Mobilome, adaptation and crop genome stability – CropCircle

Plants are sessile organisms and naturally adapt to rapidly changing environmental conditions. Recent evidence showed that extrachromosomal circular DNA (eccDNA) can drive rapid adaptation to a stressful environment, in yeast, cancer cells but also in herbicide resistant plants. However, in plants the role of eccDNA is still poorly explored. ?We have previously developed a method (mobilome-seq) to study the repertoire of eccDNAs and shown the influence of heat stress on the repertoire of eccDNAs in rice. For the CROPCIRCLE project we also obtained preliminary results showing (1) the protective role of the epigenome in limiting the impact of eccDNAs on the Arabidopsis genome  (French DIADE/LGDP consortium) and (2) the influence of drought on the eccDNA content in rice (Swiss consortium AGROSCOPE).?In CROPCIRCLE we therefore propose to combine our expertise on epigenetic mechanisms, high-resolution live-cell imaging and genome dynamics (French consortium) and genomics and epigenomics of cultivated species (Swiss consortium) in order to answer three major questions on the role of eccDNAs:?
1- What are the stress and DNA damage conditions that promote the production of eccDNA in plants?
?2- What are the plant epigenetic mechanisms limiting eccDNA production?
?3- What is the tissue and cellular distribution of eccDNA?
?3- What are the impacts of eccDNA on genome stability??
To answer these questions, we will rely on two model plants for which we have recognized expertise and have significant genomic and genetic resources: Arabidopsis thaliana (French consortium) and cultivated rice Oryza sativa (Swiss consortium). The complementarity of the French and Swiss partners will favor the reciprocal exchanges of protocols linked to the sequencing of eccDNA and their bioinformatics processing. Thus, the partners will be able to compare the results obtained in parallel on the two species in order to draw more general conclusions allowing a better understanding of the control of the extrachromosomal DNA compartment in plants.?The CROPCIRCLE project will contribute to fundamental knowledge through a better understanding of eccDNAs in plants. We hope that the network created thanks to the CROPCIRCLE project will foster a larger network at the European level in the merging field of eccDNA biology in order to be able to apply to future European research funding calls. In the medium term our project objectives fit with a science of sustainability by exploring the natural role of eccDNAs in the rapid adaptation of plants to changing environmental conditions.