Microbe-ID: an open source toolbox for microbial genotyping and species identification.
Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.
Department of Botany and Plant Pathology, Oregon State University , Corvallis , OR , United States.
Javier F
JF
Tabima
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States; Current affiliation: Department of Plant Pathology, University of Nebraska, Lincoln, NE, United States.
Sydney E
SE
Everhart
Horticultural Crops Research Laboratory, USDA Agricultural Research Service , Corvallis , OR , United States.
Meredith M
MM
Larsen
Department of Botany and Plant Pathology, Oregon State University , Corvallis , OR , United States.
Alexandra J
AJ
Weisberg
Department of Botany and Plant Pathology, Oregon State University , Corvallis , OR , United States.
Zhian N
ZN
Kamvar
Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University , Geneva , NY , United States.
Matthew A
MA
Tancos
Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University , Geneva , NY , United States.
Christine D
CD
Smart
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States; Molecular and Cellular Biology Graduate Program and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States.
Jeff H
JH
Chang
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States; Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR, United States; Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, United States; Molecular and Cellular Biology Graduate Program and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States.
Niklaus J
NJ
Grünwald
Genotyping; Identification; Molecular diagnostics; Pathogen; Phytophthora; Taxonomy