A Singapore-centric Fungal Dataset of 518 Cultivated Strains with Visual Phenotypes and Taxonomic Identity
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Abstract
The fungal kingdom represents a greatly untapped resource to produce a wide range of bioactive secondary metabolites, including antibiotics, anticancer agents, industrially significant dyes and enzymes. To-date, it is estimated only less than 5% of all fungi have been characterised, a deficit that is especially pronounced in tropical regions like Singapore, where fungal diversity remains underexplored compared to northern hemisphere counterparts. This underlines the urgency and importance of our research which motivated the creation of our curated dataset, aiming to address this gap and contribute to understanding the broader ecosystem. We developed a generalisable cultivation workflow that enables systematic strain preparation, supports high-resolution imaging, and yields sufficient fungal biomass amenable for genomic analyses. This resulted in a diverse collection of 518 phylogenetically and ecologically varied fungal strains from both terrestrial and marine environments in biodiverse Singapore. The curated dataset from this project captures both taxonomic identity and colony-level morphological traits serving as a foundation for visual phenotype to taxonomy mapping through the integration of computer vision.
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. Users can identify fungal clusters of interest based on its phenotypic characteristics and rapidly relate its underlying genomics, creating a systematic and targeted exploration strategy for downstream functional or genomic studies.
How would users access any of the data here, and is it possible to obtain these strains?
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I tried to look at this repo on github, but it does not appear to exist. Please make sure that it is public.
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we performed multiple sequence alignment (MSA) on the 518 fungal 18S rRNA sequences
Have you deposited these sequences publicly anywhere? It would be especially helpful if they were directly paired/associated with the culture collection they came from. I couldn't easily find a way to explore the NPL collection, but if such a site exists, it would be good to link it here
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Fungal DNA was extracted from biomass and sequenced on the Illumina NovaSeq 6000 platform.
I think it is important to provide more detail here. Extraction of fungal DNA from environmental isolates is not trivial, especially for a large collection. What method did you use? Also, I assume you only sequenced 18S amplicons, but you don't provide any details here on the methods you used (primers used, PCR method, sequencing read length, where was the sequencing done, etc.). Was the sequencing done by a commercial service? Without these details, it is impossible for anyone to replicate what you have done.
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the phylogenetic tree offers a comprehensive overview of Singapore’s fungal diversity.
Are there any existing amplicon/ shotgun metagenomic surveys of Singapore's fungal biodiversity across different environments? It would be interesting to compare the genera you recovered to know how representative this culture collection is of the full biodiversity present in these environments.
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omprises 518 diverse fungal strains,
Could you clarify why you focused on these 518 strains, out the 857 that you were able to revive and get DNA from? Were you trying to select unique morphologies?
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