Abstract
The yeast Metschnikowia fructicola was reported as an efficient biological control agent of postharvest diseases of fruits and vegetables, and it is the bases of the commercial formulated product “Shemer.” Several mechanisms of action by which M. fructicola inhibits 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 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 contigs, with an estimated genome size of approximately 26 Mb, was obtained. Comparative analysis of M. fructicola proteins with the other 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 homologous SNPs with 2,004 predicted high impact mutations. The size of the genome is exceptionally high when compared with those of available closely related organisms, and the high rate of homology among M. fructicola genes points toward a recent whole-genome duplication event as the cause of this large genome. Based on the assembled genome, sequences were annotated with a gene description and gene ontology (GO term) and clustered in functional groups. Analysis of CAZymes family genes revealed 1,145 putative genes, and 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.
Highlights
The yeast Metschnikowia fructicola was first isolated from grapes and identified as a new species by Kurtzman and Droby (2001)
A new assembly of the M. fructicola genome (Genbank accession ANFW02000000) was constructed using sequence data obtained from the Pacific Biosciences (PacBio) RS II Sequencer
The PacBio genomic sequences were assembled with the HGAP3.0 program (Chin et al, 2013) and yielded a high-quality draft genome consisting of 93 contigs with an N50 of 957,836 bp
Summary
The yeast Metschnikowia fructicola (type strain NRRL Y-27328, CBS 8853) was first isolated from grapes and identified as a new species by Kurtzman and Droby (2001). Yeasts have been identified by many workers as potential biological control agents suitable for the prevention of postharvest diseases, especially since they are naturally occurring on fruits and vegetables, and exhibit a number of traits that favor their use as fungal antagonists These traits include high tolerance to environmental stresses (low and high temperatures, desiccation, wide fluctuations in relative humidity, low oxygen levels, pH fluctuations, UV radiation) encountered during fruit and vegetable production before and after harvest, and their ability to adapt to the micro-environment present in wounded fruit tissues, characterized by high sugar concentration, high osmotic pressure, low pH and conditions that conducive to oxidative stress. In contrast to filamentous fungi, the vast majority of naturally occurring yeasts do not produce allergenic spores or mycotoxins, and have simple nutritional requirements that enable them to colonize dry surfaces for long periods of time (Spadaro et al, 2008)
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