Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

SYRINGAE: A web-based application for Pseudomonas syringae isolate characterization

View ORCID ProfileChad Fautt, View ORCID ProfileEstelle Couradeau, View ORCID ProfileKevin L. Hockett
doi: https://doi.org/10.1101/2022.11.04.515192
Chad Fautt
1Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania, United States
2Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, United States
3Intercollege Graduate Degree Program in Ecology, Pennsylvania State University, University Park, Pennsylvania, United States
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Chad Fautt
  • For correspondence: cwf30@psu.edu
Estelle Couradeau
2Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, United States
3Intercollege Graduate Degree Program in Ecology, Pennsylvania State University, University Park, Pennsylvania, United States
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Estelle Couradeau
Kevin L. Hockett
1Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania, United States
3Intercollege Graduate Degree Program in Ecology, Pennsylvania State University, University Park, Pennsylvania, United States
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kevin L. Hockett
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

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 Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted November 04, 2022.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
SYRINGAE: A web-based application for Pseudomonas syringae isolate characterization
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
SYRINGAE: A web-based application for Pseudomonas syringae isolate characterization
Chad Fautt, Estelle Couradeau, Kevin L. Hockett
bioRxiv 2022.11.04.515192; doi: https://doi.org/10.1101/2022.11.04.515192
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
SYRINGAE: A web-based application for Pseudomonas syringae isolate characterization
Chad Fautt, Estelle Couradeau, Kevin L. Hockett
bioRxiv 2022.11.04.515192; doi: https://doi.org/10.1101/2022.11.04.515192

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Microbiology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4246)
  • Biochemistry (9173)
  • Bioengineering (6806)
  • Bioinformatics (24064)
  • Biophysics (12157)
  • Cancer Biology (9565)
  • Cell Biology (13825)
  • Clinical Trials (138)
  • Developmental Biology (7660)
  • Ecology (11737)
  • Epidemiology (2066)
  • Evolutionary Biology (15544)
  • Genetics (10672)
  • Genomics (14362)
  • Immunology (9515)
  • Microbiology (22907)
  • Molecular Biology (9130)
  • Neuroscience (49155)
  • Paleontology (358)
  • Pathology (1487)
  • Pharmacology and Toxicology (2584)
  • Physiology (3851)
  • Plant Biology (8351)
  • Scientific Communication and Education (1473)
  • Synthetic Biology (2301)
  • Systems Biology (6206)
  • Zoology (1303)