Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genes.

Maria Paula Rueda-Mejia,Lukas Nägeli,Richard D Hayes,Adithi R Varadarajan,Igor V Grigoriev,Christian H Ahrens,Florian M Freimoser,Stefanie Lutz

doi:10.15698/mic2021.08.757

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.

Highlights

Aureobasidium pullulans belongs to the Dothideales, not the classical yeast order Saccharomycetales, and exhibits both yeast-like and hyphal growth morphology [1]
Genome analysis of A. pullulans NBB 7.2.1 We sequenced the genome of A. pullulans NBB 7.2.1 using PacBio Sequel long read and Illumina short read sequencing technologies (2x300 bp, 29x coverage, 100% of reads mapped to final assembly) (Supplementary Table 1)
The study presented here reports a reference genome, transcriptome datasets, and a secretome analysis of the A. pullulans strain NBB 7.2.1, which strongly inhibits the growth of filamentous fungi

Summary

Introduction

Aureobasidium pullulans belongs to the Dothideales, not the classical yeast order Saccharomycetales, and exhibits both yeast-like and hyphal growth morphology [1]. The species is often referred to as a yeast, black yeast, or yeast-like fungus and biocontrol species. Fungi of the genus Aureobasidium, and in particular A. pullulans, are frequently isolated from phyllosphere and soil samples worldwide. Their phenotypic plasticity and tolerance of harsh environmental conditions are likely the reason for the competitiveness of these ascomycetes in a wide range of ecological niches [1, 2]. Potential biocontrol genes of A. pullulans strains from different environments and geographical regions revealed a homogenous population structure and limited genome variability. It has been concluded that A. pullulans is an efficiently spreading and recombining fungus [3]

Methods

Results

Conclusion