Phymyco-DB

Phymyco-DB curates high-quality nuclear SSU rRNA and EF1-α sequences to support fungal molecular taxonomy and phylogenetic analyses.

Key Features:

• Curated Sequence Quality: Sequences undergo automatic filtering followed by manual curation, with approximately 20% of automatically filtered sequences removed to eliminate problematic entries while preserving phylogenetically informative records.
• Focus on Molecular Taxonomic Markers: Targets nuclear SSU rRNA and EF1-α gene sequences that are widely used for fungal taxonomy and phylogenetic inference.
• Extensive Sequence Repository: Contains 9,120 high-quality SSU rRNA sequences and 672 EF1-α sequences spanning all five fungal phyla and multiple taxonomic levels.
• Functional Tools: Provides extraction of high-quality fungal sequences across phyla, access to pre-performed "reference alignments", and the capability to align personal sequence data with the stored sequences for comparative analyses.
• Application Demonstration: Has been applied to assign environmental Chytridiomycota sequences obtained from deep-sea samples, illustrating its use in environmental phylogenetic assignments.

Scientific Applications:

• Environmental sequencing: Supports accurate fungal identification and classification in environmental sequencing studies.
• Phylogenetic species concept: Enables adoption of the phylogenetic species concept through curated reference sequences and alignments for species delimitation.
• Complex and deep-sea ecosystems: Facilitates phylogenetic analyses in complex environments such as deep-sea ecosystems where traditional taxonomic methods may be insufficient.

Methodology:

Initial automatic extraction and filtration of sequences from GenBank based on predefined quality criteria followed by manual expert curation to remove problematic entries while retaining phylogenetically informative sequences.