fPoxDB: fungal peroxidase database for comparative genomics

Area of Science:

• Biochemistry and Molecular Biology
• Genomics
• Mycology

Background:

• Peroxidases are oxidoreductases crucial for industrial applications and fungal biology, impacting pollutant degradation, lignin breakdown, and pathogenicity.
• Understanding fungal peroxidases at the genome level requires a dedicated genomics platform.
• The Fungal Peroxidase Database (fPoxDB) was developed to address this need for the peroxidase gene family.

Purpose of the Study:

• To develop and present fPoxDB, a novel genomics platform for the comprehensive study of fungal peroxidases.
• To facilitate genome-level analysis and understanding of the peroxidase gene family in fungi.

Main Methods:

• Developed 24 sequence profiles to identify and classify fungal peroxidases across 331 genomes (216 fungi and Oomycetes).
• Integrated NoxR regulation of NADPH oxidases into the analysis pipeline.
• Utilized sequence profiles and bioinformatics tools to predict gene families and analyze their distribution.

Main Results:

• Identified 6,113 genes encoding 25 peroxidase gene families with distinct taxonomic distributions.
• Lignin, manganese, and versatile peroxidases were found concentrated in rot-causing basidiomycetes, indicating ligninolytic capabilities.
• fPoxDB offers prediction tools, pre-computed bioinformatics results, similarity searches, multiple sequence alignment, and domain analysis.

Conclusions:

• fPoxDB is a specialized genomics platform for fungal peroxidases, enhancing comparative and evolutionary studies.
• The platform's sequence-based predictions and analysis toolkits provide a valuable resource for researchers.
• fPoxDB's user-friendly interface supports in-depth investigation of fungal peroxidases.