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      Analysis of ginseng rusty root symptoms transcriptome and its pathogenesis directed by reactive oxygen species theory

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          Abstract

          Ginseng rusty root symptoms (GRS) is a primary disease of ginseng, which seriously decreases the yield and quality of ginseng and causes enormous losses to ginseng production. GRS prevention and control is still challenging due to its unclear etiology. In this study, the phloem tissue of healthy Panax ginseng (AG), the nonred tissue of the phloem epidermis around the lesion (BG), and the red lesion site tissue of GRS (CG) were extracted for mRNA transcriptomic analysis; 35,958 differentially expressed genes (DEGs) were identified and were associated with multiple stress resistance pathways, reactive oxygen species (ROS), and iron ion binding. Further study showed that the contents of O 2 •‐, H 2O 2, and malondialdehyde (MDA) were significantly increased in BG and CG tissues. Under anaerobic conditions caused by excessive soil moisture, the overproduction of ROS destroys cell membranes, simultaneously converting Fe 2+ to Fe 3+ and depositing it in the cell wall, which results in GRS, as evidenced by the success of the GRS induction test.

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

          Michael Love, Wolfgang Huber, Simon Anders (2014)
          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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            Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data

            Manfred Grabherr, Brian Haas, Moran Yassour … (2011)
            Massively-parallel cDNA sequencing has opened the way to deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here, we present the Trinity methodology for de novo full-length transcriptome reconstruction, and evaluate it on samples from fission yeast, mouse, and whitefly – an insect whose genome has not yet been sequenced. Trinity fully reconstructs a large fraction of the transcripts present in the data, also reporting alternative splice isoforms and transcripts from recently duplicated genes. In all cases, Trinity performs better than other available de novo transcriptome assembly programs, and its sensitivity is comparable to methods relying on genome alignments. Our approach provides a unified and general solution for transcriptome reconstruction in any sample, especially in the complete absence of a reference genome.
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              Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants.

              Sarvajeet Gill, Narendra Tuteja (2010)
              Various abiotic stresses lead to the overproduction of reactive oxygen species (ROS) in plants which are highly reactive and toxic and cause damage to proteins, lipids, carbohydrates and DNA which ultimately results in oxidative stress. The ROS comprises both free radical (O(2)(-), superoxide radicals; OH, hydroxyl radical; HO(2), perhydroxy radical and RO, alkoxy radicals) and non-radical (molecular) forms (H(2)O(2), hydrogen peroxide and (1)O(2), singlet oxygen). In chloroplasts, photosystem I and II (PSI and PSII) are the major sites for the production of (1)O(2) and O(2)(-). In mitochondria, complex I, ubiquinone and complex III of electron transport chain (ETC) are the major sites for the generation of O(2)(-). The antioxidant defense machinery protects plants against oxidative stress damages. Plants possess very efficient enzymatic (superoxide dismutase, SOD; catalase, CAT; ascorbate peroxidase, APX; glutathione reductase, GR; monodehydroascorbate reductase, MDHAR; dehydroascorbate reductase, DHAR; glutathione peroxidase, GPX; guaicol peroxidase, GOPX and glutathione-S- transferase, GST) and non-enzymatic (ascorbic acid, ASH; glutathione, GSH; phenolic compounds, alkaloids, non-protein amino acids and α-tocopherols) antioxidant defense systems which work in concert to control the cascades of uncontrolled oxidation and protect plant cells from oxidative damage by scavenging of ROS. ROS also influence the expression of a number of genes and therefore control the many processes like growth, cell cycle, programmed cell death (PCD), abiotic stress responses, pathogen defense, systemic signaling and development. In this review, we describe the biochemistry of ROS and their production sites, and ROS scavenging antioxidant defense machinery. Copyright © 2010 Elsevier Masson SAS. All rights reserved.
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                Author and article information

                Contributors
                Xiangcai Meng:
                ORCID: https://orcid.org/0000-0003-1868-4810
                mengxiangcai000@163.com
                Journal
                Journal ID (nlm-ta): Plant Direct
                Journal ID (iso-abbrev): Plant Direct
                Journal ID (doi): 10.1002/(ISSN)2475-4455
                Journal ID (publisher-id): PLD3
                Title: Plant Direct
                Publisher: John Wiley and Sons Inc. (Hoboken )
                ISSN (Electronic): 2475-4455
                Publication date (Electronic): 17 May 2024
                Publication date Collection: May 2024
                Volume: 8
                Issue: 5 ( doiID: 10.1002/pld3.v8.5 )
                Electronic Location Identifier: e586
                Affiliations
                [ 1 ] Country College of Pharmacy Heilongjiang University of Chinese Medicine Harbin China
                Author notes
                [*] [* ] Correspondence

                Xiangcai Meng, Country College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150006, China.

                Email: mengxiangcai000@ 123456163.com

                Author information
                https://orcid.org/0000-0002-3793-4013
                https://orcid.org/0000-0003-1868-4810
                Article
                Publisher ID: PLD3586
                DOI: 10.1002/pld3.586
                PMC ID: 11099884
                SO-VID: 3a5f3088-b79a-4c0e-8d9a-ada6d0c7e079
                Copyright © © 2024 The Authors. Plant Direct published by American Society of Plant Biologists and the Society for Experimental Biology and John Wiley & Sons Ltd.
                License:

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                Date revision received : 07 April 2024
                Date received : 12 December 2023
                Date accepted : 12 April 2024
                Page count
                Figures: 9, Tables: 3, Pages: 15, Words: 9200
                Funding
                Funded by: National Natural Science Foundation of China
                Award ID: 20012210001
                Funded by: University Nursing Program for Young Scholars with Creative Talents in Heilongjiang Province , doi 10.13039/501100012676;
                Award ID: UNPYSCT‐2020224
                Categories
                Subject: Research Article
                Subject: Research Articles
                Custom metadata
                source-schema-version-number 2.0
                cover-date May 2024
                details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_JATSPMC version:6.4.3 mode:remove_FC converted:17.05.2024

                Keywords: ginseng rusty root symptoms,gsea, fe3+ ,ros,transcriptomics
                Data availability:
                Keywords: ginseng rusty root symptoms, gsea, fe3+ , ros, transcriptomics

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