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High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection

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A Correction to this article was published on 17 October 2019

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Abstract

Key message

We provide a transcriptional profile of coffee rust interaction and identified putative up regulated resistant genes

Abstract

Coffee rust disease, caused by the fungus Hemileia vastatrix, is one of the major diseases in coffee throughout the world. The use of resistant cultivars is considered to be the most effective control strategy for this disease. To identify candidate genes related to different mechanism defense in coffee, we present a time-course comparative gene expression profile of Caturra (susceptible) and Híbrido de Timor (HdT, resistant) in response to H. vastatrix race XXXIII infection. The main objectives were to obtain a global overview of transcriptome in both interaction, compatible and incompatible, and, specially, analyze up-regulated HdT specific genes with inducible resistant and defense signaling pathways. Using both Coffea canephora as a reference genome and de novo assembly, we obtained 43,159 transcripts. At early infection events (12 and 24 h after infection), HdT responded to the attack of H. vastatrix with a larger number of up-regulated genes than Caturra, which was related to prehaustorial resistance. The genes found in HdT at early hours were involved in receptor-like kinases, response ion fluxes, production of reactive oxygen species, protein phosphorylation, ethylene biosynthesis and callose deposition. We selected 13 up-regulated HdT-exclusive genes to validate by real-time qPCR, which most of them confirmed their higher expression in HdT than in Caturra at early stage of infection. These genes have the potential to assist the development of new coffee rust control strategies. Collectively, our results provide understanding of expression profiles in coffee—H. vastatrix interaction over a time course in susceptible and resistant coffee plants.

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Change history

  • 17 October 2019

    All the transcriptome sequencing data mentioned in the original article is publicly available at the National Center of Biotechnology Information (NCBI).

  • 17 October 2019

    All the transcriptome sequencing data mentioned in the original article is publicly available at the National Center of Biotechnology Information (NCBI).

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Acknowledgements

We thank Jorge Badel for his helpful suggestions during the preparation of the manuscript. We are also grateful to CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) for the scholarship and Brazilian Coffee Research and Development Consortium (Consórcio Brasileiro de Pesquisa e Desenvolvimento do Café – CBP&D/Café), the Foundation for Research Support of the state of Minas Gerais (FAPEMIG), National Council of Scientific and Technological Development (CNPq), and National Institutes of Science and Technology of Coffee (INCT/Café) for the financial support, DTI (Diretoria de Tecnologia da Informação) of the Universidade Federal de Viçosa and LGE (Laborátorio de Genômica e Expressão) of the Universidade Estadual de Campinas for providing bioinformatics facilities.

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    Authors and Affiliations

    1. Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), BioCafé, Universidade Federal de Viçosa, Campus Universitário, Avenida P.H. Rolfs, s/n, Viçosa, MG, Brazil

      Juan Carlos Florez, Rejane do Livramento Freitas-Lopes, Sávio Siqueira Ferreira, Eunize Maciel Zambolim & Eveline Teixeira Caixeta

    2. Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Distrito de Barão Geraldo, Campinas, SP, 13083-970, Brazil

      Luciana Souto Mofatto & Marcelo Falsarella Carazzolle

    3. Departamento de Fitopatologia, Universidade Federal de Viçosa, Campus Universitário, Avenida P.H. Rolfs, s/n, Viçosa, MG, Brazil

      Laércio Zambolim

    4. Embrapa Café, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Campus Universitário, Avenida P.H. Rolfs, s/n, Viçosa, MG, Brazil

      Eveline Teixeira Caixeta

    Authors
    1. Juan Carlos Florez
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    2. Luciana Souto Mofatto
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    3. Rejane do Livramento Freitas-Lopes
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    4. Sávio Siqueira Ferreira
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    5. Eunize Maciel Zambolim
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    6. Marcelo Falsarella Carazzolle
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    7. Laércio Zambolim
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    8. Eveline Teixeira Caixeta
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    Contributions

    JCF, LCM and MFC analyzed the sequencing data for transcriptome assembly; RDLFL and EMZ developed the biological experiments for the sequencing; JCF and SSF developed the qPCR experiments; Wrote the manuscript draft: JCF, SSF and ETC edited and revised the manuscript; ETC and LZ formulated the idea.

    Corresponding author

    Correspondence to Eveline Teixeira Caixeta.

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    Conflict of interest

    The authors have no conflict of interest to declare.

    Additional information

    Juan Carlos Florez and Luciana Souto Mofatto have contributed equally to this work.

    Electronic supplementary material

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    Supplementary material 1 (DOC 623 KB)

    Supplementary material 2 (DOC 445 KB)

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    Cite this article

    Florez, J.C., Mofatto, L.S., do Livramento Freitas-Lopes, R. et al. High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection. Plant Mol Biol 95, 607–623 (2017). https://doi.org/10.1007/s11103-017-0676-7

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    • DOI: https://doi.org/10.1007/s11103-017-0676-7

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