RNAs (lncRNA) and enhancer RNAs (eRNA) are found to be most copious. While their exact biological functions and mechanisms of action are currently unknown, technologies such as next-generation RNA sequencing (RNA-seq) and global nuclear run-on sequencing (GRO-seq) have begun deciphering their expression patterns and biological significance. In addition to their identification, it has been shown that the expression of long non-coding RNAs and enhancer RNAs can vary due to spatial, temporal, developmental, or hormonal variations. In this review, we explore newly reported information on estrogen-regulated eRNAs and lncRNAs and their associated biological functions to help outline their markedly prominent roles in estrogen-dependent signaling.

scholarly journals Antioxidant and Antiplatelet Activities in Extracts from Green and Fully Ripe Tomato Fruits (Solanum lycopersicum) and Pomace from Industrial Tomato Processing

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Eduardo Fuentes ◽  
Reinhold Carle ◽  
Luis Astudillo ◽  
Luis Guzmán ◽  
Margarita Gutiérrez ◽  
...  
Keyword(s):  
Fruits And Vegetables ◽  
Tomato Fruit ◽  
Antioxidant Effect ◽  
Maturation Stage ◽  
Total Phenol Content ◽  
Antiplatelet Activity ◽  
Tomato Fruits ◽  
Tomato Paste ◽  
Tomato Processing ◽  
Reduce Risk

The consumption of fruits and vegetables is accepted to be one of the strategies to reduce risk factors for these diseases. The aim of this study was to examine potential relationships between the antioxidant and the antiplatelet activities in green mature and fully ripe (red) tomatoes and of lycopene-rich byproducts of tomato paste processing such as pomace. The total phenol content of tomato components was the highest in peels, pulp, and in the mucilaginous myxotesta covering the tomato seeds with values36.9±0.8,33.3±00.5, and17.6±0.9 mg GAE/100 g, respectively (P<0.05). Tomato peels had the highest antioxidant activity, both, as measured by the FRAP (46.9±0.9 μmol Fe+2/g,P<0.05) and the DPPH assays (97.4±0.2%, 1000 μg/mL,P<0.05). Pomace extracts showed the highest antiplatelet activity induced by ADP, collagen, TRAP-6, and arachidonic acid. While the maturation stage of the tomato fruit affected the antioxidant effect, antiplatelet activity was independent of fruit ripeness. Finally, based on the present results, tomato and its byproducts may be considered as a valuable source of antioxidant and antiplatelet activities.

scholarly journals Influence of Cold Plasma Treatment on Textural and Color Characteristics of Two Tomato Varieties

2016 ◽  
Vol 13 (1-2) ◽  
Author(s):  
Milan Vukić ◽  
Dragan Vujadinović ◽  
Vesna Gojković ◽  
Radoslav Grujić
Keyword(s):  
Plasma Treatment ◽  
Cold Plasma ◽  
Fruits And Vegetables ◽  
New Technologies ◽  
Tomato Fruit ◽  
Vegetable Crops ◽  
Negative Effects ◽  
Horticultural Crops ◽  
Color Characteristics ◽  
Hot Air Treatment

New technologies had been developed to prolong postharves sustainability of horticultural crops. Technologies as hot air treatment or iridation with UV-C spectral emissions are among them. Al of them have positive and negative effects on quality of horticultural crops. Increasingly under research for decontamination of foods is cold plasma technology, especially fresh fruits and vegetables. Possibility of creating cold plasma under atmosferic presures (ACP) offers new preservation tool to reduce microbial infections of vegetable crops. Effects of atmosferic cold plasma on food quality, however, remains under researched.. In this study, tomato is treated with air ACP generated with an dielectric barrier discharge reactor (DBD). Changes in textural and color characteristics of two tomato fruit varieties after cold plasma treatment were analysed by performing TPA test and color measurements. The effect of air ACP on tomato texture and color was insignificant.

