PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution

Abstract

BackgroundIn environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylogenetic analyses and the adoption of the phylogenetic species concept.Such analysis requires that the reference sequences are well identified and deposited in public-access databases. However, many entries in the public sequence databases are problematic in terms of quality and reliability and these data require screening to ensure correct phylogenetic interpretation.Methods and Principal FindingsTo facilitate phylogenetic inferences and phylogenetic assignment, we introduce a fungal sequence database. The database PHYMYCO-DB comprises fungal sequences from GenBank that have been filtered to satisfy stringent sequence quality criteria. For the first release, two widely used molecular taxonomic markers were chosen: the nuclear SSU rRNA and EF1-α gene sequences. Following the automatic extraction and filtration, a manual curation is performed to remove problematic sequences while preserving relevant sequences useful for phylogenetic studies. As a result of curation, ∼20% of the automatically filtered sequences have been removed from the database. To demonstrate how PHYMYCO-DB can be employed, we test a set of environmental Chytridiomycota sequences obtained from deep sea samples.ConclusionPHYMYCO-DB offers the tools necessary to: (i) extract high quality fungal sequences for each of the 5 fungal phyla, at all taxonomic levels, (ii) extract already performed alignments, to act as ‘reference alignments’, (iii) launch alignments of personal sequences along with stored data. A total of 9120 SSU rRNA and 672 EF1-α high-quality fungal sequences are now available.The PHYMYCO-DB is accessible through the URL http://phymycodb.genouest.org/.

Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions of Rhizophagus irregularis and Gigaspora margarita is high and isolate‐dependent

“…), PHYMYCO‐DB for fungi in general (SSU, EF‐1α; Mahe et al . ), UNITE for fungi in general (ITS; Abarenkov et al . ), and for LSU, a hand‐curated set of fungal sequences deposited at the Ribosomal Database Project website (Liu et al .…”

Past spatial structure of plant communities determines arbuscular mycorrhizal fungal community assembly

“…The resulting rarefied matrix was used for the statistical analyses (see below). The most abundant sequence within each OTU was selected as the representative sequence for the phylogenetic analyses and taxonomic assignation using Phymyco‐DB, a curated SSU rRNA fungal database (Mahé et al, ). At the last release, this database contained 1,400 non‐redundant Glomeromycota SSU rRNA sequences and hundreds to thousands of sequences from other fungal phyla (see http://phymycodb.genouest.org/).…”

Navigating the labyrinth: a guide to sequence‐based, community ecology of arbuscular mycorrhizal fungi

“…However, the majority of these sequences (67%) are identified only to genus level (http://unite.ut.ee; accessed November 2014). Full‐length SSU rRNA gene sequences are available in the PHYMYCO‐DB database of fungal SSU and EF1‐alpha (Mahé et al ., ). The SILVA database (Quast et al ., ) contains curated and aligned sets of rRNA gene sequences from various organisms, including Glomeromycota, but the numbers of sequences are limited.…”