Using bioinformatics and molecular biology to streamline construction of effector libraries for phytopathogenic pseudomonas syringae strains

Abstract

The war between plants and their pathogens is endless, with plant resistance genes offering protection against pathogens until the pathogen evolves a way to overcome this resistance. Given how quickly new pathogen strains can arise and defeat plant defenses, it is critical to more rapidly identify and examine the specific genomic characteristics new virulent strains have gained which give them the upper hand. An indispensable tool is bioinformatics. Genome sequencing has advanced rapidly in the last decade, and labs are frequently uploading high-quality genomes of various organisms, including plant pathogenic bacteria such as Pseudomonas syringae. Pseudomonas syringae strains inject several effector proteins into host cells which often overcome host defenses. Probing online genomes provides a way to quickly and accurately predict effector repertoires of Pseudomonas, enabling the cloning of complete effector libraries of newly emerged strains. Here, we describe detailed protocols to rapidly clone bioinformatically predicted P. syringae effectors for various screening applications. © Springer Science+Business Media, LLC, part of Springer Nature 2019.