scholarly journals Genome-wide cis-decoding for expression designing in tomato using cistrome data and explainable deep learning

2021 ◽  
Author(s):  
Takashi Akagi ◽  
Kanae Masuda ◽  
Eriko Kuwada ◽  
Kouki Takeshita ◽  
Taiji Kawakatsu ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Dna Sequences ◽  
Regulatory Networks ◽  
Tomato Fruit ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Tomato Fruits ◽  
Genome Wide ◽  
Tomato Fruit Ripening ◽  
Single Cell Type

In the evolutionary paths of plants, variations of the cis-regulatory elements (CREs) resulting in expression diversification have played a central role in driving the establishment of lineage-specific traits. However, it is difficult to predict expression behaviors from the CRE patterns to properly harness them, mainly because the biological processes are complex. In this study, we used cistrome datasets and explainable convolutional neural network (CNN) frameworks to predict genome-wide expression patterns in tomato fruits from the DNA sequences in gene regulatory regions. By fixing the effects of trans-elements using single cell-type spatiotemporal transcriptome data for the response variables, we developed a prediction model of a key expression pattern for the initiation of tomato fruit ripening. Feature visualization of the CNNs identified nucleotide residues critical to the objective expression pattern in each gene and their effects, were validated experimentally in ripening tomato fruits. This cis-decoding framework will not only contribute to understanding the regulatory networks derived from CREs and transcription factor interactions, but also provide a flexible way of designing alleles with optimized expression.

scholarly journals Effects of High Nutrient Solution EC and Its Application Timing on Lycopene, Soluble Sugars, and Chlorophyll Concentrations of Tomato (Lycopersicon esculentum Mill.) Fruit

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1108A-1108
Author(s):  
Min Wu ◽  
Chieri Kubota
Keyword(s):  
Nutrient Solution ◽  
Developmental Stages ◽  
Tomato Fruit ◽  
Chlorophyll Concentration ◽  
Soluble Sugars ◽  
Maximum Size ◽  
Tomato Fruits ◽  
Application Timing ◽  
Significant Difference ◽  
Ripe Tomato

Manipulation of the electrical conductivity (EC) of the hydroponic nutrient solution has been studied as an effective method to enhance flavor and nutritional value of tomato fruit. The objective of this research was to quantitatively understand the accumulation of lycopene, soluble sugars, and the degradation of chlorophyll in fruits as affected by EC and EC application timing relative to fruit ripeness stages. `Durinta' tomato was grown hydroponically inside the greenhouse under two EC (2.3 and 4.5 dS·m-1). The high EC treatment began immediately after anthesis (HEC treatment) or 4 weeks later (DHEC treatment), when fruits had reached maximum size, but still were green. Fruits were harvested weekly beginning 2 weeks after anthesis, until they reached red ripe stage. The chlorophyll concentration in tomato fruits showed no difference between treatments when compared at the same ripeness stages. The lycopene concentration of red ripe tomato fruits in HEC and DHEC treatments was 29% greater than that in low EC control (LEC treatment). However, there was no significant difference in lycopene concentration between HEC and DHEC. Both DHEC and HEC increased total soluble solid concentration (TSS) of red ripe tomato fruits compared with those grown in LEC; while the DHEC showed an increase of fruit TSS of 12%, the HEC had a greater enhancement of TSS of 19%. In addition, the fruit ripeness was accelerated under high EC, regardless of the timing of treatment. High EC treatment at early and mature green fruit developmental stages enhanced both fruit TSS and lycopene concentration; however, the nutrient solution EC effect on lycopene concentration was not dependent on the time of application during fruit development.

scholarly journals Molecular and Hormonal Mechanisms Regulating Fleshy Fruit Ripening

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1136
Author(s):  
Shan Li ◽  
Kunsong Chen ◽  
Donald Grierson
Keyword(s):  
Fruit Ripening ◽  
Tomato Fruit ◽  
Ethylene Biosynthesis ◽  
Fleshy Fruit ◽  
Regulatory Interactions ◽  
Expression Of Genes ◽  
Regulatory Circuits ◽  
Ripening Genes ◽  
Different Types ◽  
Non Coding Rnas

