New smut-specific primers for multilocus genotyping and phylogenetics of Ustilaginaceae

Article


Kruse, Julia, Mishra, Bagdevi, Choi, Young-Joon, Sharma, Rahul and Thines, Marco. 2017. "New smut-specific primers for multilocus genotyping and phylogenetics of Ustilaginaceae." Mycological Progress: international journal of fungal sciences. 16 (9), pp. 917-925. https://doi.org/10.1007/s11557-017-1328-7
Article Title

New smut-specific primers for multilocus genotyping
and phylogenetics of Ustilaginaceae

ERA Journal ID2503
Article CategoryArticle
AuthorsKruse, Julia (Author), Mishra, Bagdevi (Author), Choi, Young-Joon (Author), Sharma, Rahul (Author) and Thines, Marco (Author)
Journal TitleMycological Progress: international journal of fungal sciences
Journal Citation16 (9), pp. 917-925
Number of Pages9
Year2017
PublisherSpringer
Place of PublicationGermany
ISSN1617-416X
1861-8952
Digital Object Identifier (DOI)https://doi.org/10.1007/s11557-017-1328-7
Web Address (URL)https://link.springer.com/article/10.1007/s11557-017-1328-7
Abstract

The Ustilaginomycotina, often collectively referred to as smut fungi, represent one of the three subphyla of the Basidiomycota. Smut fungi predominantly parasitize Angiosperms, are globally distributed, and contain several economically important pathogens. The most species-rich family of the smut fungi is the Ustilaginaceae. To investigate the molecular phylogeny of smut fungi, most studies rely on nrDNA loci, such as ITS and LSU. Protein coding genes, like rpb1, rpb2, TeF1a, Atp6, and ß-tubulin, have been used in some studies. However, because of the huge diversity of smut fungi and the lack o dedicated primers, amplification of these loci has proven difficult for several groups. Thus, it was the aim of the current study to develop primers for new loci for the smut fungi with the focus on the largest family, the Ustilaginaceae. Here, the development and testing of new primers for nine loci based on protein-coding genes is reported (myosin, map, rpl3, tif2, ssc1, ß-tubulin, sdh1, rpl4A and atp2). A list of various primer combinations for the amplification of the new loci is given, with the corresponding PCR conditions and the best combinations for several genera of the Ustilaginaceae and some other Ustilaginomycetes. We hope that the primers presented in this study will be useful in overcoming the limitations of currently-used loci in terms of phylogenetic resolution, especially with respect to resolving species complexes and providing a better resolution of the higher-level phylogenetic relationships of smut fungi.

Keywordsmolecular phylogeny; multilocus; new primers; primer development, protein coding genes, smut fungi
ANZSRC Field of Research 2020310705. Mycology
310299. Bioinformatics and computational biology not elsewhere classified
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Byline AffiliationsSenckenberg Biodiversity and Climate Research Centre, Germany
Goethe University, Germany
Institution of OriginUniversity of Southern Queensland
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