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Using pathogen genome-informed strategies to understand the molecular mechanism plant disease

A key feature of our Congresses is the opportunity given to early career researchers to present their work.

At the upcoming 7th Plant Genomics & Gene Editing Congress: EuropeEgem Ozbudak will be one of four early career researchers to be given a 15-minute platform to present their work and receive a free registration pass for both days of the conference.

He will be discussing his research project on Colletotrichum acutatum, the causative agent of anthracnose crown and fruit rot, recognized as the second most important pathogen of strawberries on the globe due to its economic impacts.

Effector proteins are secreted proteins released by phytopathogens directly into plant tissue cell or the apoplast. When secreted into plant cells, their function is to suppress plant immunity and promote the colonization of the plant.

Most projects in our laboratory are linked to pathogen effectors. We study bacterial, fungal and oomycete diseases affecting crops like citrus plants, strawberries, avocado and also we use model plants such as Nicotiana benthamiana and periwinkle. In our projects, we generate genome resources if not available for the major plant pathogens of these plants affecting Florida state.

My main project focus is on a fungal disease affecting strawberries. In our lab, we have five plant cultivars– Florida Beauty, Sensation, Winterstar, Fortuna, and Festival. These five cultures were generated by the University of Florida Horticulture Department and have different properties like different photoperiodism or fruit properties etc. Most importantly, they have different resistance to plant pathogens, specifically to the pathogen that currently I am working on, Colletotrichum acutatum. This fungal pathogen is globally recognized as a pathogen of strawberry plants. We are working in collaboration with Dr. Natalia Peres from the University of Florida who facilitated many strains of C. acutatum isolated from diseases strawberry tissues.

This project offered the opportunity to learn bioinformatics, as one primary step is the in silico sequence identification of secreted proteins. I have adapted a reported pipeline used for rust fungi that basically question C. acutatum proteome in search for proteins predicted to be secreted into the host cells, usually about 5% of all proteins (~2,000). Besides containing secretion signals we looked at the size of these proteins, these should be small and no larger than 250 amino acids.

I am working at the bench and greenhouse since I am generating RNA material from infections of strawberry tissues for RNA-sequencing. From the RNA-sequencing data, I am specifically trying to detect in planta expressed candidate effectors genes. These candidate effectors can be used as a molecular marker to screen new strawberry varieties for resistance traits but also can be used as baits to identify and functionally characterize novel susceptible or resistance gene factors from the host plant.

My take-home message is that to understand the molecular mechanism of a plant disease it is essential to use pathogen genome-informed strategies.


Egem Ozbudak is a Ph.D. Student in the Plant Pathology Department at the University of Florida, USA. He will be presenting at the 7th Plant Genomics & Gene Editing Congress: Europe.


Attracting over 300 experts working in all areas of plant science, the 7th Plant Genomics & Gene Editing Congress: Europe will examine the latest in gene editing methods for plant genomics research. Click here to download the agenda.

One Response to “Using pathogen genome-informed strategies to understand the molecular mechanism plant disease”

  1. Adriana Vanegas N

    This publicaciones are very interesting for my Jon and my studi in phitopathology


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