This article focuses on the molecular and hormonal mechanisms underlying the control of fleshy fruit ripening and quality. Recent research on tomato shows that ethylene, acting through transcription factors, is responsible for the initiation of tomato ripening. Several other hormones, including abscisic acid (ABA), jasmonic acid (JA) and brassinosteroids (BR), promote ripening by upregulating ethylene biosynthesis genes in different fruits. Changes to histone marks and DNA methylation are associated with the activation of ripening genes and are necessary for ripening initiation. Light, detected by different photoreceptors and operating through ELONGATED HYPOCOTYL 5(HY5), also modulates ripening. Re-evaluation of the roles of ‘master regulators’ indicates that MADS-RIN, NAC-NOR, Nor-like1 and other MADS and NAC genes, together with ethylene, promote the full expression of genes required for further ethylene synthesis and change in colour, flavour, texture and progression of ripening. Several different types of non-coding RNAs are involved in regulating expression of ripening genes, but further clarification of their diverse mechanisms of action is required. We discuss a model that integrates the main hormonal and genetic regulatory interactions governing the ripening of tomato fruit and consider variations in ripening regulatory circuits that operate in other fruits.

scholarly journals Effect of Fluridone on Some Physiological and Qualitative Features of Ripening Tomato Fruit

2017 ◽  
Vol 59 (2) ◽  
pp. 41-49
Author(s):  
Justyna Góraj-Koniarska ◽  
Marian Saniewski ◽  
Ryszard Kosson ◽  
Wiesław Wiczkowski ◽  
Marcin Horbowicz
Keyword(s):  
Ethylene Production ◽  
Tomato Fruit ◽  
Carotenoid Biosynthesis ◽  
Tomato Fruits ◽  
Tomato Plants ◽  
Tomato Fruit Ripening ◽  
Chlorophyll Production ◽  
Carotenoid Biosynthesis Pathway ◽  
Metabolic Significance

AbstractIn tomato fruits, chlorophyll, lycopene and ß-carotene are mostly responsible for the color. During ripening of tomato fruits, the color of the pericarp changes from green to red as chlorophyll is degraded and carotenoids accumulate. These changes are associated with an increase in respiration and ethylene production. Carotenoid biosynthesis pathway in plants can be disturbed by herbicide fluridone (1-methyl-3-phenyl-5-[3-trifluoromethyl(phenyl)]- 4(1H)-pyridinone), which inhibits the activity of phytoene desaturase, an enzyme responsible for conversion of phytoene to phytofluene. Fluridone is also used as an inhibitor of biosynthesis of abscisic acid (ABA) and strigolactones, and it reduces chlorophyll production in plants. In our research we studied the effect of fluridone on some physiological parameters, such as color, firmness, ethylene production, lycopene and chlorophyll content during ripening of the tomato fruit. Tomato plants cv. Altadena (Syngenta) were cultivated in a greenhouse in controlled temperature and both immature and mature fruits were used for the experiments, performed between August and November 2016. Fluridone at concentrations of 0.1% and 1.0% in lanolin paste was applied as a 2-3 mm stripe from the top to the base of tomato fruits, and as a control a stripe of lanolin was applied in the same way on the opposite side of the fruits. Fluridone at a concentration of 1.0% greatly inhibited lycopene accumulation in the pericarp of tomato fruits from the treated side. The measurements of fruit firmness have shown no significant differences between firmness of the part of the tomato fruits treated with fluridone, and the non-treated ones. Tomato fruits treated with fluridone produced amounts of ethylene similar to those found in control tissues on the opposite side of the same fruit. Fluridone delayed chlorophyll degradation in tomato fruits. The metabolic significance of these findings is discussed with the role of carotenogenesis inhibition in tomato fruit ripening.

