RT Journal Article SR Electronic T1 SYRINGAE: A web-based application for Pseudomonas syringae isolate characterization JF bioRxiv FD Cold Spring Harbor Laboratory SP 2022.11.04.515192 DO 10.1101/2022.11.04.515192 A1 Chad Fautt A1 Estelle Couradeau A1 Kevin L. Hockett YR 2022 UL http://biorxiv.org/content/early/2022/11/04/2022.11.04.515192.abstract AB The Pseudomonas syringae species complex (PSSC) is a diverse group of plant pathogens with a collective host range encompassing almost every food crop grown throughout the world. As a threat to global food security, rapid detection and characterization of epidemic and emerging pathogenic lineages is essential. However, phylogenetic identification and prediction of virulence is often complicated by an unclarified taxonomy and the diversity of virulence factor repertoires carried by PSSC isolates. To address these issues, we have built SYRINGAE (www.syringae.org), a web-based phylogenetic placement and functional inference pipeline for PSSC. SYRINGAE contains a comprehensive phylogeny of 2,161 quality-checked genome assemblies annotated with 120 virulence genes. From this dataset, naïve Baye classification models trained from life identification numbers (LINs) and common marker gene sequences can be used for accurate identification of isolates. SYRINGAE efficiently articulates taxonomical and functional data generated over the last several decades on PSSC and constitutes a unique tool tailored towards the rapid characterization of PSSC emerging strains of concern.Competing Interest StatementThe authors have declared no competing interest.