Solanum elaeagnifolium, an invasive weed of the Solanaceae family, is poorly studied although it poses a significant threat to crops. Here the analysis of the transcriptome of S. elaeagnifolium is presented, as a means to explore the... more
Solanum elaeagnifolium, an invasive weed of the Solanaceae family, is poorly studied although it poses a significant threat to crops. Here the analysis of the transcriptome of S. elaeagnifolium is presented, as a means to explore the biology of this species and to identify genes related to its adaptation to environmental stress. One of the basic mechanisms by which plants respond to environmental stress is through the synthesis of specific secondary metabolites that protect the plant from herbivores and microorganisms, or serve as signaling molecules. One important such group of secondary metabolites are terpenes. By next-generation sequencing, the flower/leaf transcriptome of S. elaeagnifolium was sequenced and de novo assembled into 75,618 unigenes. Among the unigenes identified, several corresponded to genes involved in terpene biosynthesis; these included terpene synthases (TPSs) and genes of the mevalonate (MVA) and the methylerythritol phosphate (MEP) pathways. Functional characterization of two of the TPSs showed that one produced the sesquiterpene (E)-caryophyllene and the second produced the monoterpene camphene. Analysis of wounded S. elaeagnifolium leaves has shown significant increase of the concentration of (E)-caryophyllene and geranyl linalool, two terpenes implicated in stress responses. The increased production of (E)-caryophyllene was matched to the induced expression of the corresponding TPS gene. Wounding also led to the increased expression of the putative 1-deoxy-D-xylulose-5-phosphate synthase 2 (DXS2) gene, a key enzyme of the MEP pathway, corroborating the overall increased output of terpene biosynthesis. The reported S. elaeagnifolium de novo transcriptome provides a valuable sequence database that could facilitate study of this invasive weed and contribute to our understanding of the highly diverse Solanaceae family. Analysis of genes and pathways involved in the plant's interaction with the environment will help to elucidate the mechanisms that underly the intricate features of this unique Solanum species.
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Solanum elaeagnifolium, an invasive weed of the Solanaceae family, is poorly studied although it poses a significant threat to crops. Here the analysis of the transcriptome of S. elaeagnifolium is presented, as a means to explore the... more
Solanum elaeagnifolium, an invasive weed of the Solanaceae family, is poorly studied although it poses a significant threat to crops. Here the analysis of the transcriptome of S. elaeagnifolium is presented, as a means to explore the biology of this species and to identify genes related to its adaptation to environmental stress. One of the basic mechanisms by which plants respond to environmental stress is through the synthesis of specific secondary metabolites that protect the plant from herbivores and microorganisms, or serve as signaling molecules. One important such group of secondary metabolites are terpenes. By next-generation sequencing, the flower/leaf transcriptome of S. elaeagnifolium was sequenced and de novo assembled into 75,618 unigenes. Among the unigenes identified, several corresponded to genes involved in terpene biosynthesis; these included terpene synthases (TPSs) and genes of the mevalonate (MVA) and the methylerythritol phosphate (MEP) pathways. Functional characterization of two of the TPSs showed that one produced the sesquiterpene (E)-caryophyllene and the second produced the monoterpene camphene. Analysis of wounded S. elaeagnifolium leaves has shown significant increase of the concentration of (E)-caryophyllene and geranyl linalool, two terpenes implicated in stress responses. The increased production of (E)-caryophyllene was matched to the induced expression of the corresponding TPS gene. Wounding also led to the increased expression of the putative 1-deoxy-D-xylulose-5-phosphate synthase 2 (DXS2) gene, a key enzyme of the MEP pathway, corroborating the overall increased output of terpene biosynthesis. The reported S. elaeagnifolium de novo transcriptome provides a valuable sequence database that could facilitate study of this invasive weed and contribute to our understanding of the highly diverse Solanaceae family. Analysis of genes and pathways involved in the plant's interaction with the environment will help to elucidate the mechanisms that underly the intricate features of this unique Solanum species.
