Evolutionary genomics of pathogens Croll lab at University of Neuchatel

Adventures with a rubber tree pathogen

Blog post written by Sandra Milena Gonzalez Sayer (visiting PhD student from Colombia)

One of my biggest passions is facing challenges related to molecular pattern discovery. Ever since I was doing my undergraduate program, I have been interested in understanding the pathogen role in plant disease and the molecular component in the pathogenicity process. My study model since that time has been Pseudocercospora ulei, an ascomycete biotrophic pathogenic fungus that causes a disease known as the South American Leaf Blight (SALB) in natural rubber plants (Hevea brasiliensis). Because of P. ulei’s biotrophic lifestyle, the isolation and in vitro culture has been one of the biggest challenges studying this pathogen. The obtention of P. ulei isolates from infected leaves could take up to 50 days, but once it occurs, maintaining the strains alive becomes another challenge. The common practice to preserve them is through periodic transference to fresh medium. However, it is well-known that this practice can affect the isolates genetic stability and generate phenotypic changes like the loss of pathogenicity. In my undergraduate thesis, I assessed long term preservation methods to maintain the P. ulei strains collection. As a result, I standardized conidia lyophilization conditions which allow maintaining the P. ulei isolations viability for more than one year.

H. brasiliensis is a perennial species which presents an unproductive period of approximately six years. Because of that, plant breeding programs advance slowly, and unconventional genetic breeding strategies based on genetic engineering technics are still necessary. Aware that molecular knowledge is crucial to improving plant breeding programs and before to its draft genome release, I worked in searching for polymorphic molecular markers (Microsatellites and RAPDs) for discriminating a natural rubber population constituted by Asiatic and Latin American clones. These markers were used in a national service of H. brasiliensis varieties identification whose aim was organizing the clonal gardens that produce seedlings for future rubber plantations in Colombia. In this sense, the farmers could know the identity of the planted clones (SALB resistance or highly rubber yield clones) before the economic investment during the unproductive period.

My scientific career has been developed in the natural rubber group from the biotechnology institute of the National University of Colombia. The work of this group is focused on studying the natural rubber crop since a holistic perspective encompassing the pre and post cultivate stages as well as the productive period. It has been amazing to me having the opportunity to choose my research line through this integral view, so my decision was studying the SALB disease. Currently, I am doing my PhD studying the P. ulei pathogenicity mechanisms through genomic and transcriptomic perspective. The main goal of my thesis project is to improve the knowledge of P. ulei genome architecture and identify pathogenicity determinants deployed by this fungus to cause SALB disease. For this purpose, whole-genome shotgun sequencing and assembly of the P. ulei genome was done using Pacific BioScience, Oxford nanopore, and Illumina platforms. One of my more relevant findings is the P. ulei size genome is the biggest genome so far reported in the Mycosphaerellaceae family. Furthermore, this genome showed an exceptionally high repeat content that could be associated with a genome a size expansion event and could play an essential role in the environment fungal adaptation as well in the pathogenicity mechanism evolved.

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