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      Candidatus Phytoplasma solani’ interferes with the distribution and uptake of iron in tomato

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          Abstract

          Background

          Candidatus Phytoplasma solani’ is endemic in Europe and infects a wide range of weeds and cultivated plants. Phytoplasmas are prokaryotic plant pathogens that colonize the sieve elements of their host plant, causing severe alterations in phloem function and impairment of assimilate translocation. Typical symptoms of infected plants include yellowing of leaves or shoots, leaf curling, and general stunting, but the molecular mechanisms underlying most of the reported changes remain largely enigmatic. To infer a possible involvement of Fe in the host-phytoplasma interaction, we investigated the effects of ‘ Candidatus Phytoplasma solani’ infection on tomato plants ( Solanum lycopersicum cv. Micro-Tom) grown under different Fe regimes.

          Results

          Both phytoplasma infection and Fe starvation led to the development of chlorotic leaves and altered thylakoid organization. In infected plants, Fe accumulated in phloem tissue, altering the local distribution of Fe. In infected plants, Fe starvation had additive effects on chlorophyll content and leaf chlorosis, suggesting that the two conditions affected the phenotypic readout via separate routes. To gain insights into the transcriptional response to phytoplasma infection, or Fe deficiency, transcriptome profiling was performed on midrib-enriched leaves. RNA-seq analysis revealed that both stress conditions altered the expression of a large (> 800) subset of common genes involved in photosynthetic light reactions, porphyrin / chlorophyll metabolism, and in flowering control. In Fe-deficient plants, phytoplasma infection perturbed the Fe deficiency response in roots, possibly by interference with the synthesis or transport of a promotive signal transmitted from the leaves to the roots.

          Conclusions

          Candidatus Phytoplasma solani’ infection changes the Fe distribution in tomato leaves, affects the photosynthetic machinery and perturbs the orchestration of root-mediated transport processes by compromising shoot-to-root communication.

          Electronic supplementary material

          The online version of this article (10.1186/s12864-019-6062-x) contains supplementary material, which is available to authorized users.

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          Most cited references99

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          The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

          Summary: Experimental techniques that survey an entire genome demand flexible, highly interactive visualization tools that can display new data alongside foundation datasets, such as reference gene annotations. The Integrated Genome Browser (IGB) aims to meet this need. IGB is an open source, desktop graphical display tool implemented in Java that supports real-time zooming and panning through a genome; layout of genomic features and datasets in moveable, adjustable tiers; incremental or genome-scale data loading from remote web servers or local files; and dynamic manipulation of quantitative data via genome graphs. Availability: The application and source code are available from http://igb.bioviz.org and http://genoviz.sourceforge.net. Contact: aloraine@uncc.edu
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            A ferric-chelate reductase for iron uptake from soils.

            Iron deficiency afflicts more than three billion people worldwide, and plants are the principal source of iron in most diets. Low availability of iron often limits plant growth because iron forms insoluble ferric oxides, leaving only a small, organically complexed fraction in soil solutions. The enzyme ferric-chelate reductase is required for most plants to acquire soluble iron. Here we report the isolation of the FRO2 gene, which is expressed in iron-deficient roots of Arabidopsis. FRO2 belongs to a superfamily of flavocytochromes that transport electrons across membranes. It possesses intramembranous binding sites for haem and cytoplasmic binding sites for nucleotide cofactors that donate and transfer electrons. We show that FRO2 is allelic to the frd1 mutations that impair the activity of ferric-chelate reductase. There is a nonsense mutation within the first exon of FRO2 in frd1-1 and a missense mutation within FRO2 in frd1-3. Introduction of functional FRO2 complements the frd1-1 phenotype in transgenic plants. The isolation of FRO2 has implications for the generation of crops with improved nutritional quality and increased growth in iron-deficient soils.
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              Processing of gene expression data generated by quantitative real-time RT-PCR.

              Quantitative real-time PCR represents a highly sensitive and powerful technique for the quantitation of nucleic acids. It has a tremendous potential for the high-throughput analysis of gene expression in research and routine diagnostics. However, the major hurdle is not the practical performance of the experiments themselves but rather the efficient evaluation and the mathematical and statistical analysis of the enormous amount of data gained by this technology, as these functions are not included in the software provided by the manufacturers of the detection systems. In this work, we focus on the mathematical evaluation and analysis of the data generated by quantitative real-time PCR, the calculation of the final results, the propagation of experimental variation of the measured values to the final results, and the statistical analysis. We developed a Microsoft Excel-based software application coded in Visual Basic for Applications, called Q-Gene, which addresses these points. Q-Gene manages and expedites the planning, performance, and evaluation of quantitative real-time PCR experiments, as well as the mathematical and statistical analysis, storage, and graphical presentation of the data. The Q-Gene software application is a tool to cope with complex quantitative real-time PCR experiments at a high-throughput scale and considerably expedites and rationalizes the experimental setup, data analysis, and data management while ensuring highest reproducibility.
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                Author and article information

                Contributors
                sara.buoso@uniud.it
                laura.pagliari@uniud.it
                rita.musetti@uniud.it
                marta.martini@uniud.it
                fabio.marroni@uniud.it
                wosh@gate.sinica.edu.tw
                simonetta.santi@uniud.it
                Journal
                BMC Genomics
                BMC Genomics
                BMC Genomics
                BioMed Central (London )
                1471-2164
                10 September 2019
                10 September 2019
                2019
                : 20
                : 703
                Affiliations
                [1 ]ISNI 0000 0001 2113 062X, GRID grid.5390.f, Department of Agricultural, Food, Environmental and Animal Sciences, , University of Udine, ; Via delle Scienze 206, 33100 Udine, Italy
                [2 ]GRID grid.452691.d, IGA Technology Services, ; Via Jacopo Linussio, 51, 33100 Udine, Italy
                [3 ]ISNI 0000 0001 2287 1366, GRID grid.28665.3f, Institute of Plant and Microbial Biology, Academia Sinica, ; 11529 Taipei, Taiwan
                [4 ]ISNI 0000 0004 0532 3749, GRID grid.260542.7, Biotechnology Center, , National Chung Hsing University, ; 40227 Taichung, Taiwan
                Author information
                http://orcid.org/0000-0003-2967-7579
                Article
                6062
                10.1186/s12864-019-6062-x
                6734453
                31500568
                bc892918-b6e0-4097-803f-311ac03caf03
                © The Author(s). 2019

                Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 13 June 2019
                : 26 August 2019
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2019

                Genetics
                iron deficiency,leaves,porphyrin,chlorophyll,carotenoids metabolism,phytoplasma,phloem,roots,tomato,ngs
                Genetics
                iron deficiency, leaves, porphyrin, chlorophyll, carotenoids metabolism, phytoplasma, phloem, roots, tomato, ngs

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