Exploring natural genetic variation in tomato sucrose synthases on the basis of increased kinetic properties

Dinh, Quy Dung; Finkers, Richard; Westphal, Adrie H.; Dongen, W.M.A.M. van; Visser, Richard G. F.; Trindade, Luisa M.

doi:10.1371/journal.pone.0206636

Cited by 13 publications

(3 citation statements)

References 41 publications

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“…The data used for comparison were publicly available tomato genomes from two studies (Dinh et al 2018;Lin et al 2014;Tomato Genome Sequencing et al 2014), for a total of 444 re-sequenced genomes of tomato cultivars and closely related species.…”

Section: Resultsmentioning

confidence: 99%

Tersect: a set theoretical utility for exploring sequence variant data

Kurowski

Mohareb

2019

Bioinformatics

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Summary Comparing genomic features among a large panel of individuals across the same species is considered nowadays a core part of the bioinformatics analyses. This typically involves a series of complex theoretical expressions to compare, intersect, extract symmetric differences between individuals within a large set of genotypes. Several publically available tools are capable of performing such tasks; however, due to the sheer size of variants being queried, such tasks can be computationally expensive with a runtime ranging from few minutes up to several hours depending on the dataset size. This makes existing tools unsuitable for interactive data query or as part of genomic data visualization platforms such as genome browsers. Tersect is a lightweight, high-performance command-line utility which interprets and applies flexible set theoretical expressions to sets of sequence variant data. It can be used both for interactive data exploration and as part of a larger pipeline thanks to its highly optimized storage and indexing algorithms for variant data. Availability and implementation Tersect was implemented in C and released under the MIT license. Tersect is freely available at https://github.com/tomkurowski/tersect. Supplementary information Supplementary data are available at Bioinformatics online.

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Section: Resultsmentioning

confidence: 99%

Tersect: a set theoretical utility for exploring sequence variant data

Kurowski

Mohareb

2019

Bioinformatics

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“…Sucrose synthases are a group of key enzymes responsible for catalyzing reversible reactions of sucrose decomposition and synthesis [ 38 ]. It has been reported that in the sucrose metabolism pathway, gene expression and enzyme activity associated with sucrose catabolism (SUS, invertase, etc.)…”

Section: Discussionmentioning

confidence: 99%

The Sink-Source Relationship in Cucumber (Cucumis sativus L.) Is Modulated by DNA Methylation

Wang,

Zhang,

et al. 2023

Plants

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The optimization of the sink-source relationship is of great importance for crop yield regulation. Cucumber is a typical raffinose family oligosaccharide (RFO)-transporting crop. DNA methylation is a common epigenetic modification in plants, but its role in sink-source regulation has not been demonstrated in RFO-translocating species. Here, whole-genome bisulfite sequencing (WGBS-seq) was conducted to compare the nonfruiting-node leaves (NFNLs) and leaves of fruit setting (FNLs) at the 12th node by removing all female flowers in other nodes of the two treatments. We found considerable differentially methylated genes enriched in photosynthesis and carbohydrate metabolic processes. Comparative transcriptome analysis between FNLs and NFNLs indicated that many differentially expressed genes (DEGs) with differentially methylated regions were involved in auxin, ethylene and brassinolide metabolism; sucrose metabolism; and RFO synthesis pathways related to sink-source regulation. Moreover, DNA methylation levels of six sink-source-related genes in the pathways mentioned above decreased in leaves after 5-aza-dC-2′-deoxycytidine (5-Aza-dC, a DNA methyltransferase inhibitor) treatment on FNLs, and stachyose synthase (CsSTS) gene expression, enzyme activity and stachyose content in RFO synthesis pathway were upregulated, thereby increasing fruit length and dry weight. Taken together, our findings proposed an up-to-date inference for the potential role of DNA methylation in the sink-source relationship, which will provide important references for further exploring the molecular mechanism of DNA methylation in improving the yield of RFO transport plants.

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“…This finding implies that the distinct sucrose metabolism in both leaves and fruits of wild accession LA385 could be one of the keys to support its higher photosynthetic capacity compared to that in Moneymaker. We have shown in a recent study that the heterologously expressed protein sucrose synthase 3 (SUSY3) of LA385 could hydrolyze sucrose more efficiently compared to the counterpart of Moneymaker (Dinh et al, 2018). Additionally, SUSY has been shown to interact with multiprotein complex involved in cellulose/callose biosynthesis in main crops such as cotton, tobacco, and wood (Nakai et al, 1999, Persia et al, 2008, Coleman et al, 2009, Fujii et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

High-Altitude Wild Species Solanum arcanum LA385—A Potential Source for Improvement of Plant Growth and Photosynthetic Performance at Suboptimal Temperatures

et al. 2019

Self Cite

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Plant growth, development, and yield of current tomato cultivars are directly affected by low temperatures. Although wild tomato species have been suggested as a potential source for low temperature tolerance, very little is known about their behavior during the reproductive phase. Here, we investigated the impact of suboptimal temperatures (SOT, 16/14°C), as compared to control temperatures (CT, 22/20°C), on plant growth, photosynthetic capacity, and carbohydrate metabolism. Under these conditions, two genotypes were analyzed: a Solanum lycopersicum cultivar Moneymaker and a high-altitude wild species Solanum arcanum LA385, from flowering onset until a later stage of fruit development. Total dry matter production in cv. Moneymaker was reduced up to 30% at SOT, whereas it was hardly affected in wild accession LA385. Specific leaf area, total leaf area, and number of fruits were also decreased at SOT in cv. Moneymaker. In contrast, wild accession LA385 showed an acclimation to SOT, in which ΦPSII and net CO2 assimilation rates were less affected; a similar specific leaf area; higher total leaf area; and higher number of fruits compared to those at CT. In addition, LA385 appeared to have a more distinct sucrose metabolism than cv. Moneymaker at both temperatures, in which it had higher contents of sucrose-6-phosphate, sucrose, and ratio of sucrose: starch in leaves and higher ratio of sucrose: hexose in fruits. Overall, our findings indicate that wild accession LA385 is able to acclimate well to SOT during the reproductive phase, whereas growth and development of cv. Moneymaker is reduced at SOT.

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Exploring natural genetic variation in tomato sucrose synthases on the basis of increased kinetic properties

Cited by 13 publications

References 41 publications

Tersect: a set theoretical utility for exploring sequence variant data

Tersect: a set theoretical utility for exploring sequence variant data

The Sink-Source Relationship in Cucumber (Cucumis sativus L.) Is Modulated by DNA Methylation

High-Altitude Wild Species Solanum arcanum LA385—A Potential Source for Improvement of Plant Growth and Photosynthetic Performance at Suboptimal Temperatures

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