Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genes
Authors:Maria Paula Rueda-Mejia1, Lukas Nägeli1, Stefanie Lutz2, Richard D. Hayes3, Adithi R. Varadarajan2, Igor V. Grigoriev3,4, Christian H. Ahrens2,5 and Florian M. Freimoser1
1 Agroscope, Research Division Plant Protection, Müller-Thurgau-Strasse 29, 8820 Wädenswil, Switzerland.
2 Agroscope, Competence Division Method Development and Analytics, Müller-Thurgau-Strasse 29, 8820, Wädenswil, Switzerland.
3 U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California 94720, USA.
4 Department of Plant and Microbial Biology, University of California Berkeley, Koshland Hall, Berkeley, CA, USA.
5 SIB, Swiss Institute of Bioinformatics, Wädenswil, Switzerland.
Keywords:
antagonism, Aureobasidium, biocontrol, Fusarium, genome, proteome, secretome, transcriptome, yeast.
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Conflict of interest statement:
The authors declare no conflict of interest.
Please cite this article as:
Maria Paula Rueda-Mejia, Lukas Nägeli, Stefanie Lutz, Richard D. Hayes, Adithi R. Varadarajan, Igor V. Grigoriev, Christian H. Ahrens and Florian M. Freimoser (2021). Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genes. Microbial Cell 8(8): 184-202. doi: 10.15698/mic2021.08.757
© 2021 Rueda-Mejia et al. This is an open-access article released under the terms of the Creative Commons Attribution (CC BY) license, which allows the unrestricted use, distribution, and reproduc-tion in any medium, provided the original author and source are acknowledged.
Abstract:
Aureobasidium pullulans is an extremotolerant, cosmopolitan yeast-like fungus that successfully colonises vastly different ecological niches. The species is widely used in biotechnology and successfully applied as a commercial biocontrol agent against postharvest diseases and fireblight. However, the exact mechanisms that are responsible for its antagonistic activity against diverse plant pathogens are not known at the molecular level. Thus, it is difficult to optimise and improve the biocontrol applications of this species. As a foundation for elucidating biocontrol mechanisms, we have de novo assembled a high-quality reference genome of a strongly antagonistic A. pullulans strain, performed dual RNA-seq experiments, and analysed proteins secreted during the interaction with the plant pathogen Fusarium oxysporum. Based on the genome annotation, potential biocontrol genes were predicted to encode secreted hydrolases or to be part of secondary metabolite clusters (e.g., NRPS-like, NRPS, T1PKS, terpene, and β-lactone clusters). Transcriptome and secretome analyses defined a subset of 79 A. pullulans genes (among the 10,925 annotated genes) that were transcriptionally upregulated or exclusively detected at the protein level during the competition with F. oxysporum. These potential biocontrol genes comprised predicted secreted hydrolases such as glycosylases, esterases, and proteases, as well as genes encoding enzymes, which are predicted to be involved in the synthesis of secondary metabolites. This study highlights the value of a sequential approach starting with genome mining and consecutive transcriptome and secretome analyses in order to identify a limited number of potential target genes for detailed, functional analyses.
doi: 10.15698/mic2021.08.757
Volume 8, pp. 184 to 202, published 08/06/2021.