Epsilon Archive for Student Projects

Abstract

Plants and pathogenic microorganisms undergo co-evolution in the wild and in agricultural fields. Understanding the mechanisms driving specific host-pathogen-pathogen interactions might reveal new sources of pathogen resistance for important crops, like wheat. For this staple crop, omics and sequencing data have allowed to elucidate some molecular mechanisms involved in defense emergence and pathogen immune evasion. In this context, coinfection experiments, which remain largely unexplored conditions, might provide new information to reveal novelty in plant immunity. In this work, we first confirm the success of a fungal coinfection experiment in wheat leaves (Triticum turgidum ssp. dicoccum inoculated with Zymoseptoria tritici and Puccinia graminis) using short-read next generation sequencing (NGS) RNA sequencing data (RNA-seq). Then, we present an overview of genetic variation in Z. tritici isolates exposed to different prolonged temperature treatments, illustrating the pathogen’s genetic plasticity through short-read NGS DNA sequencing data. Finally, we analyse long-read RNA-seq datasets from more fungal coinfections of wheat leaves (Triticum aestivum and T. turgidum ssp. dicoccum, infected with Z. tritici and P. graminis or Z. tritici and Fusarium graminearum), filtering and scouting libraries for unannotated wheat transcripts that could bear potential novelty in plant defense responses. We exemplify this potential with two examples: an mRNA showing indications of an exon fusion and a group of ncRNAs that form conserved hairpins. Our work highlights the importance of generating sequencing datasets under new conditions, expected to induce specific biological responses.