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Open Access Research article

Global analyses of Ceratocystis cacaofunesta mitochondria: from genome to proteome

Alinne Batista Ambrosio1, Leandro Costa do Nascimento1, Bruno V Oliveira1, Paulo José P L Teixeira1, Ricardo A Tiburcio1, Daniela P Toledo Thomazella1, Adriana F P Leme2, Marcelo F Carazzolle13, Ramon O Vidal12, Piotr Mieczkowski4, Lyndel W Meinhardt5, Gonçalo A G Pereira1* and Odalys G Cabrera1

Author Affiliations

1 Laboratório de Genômica e Expressão, Departamento de Genética Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CEP: 13083-970, Campinas, São Paulo, Brasil

2 Laboratório Nacional de Biociências-LNBio, Centro Nacional de Pesquisa em Energia e Materiais, CEP: 13083-970, Campinas, São Paulo, Brasil

3 Centro Nacional de Processamento de Alto Desempenho, Universidade Estadual de Campinas, CEP: 13083-970, Campinas, São Paulo, Brasil

4 High-Throughput Sequencing Facility, University of North Carolina, 2234 Nelson Highway, Chapel Hill, NC, NC 27516, USA

5 Sustainable Perennial Crops Laboratory, USDA/ARS, 10300 Baltimore Ave, Beltsville, MD, 20705, USA

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BMC Genomics 2013, 14:91  doi:10.1186/1471-2164-14-91

Published: 11 February 2013

Abstract

Background

The ascomycete fungus Ceratocystis cacaofunesta is the causal agent of wilt disease in cacao, which results in significant economic losses in the affected producing areas. Despite the economic importance of the Ceratocystis complex of species, no genomic data are available for any of its members. Given that mitochondria play important roles in fungal virulence and the susceptibility/resistance of fungi to fungicides, we performed the first functional analysis of this organelle in Ceratocystis using integrated “omics” approaches.

Results

The C. cacaofunesta mitochondrial genome (mtDNA) consists of a single, 103,147-bp circular molecule, making this the second largest mtDNA among the Sordariomycetes. Bioinformatics analysis revealed the presence of 15 conserved genes and 37 intronic open reading frames in C. cacaofunesta mtDNA. Here, we predicted the mitochondrial proteome (mtProt) of C. cacaofunesta, which is comprised of 1,124 polypeptides - 52 proteins that are mitochondrially encoded and 1,072 that are nuclearly encoded. Transcriptome analysis revealed 33 probable novel genes. Comparisons among the Gene Ontology results of the predicted mtProt of C. cacaofunesta, Neurospora crassa and Saccharomyces cerevisiae revealed no significant differences. Moreover, C. cacaofunesta mitochondria were isolated, and the mtProt was subjected to mass spectrometric analysis. The experimental proteome validated 27% of the predicted mtProt. Our results confirmed the existence of 110 hypothetical proteins and 7 novel proteins of which 83 and 1, respectively, had putative mitochondrial localization.

Conclusions

The present study provides the first partial genomic analysis of a species of the Ceratocystis genus and the first predicted mitochondrial protein inventory of a phytopathogenic fungus. In addition to the known mitochondrial role in pathogenicity, our results demonstrated that the global function analysis of this organelle is similar in pathogenic and non-pathogenic fungi, suggesting that its relevance in the lifestyle of these organisms should be based on a small number of specific proteins and/or with respect to differential gene regulation. In this regard, particular interest should be directed towards mitochondrial proteins with unknown function and the novel protein that might be specific to this species. Further functional characterization of these proteins could enhance our understanding of the role of mitochondria in phytopathogenicity.

Keywords:
Cacao wilt disease; Ceratocystis cacaofunesta; Mitogenomics; Mitochondrial proteome; Fungal virulence