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      Homeobox Transcription Factors Are Required for Fungal Development and the Suppression of Host Defense Mechanisms in the Colletotrichum scovillei-Pepper Pathosystem

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          ABSTRACT

          Colletotrichum scovillei, an ascomycete phytopathogenic fungus, is the main causal agent of serious yield losses of economic crops worldwide. The fungus causes anthracnose disease on several fruits, including peppers. However, little is known regarding the underlying molecular mechanisms involved in the development of anthracnose caused by this fungus. In an initial step toward understanding the development of anthracnose on pepper fruits, we retrieved 624 transcription factors (TFs) from the whole genome of C. scovillei and comparatively analyzed the entire repertoire of TFs among phytopathogenic fungi. Evolution and proliferation of members of the homeobox-like superfamily, including homeobox (HOX) TFs that regulate the development of eukaryotic organisms, were demonstrated in the genus Colletotrichum. C. scovillei was found to contain 10 HOX TF genes ( CsHOX1 to CsHOX10), which were functionally characterized using deletion mutants of each CsHOX gene. Notably, CsHOX1 was identified as a pathogenicity factor required for the suppression of host defense mechanisms, which represents a new role for HOX TFs in pathogenic fungi. CsHOX2 and CsHOX7 were found to play essential roles in conidiation and appressorium development, respectively, in a stage-specific manner in C. scovillei. Our study provides a molecular basis for understanding the mechanisms associated with the development of anthracnose on fruits caused by C. scovillei, which will aid in the development of novel approaches for disease management.

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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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            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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              MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

              We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                mBio
                mBio
                mbio
                mBio
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2150-7511
                24 August 2021
                Jul-Aug 2021
                24 August 2021
                : 12
                : 4
                : e01620-21
                Affiliations
                [a ] Division of Bio-Resource Sciences, BioHerb Research Institute, and Interdisciplinary Program in Smart Agriculture, Kangwon National Universitygrid.412010.6, , Chuncheon, South Korea
                [b ] Department of Research and Development, Chuncheon Bioindustry Foundation, Chuncheon, South Korea
                [c ] Department of Agricultural Biotechnology, Interdisciplinary Program in Agricultural Genomics, Center for Fungal Genetic Resources, Plant Immunity Research Center, and Research Institute of Agriculture and Life Sciences, Seoul National Universitygrid.31501.36, , Seoul, South Korea
                [d ] Department of Agricultural Life Science, Sunchon National University, Suncheon, South Korea
                Cornell University
                Author information
                https://orcid.org/0000-0003-2462-1250
                https://orcid.org/0000-0002-8249-5283
                https://orcid.org/0000-0002-0827-0844
                Article
                mBio01620-21
                10.1128/mBio.01620-21
                8406175
                34425710
                87d52bd2-42ff-474c-bb50-41e55562928b
                Copyright © 2021 Fu et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 1 June 2021
                : 20 July 2021
                Page count
                supplementary-material: 10, Figures: 7, Tables: 1, Equations: 0, References: 99, Pages: 20, Words: 15113
                Funding
                Funded by: National Research Foundation of Korea (NRF), FundRef https://doi.org/10.13039/501100003725;
                Award ID: NRF-2020R1A2C100550700
                Award Recipient :
                Funded by: Ministry of Agriculture, Food and Rural Affairs (MAFRA), FundRef https://doi.org/10.13039/501100003624;
                Award ID: 918019043HD020
                Award Recipient :
                Categories
                Research Article
                host-microbial-interactions, Host-Microbial Interactions
                Custom metadata
                July/August 2021

                Life sciences
                anthracnose,appressorium development,colletotrichum scovillei,conidiation,host defense,pathogenicity factor

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