Skip to main content
APS Plant Health 2025 Main banner
Icon Legend
This session is not in your schedule.
This session is in your schedule. Click again to remove it.
ViewAttendees 1

POSTERS: Disease Detection and Diagnosis II

P-186 - Genome-based Identification of Prokaryotic Plant Pathogens at Within-Species Resolution Using the genomeRxiv Web Server

Tuesday, August 5, 2025
9:30 AM - 10:15 AM HST
Location: Exhibit Hall 3

    Presenting Author(s)

  • RM

    Reza Mazloom

    Graduate Researcher
    Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, U.S.A.
    Blacksburg, Virginia, United States

    • Author(s)

  • CN

    Chandra Sekhar Nerella

    Graduate Researcher
    Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, U.S.A.
    Blacksburg, Virginia, United States

  • AB

    Atul Bharadwaj

    Graduate Researcher
    Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, U.S.A.
    Blacksburg, Virginia, United States

  • RS

    Rituraj Sharma

    Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, U.S.A.
    Blacksburg, Virginia, United States

  • LH

    Lenwood S. Heath

    Professor
    Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, U.S.A.
    Blacksburg, Virginia, United States

  • CB

    C.Titus Brown

    Professor
    Department of Population Health and Reproduction, University of California, Davis, CA,USA
    Davis, California, United States

  • NP

    N. Tessa Pierce-Ward

    Assistant Researcher
    Department of Population Health and Reproduction, University of California, Davis, CA,USA
    Davis, California, United States

  • LP

    Leighton Pritchard

    Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde Glasgow, Scotland
    Glasgow, Scotland, United Kingdom

  • BV

    Boris A. Vinatzer

    Professor
    School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061
    Blacksburg, Virginia, United States

Abstract Text: One of the phenotypes of plant pathogenic bacteria that is crucial for disease control and management is host range and it can vary at the strain level. However, species is the smallest unit of taxonomic nomenclature regulated by ICSP, not the strain. While several tools exist for genome-based identification at the species rank, strain-level tools are limited to a small number of plant pathogenic species, hampering genome-based identification that is relevant to disease control. To address this, we leveraged the Life Identification Number system for near-strain level classification in our legacy web server LINbase for all prokaryotes. We are excited to share with the community the genomeRxiv web server, accessible through a website and a Python client, BrookLIN. Currently, genomeRxiv contains 290,000 genomes, 48,000 species, and 50 within-species groups, with more genomes added daily. Metadata of genome-sequenced strains are visualized to provide users easy access to information about sources, time of isolation, and geographic distribution to facilitate emerging disease outbreak detection and investigations of host jumps and geographic range expansion. Moreover, users can share compressed sketches of newly sequenced genomes, preserving sequence privacy. As more genomes, sourmash sketches, and metadata are added, genomeRxiv will be a growing resource for scientists and regulators, informing them about genotypes, phenotypes, and geographic range of strains to evaluate their associated biosecurity risk and guide implementation of control and management measures.