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Continental-scale metagenomics, BLAST searches, and herbarium specimens: The Australian Microbiome Initiative and the National Herbarium of Victoria

journal contribution
posted on 2020-12-21, 06:25 authored by N Davoodian, CJ Jackson, Gareth HolmesGareth Holmes, T Lebel
© 2020 Davoodian et al. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America Premise: Motivated to make sensible interpretations of the massive volume of data from the Australian Microbiome Initiative (AusMic), we characterize the soil mycota of Australia. We establish operational taxonomic units (OTUs) from the data and compare these to GenBank and a data set from the National Herbarium of Victoria (MEL), Melbourne, Australia. We also provide visualizations of Agaricomycete diversity, drawn from our analyses of the AusMic sequences and taxonomy. Methods: The AusMic internal transcribed spacer (ITS) data were filtered to create OTUs, which were searched against the National Center for Biotechnology Information Nucleotide database and the MEL database. We further characterized a portion of our OTUs by graphing the counts of the families and orders of Agaricomycetes. We also graphed AusMic species determinations for Australian Agaricomycetes against latitude. Results: Our filtering process generated 192,325 OTUs; for Agaricomycetes, there were 27,730 OTUs. Based on the existing AusMic taxonomy at species level, we inferred the diversity of Australian Agaricomycetes against latitude to be lowest between −20 and −25 decimal degrees. Discussion: BLAST comparisons provided reciprocal insights between the three data sets, including the detection of unusual root-associated species in the AusMic data, insights into mushroom morphology from the MEL data, and points of comparison for the taxonomic determinations between AusMic, GenBank, and MEL. This study provides a tabulation of Australian fungi, different visual snapshots of a subset of those taxa, and a springboard for future studies.


The authors acknowledge support from Bioplatforms Australia through funding from the Australian Government National Collaborative Research Infrastructure Strategy, through use of the Biomes of Australian Soil Environments (BASE) data, and through contributions toward sequencing efforts for the National Herbarium of Victoria (MEL) database. This study was also supported in part by an Australian Biological Resources Study grant (RF217-63).


Publication Date



Applications in Plant Sciences





Article Number



7p. (p. 1-7)


Botanical Society of America



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