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ARS Home » Northeast Area » Kearneysville, West Virginia » Appalachian Fruit Research Laboratory » Innovative Fruit Production, Improvement, and Protection » Research » Publications at this Location » Publication #341586
Title: Genome sequence, assembly and characterization of two Metschnikowia fructicola strains used as biocontrol agents of postharvest diseases

Author
item PIOMBO, EDUARDO - University Of Torino
item SELA, NOA - Volcani Center (ARO)
item Wisniewski, Michael
item HOFFMAN, MARIA - Food And Drug Administration(FDA)
item GULLINO, MARIA LODOVICA - University Of Torino
item ALLARD, MARC - University Of Maryland
item LEVIN, ELENA - Volcani Center (ARO)
item SPADARO, DAVID - University Of Torino
item DROBY, SAMIR - Volcani Center (ARO)

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/15/2018
Publication Date: 4/3/2018
Citation: Piombo, E., Sela, N., Wisniewski, M.E., Hoffman, M., Gullino, M., Allard, M.W., Levin, E., Spadaro, D., Droby, S. 2018. Genome sequence, assembly and characterization of two Metschnikowia fructicola strains used as biocontrol agents of postharvest diseases. Frontiers in Microbiology. 9(593):1-17.

Interpretive Summary: Different strains and species of the yeast, Metschnikowia, have been identified in recent years as good biocontrol agents for controlling postharvest diseases of fruits and vegetables. In fact, numerous new strains and/or species have been reported to have potential as postharvest biocontrol agents. Despite these numerous reports, little is known about why some yeasts are good biocontrol agents and why some are not. Having a good genome sequence for these biocontrol agents will allow researchers to discover what genes are present and actively transcribed during biocontrol activity and thus provide the opportunity to understand what mechanisms are utilized by good biocontrol agents and what genes are missing or not expressed in bad biocontrol agents. The current study sequenced the genome of the postharvest biocontrol yeast, Metschnikowia fructicola, and compared the sequence of two different strains. The results provided the most comprehensive and complete sequence of this yeast species to date, as well as an annotation of the genes that were present, and genetic markers (SNPs – single nucleotide polymorphisms) that could be used to distinguish different strains from each other. In particular, a large family of enzymes (CAZymes) involved in carbohydrate utilization were identified. These genes may play a role in biocontrol activity and expression studies indicated that M. fructicola produces very high levels of these genes when it interacts with fruit tissues and the pathogen, P. digitatum. This information will serve as an excellent resource for the research community trying to identify the genes and mechanisms in yeast species associated with strong biocontrol activity.

Technical Abstract: The yeast Metschnikowia fructicola was reported as an efficient biological control agent of postharvest diseases of fruits and vegetables. Several mechanism of action by which M. fructicola inhibit postharvest pathogens were suggested including iron-binding compounds, induction of defense signaling genes, production of fungal cell wall degrading enzymes and relatively high amounts of superoxide anions. We assembled 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. Comparative analysis of M. fructicola proteins with the other three available closely-related genomes revealed a shared core of homologous proteins coded by 1,157 genes. Comparing the genomes of the two M. fructicola strains using SNP calling approach resulted in the identification of 546,356 SNPs with a total of 743 predicted high impact mutations. Based on the assembled genome sequences were annotated with a gene description, gene ontology (GO term) and clustered in functional groups. Analysis of CAZymes family genes revealed 853 putative genes, among these 343 have clear functional assignments. 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.