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      A Complex Gene Network Mediated by Ethylene Signal Transduction TFs Defines the Flower Induction and Differentiation in Olea europaea L.

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          Abstract

          The olive tree ( Olea europaea L.) is a typical Mediterranean crop, important for olive and oil production. The high tendency to bear fruits in an uneven manner, defined as irregular or alternate bearing, results in a significant economic impact for the high losses in olives and oil production. Buds from heavy loaded (‘ON’) and unloaded (‘OFF’) branches of a unique olive tree were collected in July and the next March to compare the transcriptomic profiles and get deep insight into the molecular mechanisms regulating floral induction and differentiation. A wide set of DEGs related to ethylene TFs and to hormonal, sugar, and phenylpropanoid pathways was identified in buds collected from ‘OFF’ branches. These genes could directly and indirectly modulate different pathways, suggesting their key role during the lateral bud transition to flowering stage. Interestingly, several genes related to the flowering process appeared as over-expressed in buds from March ‘OFF’ branches and they could address the buds towards flower differentiation. By this approach, interesting candidate genes related to the switch from vegetative to reproductive stages were detected and analyzed. The functional analysis of these genes will provide tools for developing breeding programs to obtain olive trees characterized by more constant productivity over the years.

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            Trimmomatic: a flexible trimmer for Illumina sequence data

            Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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              Cytoscape: a software environment for integrated models of biomolecular interaction networks.

              Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                Genes (Basel)
                Genes (Basel)
                genes
                Genes
                MDPI
                2073-4425
                09 April 2021
                April 2021
                : 12
                : 4
                : 545
                Affiliations
                [1 ]Research Centre for Olive, Citrus and Tree Fruit, Council for Agricultural Research and Economics (CREA), 87036 Rende, Italy; amelia.salimonti@ 123456crea.gov.it (A.S.); ivanoforgione@ 123456gmail.com (I.F.); tizianasirangelo@ 123456gmail.com (T.M.S.)
                [2 ]Department of Agricultural, Food and Forest Sciences, University of Palermo, 90133 Palermo, Italy; gugpuccio@ 123456gmail.com
                [3 ]Department of Agriculture, University Mediterranea of Reggio Calabria, 89124 Reggio Calabria, Italy; antonio.mauceri87@ 123456gmail.com (A.M.); francesco.sunseri@ 123456unirc.it (F.S.)
                [4 ]Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), 90129 Palermo, Italy; francesco.mercati@ 123456ibbr.cnr.it
                Author notes
                Author information
                https://orcid.org/0000-0002-2452-5309
                https://orcid.org/0000-0002-3282-1992
                https://orcid.org/0000-0003-1356-2881
                https://orcid.org/0000-0001-5201-5413
                https://orcid.org/0000-0002-0393-7099
                Article
                genes-12-00545
                10.3390/genes12040545
                8070190
                30279f77-e212-4ed2-842f-fe350df5188e
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( https://creativecommons.org/licenses/by/4.0/).

                History
                : 15 March 2021
                : 07 April 2021
                Categories
                Article

                olea europaea,flowering,alternate bearing,ngs,lateral bud,transcriptome profiling

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