fPoxDB: fungal peroxidase database for comparative genomics
- Equal contributors
1 Fungal Bioinformatics Laboratory and Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
2 Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea
3 Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
4 Department of Agricultural Sciences, University of Helsinki, 00014 Helsinki, Finland
5 Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
BMC Microbiology 2014, 14:117 doi:10.1186/1471-2180-14-117Published: 8 May 2014
Peroxidases are a group of oxidoreductases which mediate electron transfer from hydrogen peroxide (H2O2) and organic peroxide to various electron acceptors. They possess a broad spectrum of impact on industry and fungal biology. There are numerous industrial applications using peroxidases, such as to catalyse highly reactive pollutants and to breakdown lignin for recycling of carbon sources. Moreover, genes encoding peroxidases play important roles in fungal pathogenicity in both humans and plants. For better understanding of fungal peroxidases at the genome-level, a novel genomics platform is required. To this end, Fungal Peroxidase Database (fPoxDB; http://peroxidase.riceblast.snu.ac.kr/ webcite) has been developed to provide such a genomics platform for this important gene family.
In order to identify and classify fungal peroxidases, 24 sequence profiles were built and applied on 331 genomes including 216 from fungi and Oomycetes. In addition, NoxR, which is known to regulate NADPH oxidases (NoxA and NoxB) in fungi, was also added to the pipeline. Collectively, 6,113 genes were predicted to encode 25 gene families, presenting well-separated distribution along the taxonomy. For instance, the genes encoding lignin peroxidase, manganese peroxidase, and versatile peroxidase were concentrated in the rot-causing basidiomycetes, reflecting their ligninolytic capability. As a genomics platform, fPoxDB provides diverse analysis resources, such as gene family predictions based on fungal sequence profiles, pre-computed results of eight bioinformatics programs, similarity search tools, a multiple sequence alignment tool, domain analysis functions, and taxonomic distribution summary, some of which are not available in the previously developed peroxidase resource. In addition, fPoxDB is interconnected with other family web systems, providing extended analysis opportunities.
fPoxDB is a fungi-oriented genomics platform for peroxidases. The sequence-based prediction and diverse analysis toolkits with easy-to-follow web interface offer a useful workbench to study comparative and evolutionary genomics of peroxidases in fungi.