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Sireviruses are an ancient genus of the Copia superfamily of LTR retrotransposons, and the only one that has exclusively proliferated within plant genomes. Based on experimental data and phylogenetic analyses, Sireviruses have... more
Sireviruses are an ancient genus of the Copia superfamily of LTR retrotransposons, and the only one that has exclusively proliferated within plant genomes. Based on experimental data and phylogenetic analyses, Sireviruses have successfully infiltrated many branches of the plant kingdom, extensively colonizing the genomes of grass species. Notably, it was recently shown that they have been a major force in the make-up and evolution of the maize genome, where they currently occupy ~21% of the nuclear content and ~90% of the Copia population. It is highly likely, therefore, that their life dynamics have been fundamental in the genome composition and organization of a plethora of plant hosts. To assist studies into their impact on plant genome evolution and also facilitate accurate identification and annotation of transposable elements in sequencing projects, we developed MASiVEdb (Mapping and Analysis of SireVirus Elements Database), a collective and systematic resource of Sireviruses in plants. Taking advantage of the increasing availability of plant genomic sequences, and using an updated version of MASiVE, an algorithm specifically designed to identify Sireviruses based on their highly conserved genome structure, we populated MASiVEdb (http://bat.infspire.org/databases/masivedb/) with data on 16,243 intact Sireviruses (total length >158Mb) discovered in 11 fully-sequenced plant genomes. MASiVEdb is unlike any other transposable element database, providing a multitude of highly curated and detailed information on a specific genus across its hosts, such as complete set of coordinates, insertion age, and an analytical breakdown of the structure and gene complement of each element. All data are readily available through basic and advanced query interfaces, batch retrieval, and downloadable files. A purpose-built system is also offered for detecting and visualizing similarity between user sequences and Sireviruses, as well as for coding domain discovery and phylogenetic analysis. MASiVEdb is currently the most comprehensive directory of Sireviruses, and as such complements other efforts in cataloguing plant transposable elements and elucidating their role in host genome evolution. Such insights will gradually deepen, as we plan to further improve MASiVEdb by phylogenetically mapping Sireviruses into families, by including data on fragments and solo LTRs, and by incorporating elements from newly-released genomes.
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Vegetable grafting is used extensively today by farmers primarily for facing soil borne problems – among other benefits – despite some unfavorable fruit quality effects observed in certain rootstock-scion combinations. Fruit shape is a... more
Vegetable grafting is used extensively today by farmers primarily for facing soil borne problems – among other benefits – despite some unfavorable fruit quality effects observed in certain rootstock-scion combinations. Fruit shape is a characteristic known to be affected by grafting. Herein, working with pepper graftings between two pepper genotypes (cultivars) differing in fruit shape, we observed fruit shape changes after grafting the round shaped cultivar, cv. “Mytilini Round” (scion) on the long shaped cultivar, cv. “Piperaki Long” (rootstock). Furthermore, the phenotypic changes observed in scion fruits were inherited for two generations of seed derived progenies indicating that the changes imposed on scion are heritable. PCR amplifications using six inter simple sequence repeat (ISSR) primers showed that progenies developed from seeds collected from the modified scion fruits had a genetic profile more similar to the scion genetic profile and less similar to the rootstock profile indicating that only minor genetic changes occurred in the scion during grafting. The change in the fruit shape was not found to be accompanied by extended DNA sequence changes in pepper CaOvate sequence, a gene shown before to be involved in determining fruit shape in pepper, although a slight difference in CaOvate gene expression was found. Overall, understanding the molecular mechanisms that probably underline graft-induced changes paves the way to a better knowledge over the rootstock-scion interactions, the role of rootstock in scion performance and eventually the improved quality and fruit harvest from grafted vegetable plants.
