Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB)

Abstract

Fungi have crucial roles in ecosystems, and are important associates for many organisms. They are adapted to a wide variety of habitats, however their global distribution and diversity remains poorly documented. The exponential growth of DNA barcode information retrieved from the environment is assisting considerably the traditional ways for unraveling fungal diversity and detection. The raw DNA data in association to environmental descriptors of metabarcoding studies are made available in public sequence read archives. While this is potentially a valuable source of information for the investigation of Fungi across diverse environmental conditions, the annotation used to describe environment is heterogenous. Moreover, a uniform processing pipeline still needs to be applied to the available raw DNA data. Hence, a comprehensive framework to analyses these data in a large context is still lacking. We introduce the MycoDiversity DataBase, a database which includes public fungal metabarcoding data of environmental samples for the study of biodiversity patterns of Fungi. The framework we propose will contribute to our understanding of fungal biodiversity and aims to become a valuable source for large-scale analyses of patterns in space and time, in addition to assisting evolutionary and ecological research on Fungi.

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

“…Interestingly, for the specific taxonomic classification of fungal taxa affiliated to the phylum Glomeromycota, the MaarjAM database [ 219 ] was created in 2010. This database associates information about geography, habitat and climate to Glomeromycota sequences, which cluster in “Virtual Taxa”, a proxy for fungal species [ 220 ]. The MaarjAM database is manually curated, and its last update occurred on 5 June 2019.…”

DNA-based occurrence dataset on peatland fungal communities studied by metabarcoding in north-western Siberia

“…The standardised approach for data storage of metabarcoding results in general and fungal metabarcoding specifically has been developed in recent years ( Nilsson et al 2018a , Nilsson et al 2018b , Martorelli et al 2020 , Tedersoo et al 2022 ). Fungal molecular taxonomic units are being accumulated and processed on a fungi-specific web-based platform UNITE and integrated with the taxonomic backbone of the Global Biodiversity Information Facility ( Nilsson et al 2018b ).…”