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      Plant extracellular self-DNA inhibits growth and induces immunity via the jasmonate signaling pathway

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          Abstract

          Plants have evolved sophisticated mechanisms to detect various forms of danger. Damage-associated molecular patterns (DAMPs) are endogenous danger molecules that are released from damaged cells and activate the innate immunity. Recent evidence suggests that plant extracellular self-DNA (esDNA) can serve as a DAMP molecule. However, the mechanisms by which esDNA functions are largely unknown. In this study, we confirmed that esDNA inhibits root growth and triggers reactive oxygen species (ROS) production in a concentration- and species-specific manner in Arabidopsis ( Arabidopsis thaliana) and tomato ( Solanum lycopersicum L.). Furthermore, by combining RNA sequencing, hormone measurement, and genetic analysis, we found that esDNA-mediated growth inhibition and ROS production are achieved through the jasmonic acid (JA) signaling pathway. Specifically, esDNA induces JA production and the expression of JA-responsive genes. The esDNA-mediated growth inhibition, ROS production, and gene expression are impaired in the JA-related mutants. Finally, we found that the JA signaling pathway is required for the esDNA-elicited resistance against the pathogens Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000. This finding highlights the importance of JA signaling in esDNA-mediated biological effects, thereby providing insight into how esDNA functions as a DAMP.

          Abstract

          RNA-sequencing, hormone measurement, and genetic analysis show that extracellular self-DNA-mediated growth inhibition and immunity induction are achieved through the jasmonic acid signaling pathway.

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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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            Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

            In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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              Fast gapped-read alignment with Bowtie 2.

              As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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                Author and article information

                Contributors
                Journal
                Plant Physiol
                Plant Physiol
                plphys
                Plant Physiology
                Oxford University Press (US )
                0032-0889
                1532-2548
                July 2023
                01 April 2023
                01 April 2023
                : 192
                : 3
                : 2475-2491
                Affiliations
                Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University , Harbin 150030, China
                Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University , Harbin 150030, China
                College of Advanced Agriculture and Ecological Environment, Heilongjiang University , Harbin 150080, China
                Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University , Harbin 150030, China
                Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University , Harbin 150030, China
                Department of Agricultural Sciences, University of Naples Federico II , Portici 80055, Italy
                Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University , Beijing 100193, China
                Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University , Harbin 150030, China
                Author notes
                Author for correspondence: duminmin@ 123456cau.edu.cn (M.D.), wufz@ 123456neau.edu.cn (F.W.)

                The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors ( https://academic.oup.com/plphys/pages/General-Instructions) is Fengzhi Wu ( wufz@ 123456neau.edu.cn ).

                Conflict of interest statement. The authors have no conflict of interest.

                Author information
                https://orcid.org/0000-0003-2681-7177
                https://orcid.org/0000-0003-1425-8216
                https://orcid.org/0009-0006-6563-636X
                https://orcid.org/0000-0002-2545-9614
                https://orcid.org/0000-0002-1132-2625
                https://orcid.org/0000-0003-2858-8582
                https://orcid.org/0000-0003-3938-0488
                Article
                kiad195
                10.1093/plphys/kiad195
                10315318
                37002819
                b35bd2a9-c8de-46cd-8498-e5bdd5373170
                © The Author(s) 2023. Published by Oxford University Press on behalf of American Society of Plant Biologists.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence ( https://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

                History
                : 25 October 2022
                : 01 March 2023
                : 05 April 2023
                Page count
                Pages: 17
                Funding
                Funded by: National Natural Science Foundation of China, DOI 10.13039/501100001809;
                Award ID: 32072655
                Award ID: 32272792
                Funded by: China Agriculture Research System;
                Award ID: CARS-23-B-10
                Categories
                Research Article
                AcademicSubjects/SCI01270
                AcademicSubjects/SCI01280
                AcademicSubjects/SCI02286
                AcademicSubjects/SCI02287
                AcademicSubjects/SCI02288

                Plant science & Botany
                Plant science & Botany

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