DescriptionFusarium oxysporum species complex is an important group of plant pathogens. Although individual isolates have a narrow host range, the group as a whole has a wide host range, and for many crops it is ranked among the most important pathogens. This diversity and flexibility are the result of genomic diversity and mobility of genes that may spread across phylogenetically disparate groups. The consequence of this phenomenon is that phylogenetic relatedness is a weak predictor of pathogenicity, and the best predictor is the effector profile of a given strain. Within the Masterplan Fusarium project, we sequenced multiple representatives of different formae speciales to identify putative effector genes that could be used as targets for the development of TaqMan assays. The steps were the following: genome assembly, effector prediction based on homology to an earlier effector set, exploring genetic diversity of the isolates (both phylogenetic and effector-focused), identifying effectors with greatest specificity and sensitivity for the target group, mining the genomes for homologous sequences, and designing TaqMan assays based on the collection of target and non-target sequences.
Using large amount of data for this kind of analysis can improve the robustness of the prediction, but significantly complicates calculations. In our analysis, we incorporated sequence variation besides presence absence and invented a new metric for calculating sequence specificity. Data analysis relies on well curated data, which is difficult to obtain and curate. We solved this issue by closely collaborating with experts of phytopathology and data analysis to see if biological observations correspond with observed patterns. Finally, before designing TaqMan assays all sequences from the genome collection were collected, since pseudogenes or other sequences may share local similarities with effector sequences. This approach allowed us to design selective detection methods for groups where we had a sufficient sample set of the pathogen diversity.
|8 Nov 2023
|36th Meeting of the Fusarium working group of the Koninklijke Nederlandse Planteziektenkundige Vereniging