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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 21.12.2020, 06:25 by N Davoodian, CJ Jackson, Gareth 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.

Funding

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).

History

Publication Date

30/09/2020

Journal

Applications in Plant Sciences

Volume

8

Issue

9

Article Number

e11392

Pagination

7p. (p. 1-7)

Publisher

Botanical Society of America

ISSN

2168-0450

Rights Statement

The Author reserves all moral rights over the deposited text and must be credited if any re-use occurs. Documents deposited in OPAL are the Open Access versions of outputs published elsewhere. Changes resulting from the publishing process may therefore not be reflected in this document. The final published version may be obtained via the publisher’s DOI. Please note that additional copyright and access restrictions may apply to the published version.

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