Diversity of marine-derived fungal cultures exposed by DNA barcodes: the algorithm matters
Andreakis, Nikolaos, Høj, Lone, Kearns, Therese, Hall, Michael R, Ericson, Gavin, Cobb, Rose E., Gordon, Benjamin R., and Evans-Illidge, Elizabeth (2015) Diversity of marine-derived fungal cultures exposed by DNA barcodes: the algorithm matters. PLoS ONE, 10 (8). e0136130..
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Abstract
Marine fungi are an understudied group of eukaryotic microorganisms characterized by unresolved genealogies and unstable classification. Whereas DNA barcoding via the nuclear ribosomal internal transcribed spacer (ITS) provides a robust and rapid tool for fungal species delineation, accurate classification of fungi is often arduous given the large number of partial or unknown barcodes and misidentified isolates deposited in public databases. This situation is perpetuated by a paucity of cultivable fungal strains available for phylogenetic research linked to these data sets. We analyze ITS barcodes produced from a subsample (290) of 1781 cultured isolates of marine-derived fungi in the Bioresources Library located at the Australian Institute of Marine Science (AIMS). Our analysis revealed high levels of under-explored fungal diversity. The majority of isolates were ascomycetes including representatives of the subclasses Eurotiomycetidae, Hypocreomycetidae, Sordariomycetidae, Pleosporomycetidae, Dothideomycetidae, Xylariomycetidae and Saccharomycetidae. The phylum Basidiomycota was represented by isolates affiliated with the genera Tritirachium and Tilletiopsis. BLAST searches revealed 26 unknown OTUs and 50 isolates corresponding to previously uncultured, unidentified fungal clones. This study makes a significant addition to the availability of barcoded, culturable marine-derived fungi for detailed future genomic and physiological studies. We also demonstrate the influence of commonly used alignment algorithms and genetic distance measures on the accuracy and comparability of estimating Operational Taxonomic Units (OTUs) by the automatic barcode gap finder (ABGD) method. Large scale biodiversity screening programs that combine datasets using algorithmic OTU delineation pipelines need to ensure compatible algorithms have been used because the algorithm matters.
| Item ID: | 44368 |
|---|---|
| Item Type: | Article (Research - C1) |
| ISSN: | 1932-6203 |
| Additional Information: | Copyright: © 2015 Andreakis et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
| Funders: | Commonwealth Research and Environment Facilities (CREF) Marine Biodiversity Hub, University of Tasmania, CSIRO Wealth from Oceans Flagship, Geoscience Australia, Australian Institute of Marine Science, Museum Victoria |
| Date Deposited: | 17 Jun 2016 02:56 |
| FoR Codes: | 06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060310 Plant Systematics and Taxonomy @ 100% |
| SEO Codes: | 96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960803 Documentation of Undescribed Flora and Fauna @ 60% 97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 40% |
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