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Supplemental Information

Supplementary Figure 1

UPGMA dendrogram of sub-module MLST-ID of Genotype-ID. The tree was constructed using 100 bootstrap replicates and MLST analysis of 8 genes (5 housekeeping genes and 3 virulence genes) of Clavibacter michiganensis. The query used is a concatenation of a WASH sample using all 8 genes. Queries are represented in blue. Note that all queries are correctly placed amongst samples of its presumptive clonal lineage while also representing relationships between lineages in the reference dataset.

DOI: 10.7287/peerj.preprints.2005v1/supp-1

Supplemental figure 2

UPGMA dendrogram of sub-module Binary-ID of Genotype-ID using 100 bootstrap replicates for Aphanomyces euteiches. The queries used for this iteration of Binary-ID are two samples from a presumptive “Athena” origin. Queries are represented in red. Note that all queries were correctly placed amongst samples of its presumptive clonal lineage while also representing relationships between lineages in the reference dataset, indicating both queries are more closely related to the “Athena” population than the “Mt. Vernon” population.

DOI: 10.7287/peerj.preprints.2005v1/supp-2

Additional Information

Competing Interests

NJ Grünwald and JH Chang are academic editors for PeerJ.

Author Contributions

Javier F Tabima conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Sydney E Everhart conceived and designed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Meredith M Larsen performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Alexandra J Weisberg performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Zhian N Kamvar performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Matthew A Tancos performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Christine D Smart wrote the paper, reviewed drafts of the paper.

Jeff H Chang wrote the paper, reviewed drafts of the paper.

Niklaus J Grünwald conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

https://github.com/grunwaldlab/Microbe-ID

Funding

This research is supported in part by US Department of Agriculture (USDA) Agricultural Research Service Grant 5358-22000-039-00D (NJG), USDA National Institute of Food and Agriculture (NIFA) Grant 2011-68004-30154 (NJG), the USDA ARS Floriculture Nursery Research Initiative (NJG), USDA NIFA Grant 2014-51181-22384 (JHC and NJG), and USDA NIFA 2012-67012-19844 (SEE). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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