Meet FEMS Research and Training grantee Joris Alkemade

26-01-22 cameronw1986

FEMS Research and Training Grants are meant to assist early career scientists in pursuing research and training at a European host institution in another country than their own country of residence.

Joris Alkemade: Research Institute of Organic Agriculture – Crop Sciences, Frick 5070, Switzerland

Host supervisor and host laboratory: Riccardo Baroncelli, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy

Dates: 2 October 2021 to 12 December 2021

FEMS Member Society Membership: Royal Netherlands Society for Microbiology

My name is Joris Alkemade and I am from the Netherlands. I have always had an interest for plants and agriculture. After a year living in Ecuador with a family that owned a banana plantation I decided to study plant sciences at Wageningen University. During my Bachelor and Master I was mostly interested in plant pathology and I was involved in projects studying fusarium wilt in Banana, potato cyst nematodes and verticillium wilt in Tomato and its interaction with the soil microbiome. After my studies I started a PhD at the institute for organic agriculture (FiBL) in Switzerland and Hohenheim University in Germany to study anthracnose disease (Colletotrichum lupini) on white lupin. There I developed a disease resistance protocol, found a candidate resistance gene in white lupin and characterized a worldwide collection of C. lupini isolates to get insight in the current lupin anthracnose pandemic. The goal of the FEMS research visit to the University of Bologna was to improve our understanding of C. lupini by performing comparative genomics. In the future I hope to continue working in the interesting field of plant pathology and contribute to a more sustainable form of agriculture.

For my FEMS Research and Training visit I went to the plant pathology lab of the Department of Agricultural and Food Sciences of the University of Bologna. Here I worked together with Riccardo Baroncelli who was recently appointed associate professor of plant pathology. The aim of the research was to improve our understanding of the notorious lupin pathogen Colletotrichum lupini. We had access to a high resolution 3D-RADseq dataset of a global collection of 76 C. lupini isolates and 36 genomes of C. lupini and closely related Colletotrichum species. We used the 3D-RADseq dataset to perform phylogenetic analysis and asses the population structure. The whole genome sequences were assembled and checked for completeness. Together with available virulence data on white and Andean lupin we aim to further improve our understanding on C. lupini population dynamics and to identify genomic regions potentially involved in pathogenicity, virulence and host-speciation. The people in the lab were very welcoming and I had great time in the city of Bologna!

To visit another lab that is working on subject similar to my PhD subject and get more experience in population genomics.I wanted to get more experience in analyzing big genomic datasets. With help from my host supervisor I succeeded but I still want to learn more. The grant gave me the opportunity to visit another lab in a different city. This gave me a lot of experience in my research field but also let me experience the Italian lifestyle.’’

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