scholarly journals Characterization of RIN Isoforms and Their Expression in Tomato Fruit Ripening

Cells ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1739
Author(s):  
Maria A. Slugina ◽  
Gleb I. Efremov ◽  
Anna V. Shchennikova ◽  
Elena Z. Kochieva
Keyword(s):  
Fruit Ripening ◽  
Wild Species ◽  
Target Genes ◽  
Tomato Fruit ◽  
Expression Patterns ◽  
Fleshy Fruit ◽  
Sugar Accumulation ◽  
Gene Promoters ◽  
Tomato Fruit Ripening ◽  
Splicing Site

Ripening of tomato fleshy fruit is coordinated by transcription factor RIN, which triggers ethylene and carotenoid biosynthesis, sugar accumulation, and cell wall modifications. In this study, we identified and characterized complete sequences of the RIN chromosomal locus in two tomato Solanum lycopersicum cultivars, its rin/RIN genotype, and three wild green-fruited species differing in fruit color and composition. The results reveal that S. lycopersicum cultivars and some wild species (S. pennellii, S. habrochaites, and S. huaylasense) had a 3′-splicing site enabling the transcription of RIN1i and RIN2i isoforms. The other wild species (S. arcanum, S. chmielewskii, S. neorickii, and S. peruvianum) had a 3′-splicing site only for RIN2i, which was consistent with RIN1i and RIN2i expression patterns. The genotype rin/RIN, which had an extended 3′-terminal deletion in the rin allele, mainly expressed the chimeric RIN–MC transcript, which was also found in cultivars (RIN/RIN). The RIN1, but not RIN2, protein is able to induce the transcription of the reporter gene in the Y2H system, which positively correlated with the transcription profile of RIN1i and RIN target genes. We suggest that during fruit ripening, RIN1 activates ripening-related genes, whereas RIN2 and RIN–MC act as modulators by competing for RIN-binding sites in gene promoters, which should be confirmed by further studies on the association between RIN-splicing mechanisms and tomato fruit ripening.

scholarly journals Spatio-Temporal Transcriptional Dynamics of Maize Long Non-Coding RNAs Responsive to Drought Stress

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 138 ◽  
Author(s):  
Junling Pang ◽  
Xia Zhang ◽  
Xuhui Ma ◽  
Jun Zhao
Keyword(s):  
Drought Stress ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Functional Enrichment ◽  
Transcriptional Analysis ◽  
Protein Coding ◽  
Altered Expression ◽  
Protein Coding Genes ◽  
A Genome ◽  
Non Coding Rnas

Long non-coding RNAs (lncRNAs) have emerged as important regulators in plant stress response. Here, we report a genome-wide lncRNA transcriptional analysis in response to drought stress using an expanded series of maize samples collected from three distinct tissues spanning four developmental stages. In total, 3488 high-confidence lncRNAs were identified, among which 1535 were characterized as drought responsive. By characterizing the genomic structure and expression pattern, we found that lncRNA structures were less complex than protein-coding genes, showing shorter transcripts and fewer exons. Moreover, drought-responsive lncRNAs exhibited higher tissue- and development-specificity than protein-coding genes. By exploring the temporal expression patterns of drought-responsive lncRNAs at different developmental stages, we discovered that the reproductive stage R1 was the most sensitive growth stage with more lncRNAs showing altered expression upon drought stress. Furthermore, lncRNA target prediction revealed 653 potential lncRNA-messenger RNA (mRNA) pairs, among which 124 pairs function in cis-acting mode and 529 in trans. Functional enrichment analysis showed that the targets were significantly enriched in molecular functions related to oxidoreductase activity, water binding, and electron carrier activity. Multiple promising targets of drought-responsive lncRNAs were discovered, including the V-ATPase encoding gene, vpp4. These findings extend our knowledge of lncRNAs as important regulators in maize drought response.

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