Metschnikowia fructicola, a biocontrol yeast against postharvest diseases: genome sequence, assembly and characterization

Edoardo Piombo 1 Noa Sela 2 Michael Wisniewski 3 Maria Hoffmann 4 Maria Lodovica Gullino 1 Marc Allard 4 Elena Levin 5 Davide Spadaro 1 Samir Droby 5
1DISAFA and AGROINNOVA, University of Torino, Grugliasco, Italy
2Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
3Agricultural Research Service, United States Department of Agriculture, Kernersville, WV, USA
4Division of Microbiology, Office of Regulatory Science, United States Food and Drug Administration, College Park, MD, USA
5Department of Postharvest Science, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel

The yeast Metschnikowia fructicola has been reported as an efficient biocontrol agent of postharvest diseases of fruit and vegetables. Several mechanisms of action by which M. fructicola inhibit postharvest pathogens were suggested, including iron-binding compounds, induction of defence signalling genes, such as PRP and MAPK cascade genes, production of fungal cell wall degrading enzymes and relatively high amounts of superoxide anions. M. fructicola also exhibits chitinase activity and the chitinase gene, MfChi, was highly induced in response to fungal pathogen cell walls.. Several studies have examined differential gene expression during the interaction of the yeast, M. fructicola, with host fruit or with a postharvest pathogen. In the current work, we awe report the assembly of the whole genome sequence of two strains of M. fructicola using PacBio and Illumina shotgun sequencing technologies. Using the PacBio, a high-quality draft genome consisting of 93 scaffolds, with an estimated genome size of approximately 26 Mb, was obtained. Comparative analysis of M. fructicola proteins with three available closely-related genomes revealed a shared core of homologous proteins coded by 5,776 genes. Comparing the genomes of the two M. fructicola strains using a SNP calling approach resulted in the identification of 564,302 SNPs/indels with a total of 2,004 predicted high impact mutations. Based on the assembled genome, sequences were annotated with a gene description and gene ontology (GO term) and clustered in functional groups. Analysis of CAZyme family genes revealed 1,145 putative genes. Transcriptomic analysis of CAZyme expression levels in M. fructicola during its interaction with either grapefruit peel tissue or Penicillium digitatum revealed a high level of CAZyme gene expression when the yeast was placed in wounded fruit tissue. The significance of the findings in biocontrol capabilities of M. fructicola will be discussed.