Open Access Research article

De-novo assembly and characterization of the transcriptome of Metschnikowia fructicola reveals differences in gene expression following interaction with Penicillium digitatum and grapefruit peel

Vera Hershkovitz1, Noa Sela2, Leena Taha-Salaime134, Jia Liu5, Ginat Rafael1, Clarita Kessler1, Radi Aly3, Maggie Levy4, Michael Wisniewski5 and Samir Droby1*

Author Affiliations

1 Department of Postharvest and Food Sciences, ARO, the Volcani Center, Bet Dagan, 50250, Israel

2 Department of Plant Pathology and Weed Research, ARO, the Volcani Center, Bet Dagan, 50250, Israel

3 Department of Plant Pathology and Weed Research, the Volcani Center, Newe-Yaar Research Center, Ramat Yeshai, 30095, Israel

4 Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Revovot, 76100, Israel

5 U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Appalachian Fruit Research Station, Kearneysville, WV, 25430, USA

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BMC Genomics 2013, 14:168  doi:10.1186/1471-2164-14-168

Published: 12 March 2013

Abstract

Background

The yeast Metschnikowia fructicola is an antagonist with biological control activity against postharvest diseases of several fruits. We performed a transcriptome analysis, using RNA-Seq technology, to examine the response of M. fructicola with citrus fruit and with the postharvest pathogen, Penicillium digitatum.

Results

More than 26 million sequencing reads were assembled into 9,674 unigenes. Approximately 50% of the unigenes could be annotated based on homology matches in the NCBI database. Based on homology, sequences were annotated with a gene description, gene ontology (GO term), and clustered into functional groups. An analysis of differential expression when the yeast was interacting with the fruit vs. the pathogen revealed more than 250 genes with specific expression responses. In the antagonist-pathogen interaction, genes related to transmembrane, multidrug transport and to amino acid metabolism were induced. In the antagonist-fruit interaction, expression of genes involved in oxidative stress, iron homeostasis, zinc homeostasis, and lipid metabolism were induced. Patterns of gene expression in the two interactions were examined at the individual transcript level by quantitative real-time PCR analysis (RT-qPCR).

Conclusion

This study provides new insight into the biology of the tritrophic interactions that occur in a biocontrol system such as the use of the yeast, M. fructicola for the control of green mold on citrus caused by P. digitatum.

Keywords:
Antagonist-fruit interaction; Antagonist-pathogen interaction; Biological agent; RNA-seq