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Fruit shape is a very important fruit quality character frequently affected by grafting in vegetable plants like pepper. It has already been shown that, similar to tomato, fruit shape in pepper is likely controlled by an Ovate-like gene,... more
Fruit shape is a very important fruit quality character frequently affected by grafting in vegetable plants like pepper. It has already been shown that, similar to tomato, fruit shape in pepper is likely controlled by an Ovate-like gene, CaOvate, the down-regulation of which positively affects fruit elongation. To further understand the molecular mechanisms involved in pepper fruit shape control and the changes imposed by grafting, we have amplified, sequenced, and structurally characterized CaGA20ox1, the target gene of CaOvate, from a long fruit and a round fruit shaped cultivar. The results show that CaGA20ox1 has similar genomic organization to the tomato GA20ox1 and encodes a 375-amino acid polypeptide that shares 89% identity with tomato GA20ox1. We then studied CaGA20ox1 expression in different pepper plant parts and in different developmental stages of flower and fruit development. The expression of the gene was quantified by means of relative quantitative PCR in the developmental stage of 10 days after anthesis fruit of both cultivars. The results showed that there is a significant difference in the expression of the CaGA20ox1 between the two cultivars in this specific stage as well as in the expression of CaGA20ox1 after virus-induced gene silencing (VIGS) of CaOvate. Finally, the 5′ upstream sequences of CaGA20ox1 gene of the two cultivars were examined and compared. These results corroborate our previous findings, where VIGS of CaOvate alters CaGA20ox1 expression, leading to more elongated fruit, and also progress further the understanding of the genes involved in fruit shape control in pepper opening the way for understanding the molecular means of grafting effects.
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Research Interests: Genetics, Gene regulation, Plant Biology, Gene expression, Arabidopsis thaliana, and 14 morePlant Physiology, Comparative Analysis, Fruit, Gene Network, Transcription Factor, Soil sciences, Plant Physiology and Biochemistry, Fruit set and development, Molecular cloning, Prunus, Plant species, Economic Loss, Species Specificity, and Prunus Persica
Background Grafting is a widely used technique contributing to sustainable and ecological production of many vegetables, but important fruit quality characters such as taste, aroma, texture and shape are known for years to be affected by... more
Background Grafting is a widely used technique contributing to sustainable and ecological production of many vegetables, but important fruit quality characters such as taste, aroma, texture and shape are known for years to be affected by grafting in important vegetables species including pepper. From all the characters affected, fruit shape is the most easily observed and measured. From research in tomato, fruit shape is known to be controlled by many QTLs but only few of them have larger effect on fruit shape variance. In this study we used pepper cultivars with different fruit shape to study the role of a pepper Ovate-like gene, CaOvate, which encodes a negative regulator protein that brings significant changes in tomato fruit shape. Results We successfully cloned and characterized Ovate-like genes (designated as CaOvate) from two pepper cultivars of different fruit shape, cv. "Mytilini Round" and cv. "Piperaki Long", hereafter referred to as cv. "Round" and cv. "Long" after the shape of their mature fruits. The CaOvate consensus contains a 1008-bp ORF, encodes a 335 amino-acid polypeptide, shares 63% identity with the tomato OVATE protein and exhibits high similarity with OVATE sequences from other Solanaceae species, all placed in the same protein subfamily as outlined by expert sequence analysis. No significant structural differences were detected between the CaOvate genes obtained from the two cultivars. However, relative quantitative expression analysis showed that the expression of CaOvate followed a different developmental profile between the two cultivars, being higher in cv. "Round". Furthermore, down-regulation of CaOvate through VIGS in cv. "Round" changes its fruit to a more oblong form indicating that CaOvate is indeed involved in determining fruit shape in pepper, perhaps by negatively affecting the expression of its target gene, CaGA20ox1, also studied in this work. Conclusions Herein, we clone, characterize and study CaOvate and CaGA20ox1 genes, very likely involved in shaping pepper fruit. The oblong phenotype of the fruits in a plant of cv. "Round", where we observed a significant reduction in the expression levels of CaOvate, resembled the change in shape that takes place by grafting the round-fruited cultivar cv. "Round" onto the long-fruited pepper cultivar cv. "Long". Understanding the role of CaOvate and CaGA20ox1, as well as of other genes like Sun also involved in controlling fruit shape in Solanaceae plants like tomato, pave the way to better understand the molecular mechanisms involved in controlling fruit shape in Solanaceae plants in general, and pepper in particular, as well as the changes in fruit quality induced after grafting and perhaps the ways to mitigate them.