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      Bacillus velezensis CLA178-Induced Systemic Resistance of Rosa multiflora Against Crown Gall Disease

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          Abstract

          Plant growth-promoting rhizobacteria (PGPRs) are able to activate induced systemic resistance (ISR) of the plants against phytopathogens. However, whether and how ISR can be activated by PGPRs in plants of the Rosa genus is unclear. The effects of PGPR Bacillus velezensis CLA178 and the pathogen Agrobacterium tumefaciens C58 on the growth, plant defense-related genes, hormones, and reactive oxygen species (ROS) in the rose plants were compared. Pretreatment with CLA178 significantly reduced crown gall tumor biomass and relieved the negative effects of the C58 pathogen on plant biomass, chlorophyll content, and photosynthesis of roses. Pretreatment of the roots with CLA178 activated ISR and significantly reduced disease severity. Pretreatment with CLA178 enhanced plant defense response to C58, including the accumulation of ROS, antioxidants, and plant hormones. Moreover, pretreatment with CLA178 enhanced C58-dependent induction of the expression of the genes related to the salicylic acid (SA) or ethylene (ET) signaling pathways. This result suggested that SA- and ET-signaling may participate in CLA178-mediated ISR in roses. Additional experiments in the Arabidopsis mutants showed that CLA178 triggered ISR against C58 in the pad4 and jar1 mutants and not in the etr1 and npr1 mutants. The ISR phenotypes of the Arabidopsis mutants indicated that CLA178-mediated ISR is dependent on the ET-signaling pathway in an NPR1-dependent manner. Overall, this study provides useful information to expand the application of PGPRs to protect the plants of the Rosa genus from phytopathogens.

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

          Kenneth Livak, Thomas D. Schmittgen (2001)
          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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            SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

            Anton Bankevich, Sergey Nurk, Dmitry Antipov … (2012)
            The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
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              Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

              Bruce Walker, Thomas Abeel, Terrance Shea … (2014)
              Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive numbers of genomes calls for fully automated methods to produce high-quality assemblies and variant calls. We introduce Pilon, a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions. Pilon works with many types of sequence data, but is particularly strong when supplied with paired end data from two Illumina libraries with small e.g., 180 bp and large e.g., 3–5 Kb inserts. Pilon significantly improves draft genome assemblies by correcting bases, fixing mis-assemblies and filling gaps. For both haploid and diploid genomes, Pilon produces more contiguous genomes with fewer errors, enabling identification of more biologically relevant genes. Furthermore, Pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions. Pilon is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains. Pilon is freely available as open source software.
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                Author and article information

                Contributors
                Journal
                Journal ID (nlm-ta): Front Microbiol
                Journal ID (iso-abbrev): Front Microbiol
                Journal ID (publisher-id): Front. Microbiol.
                Title: Frontiers in Microbiology
                Publisher: Frontiers Media S.A.
                ISSN (Electronic): 1664-302X
                Publication date (Electronic): 22 October 2020
                Publication date Collection: 2020
                Volume: 11
                Electronic Location Identifier: 587667
                Affiliations
                [1] 1Experimental Center of Forestry in North China, Chinese Academy of Forestry , Beijing, China
                [2] 2Key Laboratory of Agricultural Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences , Beijing, China
                [3] 3Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University , Nanjing, China
                Author notes

                Edited by: Christos Zamioudis, Democritus University of Thrace, Greece

                Reviewed by: Yong-Soon Park, Chungbuk National University, South Korea; Adriana Fabra, National University of Río Cuarto, Argentina

                *Correspondence: Yunpeng Liu, liuyunpeng@ 123456caas.cn

                This article was submitted to Microbe and Virus Interactions with Plants, a section of the journal Frontiers in Microbiology

                Article
                DOI: 10.3389/fmicb.2020.587667
                PMC ID: 7642876
                PubMed ID: 33193244
                SO-VID: 5f775d83-2f3a-495a-aa3a-2b7a921f65b5
                Copyright © Copyright © 2020 Chen, Wang, Ma, Bian, Liu, Xu, Zhang, Shao and Liu.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                Date received : 27 July 2020
                Date accepted : 28 September 2020
                Page count
                Figures: 7, Tables: 0, Equations: 0, References: 67, Pages: 12, Words: 0
                Funding
                Funded by: National Natural Science Foundation of China 10.13039/501100001809
                Award ID: 31601826
                Funded by: Fundamental Research Funds for the Central Universities 10.13039/501100012226
                Categories
                Subject: Microbiology
                Subject: Original Research

                ScienceOpen disciplines: Microbiology & Virology
                Keywords: induced systemic resistance,plant growth-promoting rhizobacteria,rose,crown gall disease,hormone
                Data availability:
                ScienceOpen disciplines: Microbiology & Virology
                Keywords: induced systemic resistance, plant growth-promoting rhizobacteria, rose, crown gall disease, hormone

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