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New smut-specific primers for the ITS barcoding of Ustilaginomycotina

Abstract

The smut fungi (Ustilaginomycotina) are a highly diverse group, containing about 115 genera and 1700 species, most of which are biotrophic plant pathogens. As for other fungal groups, the ITS rDNA region is widely used to determine smut fungi at species level due to its high discriminatory power and for phylogenetic reconstructions within genera. So far, two primer sets, ITS1/ITS4 and M-ITS1/ITS4, were generally used to amplify smut fungi, but these often co-amplify host plants or contaminant fungi and do not yield satisfactory amplification for a variety of smut fungi. In the present study, based on a selection of genera that include more than 90% of the species of smut fungi (more than half of the genera of smut fungi), three new primers, smITS-F, smITS-R1 and smITS-R2, situated in the SSU or LSU region, were designed to avoid the amplification of host plants and to extend the coverage of PCR amplification for as many smut genera as possible.

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Acknowledgements

This study was funded by the LOEWE research funding programme in the framework of the Cluster for Integrative Fungal Research (IPF). We are grateful to the curators of PDD, BPI, VPRI, HBG, WSP, M, GLM and TUB (mostly HUV samples) for allowing the investigation of specimens in their keeping. We thank the private collectors, Udo and Heidrun Richter and Volker Kummer, for allowing us to include some of their collections in this study.

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Correspondence to Marco Thines.

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Section Editor: Dominik Begerow

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Kruse, J., Choi, YJ. & Thines, M. New smut-specific primers for the ITS barcoding of Ustilaginomycotina. Mycol Progress 16, 213–221 (2017). https://doi.org/10.1007/s11557-016-1265-x

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  • DOI: https://doi.org/10.1007/s11557-016-1265-x

Keywords

  • Barcoding locus
  • Basidiomycota
  • Diversity
  • DNA-extraction methods
  • Smut-specific primers