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

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.

Clinical Aureobasidium Isolates Are More Fungicide Sensitive than Many Agricultural Isolates

“…Genomic DNA was extracted as previously described ( 15 ), and whole-genome sequencing (150 bp paired end reads) was performed at BGI Genomics. The reference isolate A. pullulans NBB 7.2.1 was originally isolated from a soil sample and characterized by genome, transcriptome, and secretome analyses ( 15 , 16 ).…”

“…Many clinical Aureobasidium isolates cluster more closely with other Aureobasidium species than with A. pullulans . As references, the analysis included 5 genomes of the 4 Aureobasidium species A. pullulans (NBB 7.2.1 and EXF-150), A. namibiae (EXF-3398), A. melanogenum (CBS 110374), and A. subglaciale (EXF-2481) ( 7 , 15 ). The x axis represents the relative distances between the taxa.…”

Pantothenate auxotrophy in a naturally occurring biocontrol yeast

“…H. meyeri (APC 12.1) genomic DNA was extracted using a phenol/chloroform extraction protocol and as previously stated (38, 39). Cells from an overnight culture were collected and resuspended in 200 μL of Harju Buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA).…”

Advances and Perspectives in the Use of Biocontrol Agents against Fungal Plant Diseases

“…In another study, Zhang et al applied RNAseq to study the host response to the BCA Yarrowia lipolytica, and they found that this BCA induced host resistance through crosstalk between salicylic acid and ethylene/jasmonate pathways [240]. Rueda-Mejia et al [241] performed dual RNA-seq of A. pullulans NBB 7.2.1 during co-incubation with F. oxysporum NRRL 26381/CL57, and found that ~12% of all the A. pullulans genes were differentially expressed, with upregulated genes including secreted hydrolases such as glycosylases, esterases, and proteases, and genes encoding enzymes predicted to be involved in the synthesis of secondary metabolites. Conversely, only 80 genes were differentially expressed in F. oxysporum, with lipid and carbohydrate metabolism being the most represented Gene Ontology categories.…”