Open Access Highly Accessed Research article

Identification of mycoparasitism-related genes against the phytopathogen Sclerotinia sclerotiorum through transcriptome and expression profile analysis in Trichoderma harzianum

Andrei Stecca Steindorff1, Marcelo Henrique Soller Ramada2, Alexandre Siqueira Guedes Coelho3, Robert Neil Gerard Miller1, Georgios Joannis Pappas1, Cirano José Ulhoa4* and Eliane Ferreira Noronha1

Author Affiliations

1 Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Instituto de Ciências Biológicas, CEP 70.910-900 Brasília, DF, Brazil

2 EMBRAPA Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372 CEP 70.770-900 Brasília, DF, Brazil

3 Escola de Agronomia e Engenharia de Alimentos, Universidade Federal de Goiás, Campus Samambaia, P.O. Box 131CEP 74001-970 Goiânia, GO, Brasil

4 Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Goiás, Campus Samambaia, Instituto de Ciências Biológicas, CEP 74.090-900 Goiânia, GO, Brazil

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BMC Genomics 2014, 15:204  doi:10.1186/1471-2164-15-204

Published: 18 March 2014

Abstract

Background

The species of T. harzianum are well known for their biocontrol activity against plant pathogens. However, few studies have been conducted to further our understanding of its role as a biological control agent against S. sclerotiorum, a pathogen involved in several crop diseases around the world. In this study, we have used RNA-seq and quantitative real-time PCR (RT-qPCR) techniques in order to explore changes in T. harzianum gene expression during growth on cell wall of S. sclerotiorum (SSCW) or glucose. RT-qPCR was also used to examine genes potentially involved in biocontrol, during confrontation between T. harzianum and S. sclerotiorum.

Results

Data obtained from six RNA-seq libraries were aligned onto the T. harzianum CBS 226.95 reference genome and compared after annotation using the Blast2GO suite. A total of 297 differentially expressed genes were found in mycelia grown for 12, 24 and 36 h under the two different conditions: supplemented with glucose or SSCW. Functional annotation of these genes identified diverse biological processes and molecular functions required during T. harzianum growth on SSCW or glucose. We identified various genes of biotechnological value encoding proteins with functions such as transporters, hydrolytic activity, adherence, appressorium development and pathogenesis. To validate the expression profile, RT-qPCR was performed using 20 randomly chosen genes. RT-qPCR expression profiles were in complete agreement with the RNA-Seq data for 17 of the genes evaluated. The other three showed differences at one or two growth times. During the confrontation assay, some genes were up-regulated during and after contact, as shown in the presence of SSCW which is commonly used as a model to mimic this interaction.

Conclusions

The present study is the first initiative to use RNA-seq for identification of differentially expressed genes in T. harzianum strain TR274, in response to the phytopathogenic fungus S. sclerotiorum. It provides insights into the mechanisms of gene expression involved in mycoparasitism of T. harzianum against S.sclerotiorum. The RNA-seq data presented will facilitate improvement of the annotation of gene models in the draft T. harzianum genome and provide important information regarding the transcriptome during this interaction.

Keywords:
T. harzianum; S. sclerotiorum; RNA-seq; Gene expression; Mycoparasitism