title: Identification of mycoparasitism-related genes against the phytopathogen Sclerotinia sclerotiorum through transcriptome and expression profile analysis in Trichoderma harzianum.
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.
authors.forename: Andrei Stecca
authors.initials: AS
authors.lastname: Steindorff
authors.forename: Marcelo Henrique Soller
authors.initials: MH
authors.lastname: Ramada
authors.forename: Alexandre Siqueira Guedes
authors.initials: AS
authors.lastname: Coelho
authors.forename: Robert Neil Gerard
authors.initials: RN
authors.lastname: Miller
authors.forename: Georgios Joannis
authors.initials: GJ
authors.lastname: Pappas
authors.affiliation: Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Goiás, Campus Samambaia, Instituto de Ciências Biológicas, CEP 74,090-900 Goiânia, GO, Brazil. ulhoa@icb.ufg.br.
authors.forename: Cirano José
authors.initials: CJ
authors.lastname: Ulhoa
authors.forename: Eliane Ferreira
authors.initials: EF
authors.lastname: Noronha
mesh_terms: D001203:Ascomycota / Q000235:genetics*; D002874:Chromosome Mapping; D016000:Cluster Analysis; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D015723:Gene Library; D005800:Genes, Fungal; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D014242:Trichoderma / Q000235:genetics* / Q000254:growth & development
chemical_list: D005656:Fungal Proteins