Data and code from: Distribution of Pseudomonas amygdali pv. loropetali in the twig phylloplane of Loropetalum chinense shrubs in ornamental plant nurseries

Authors: Copes, Warren; Leep, Kenneth; LU, SHI-EN - Mississippi State University; Read, Quentin; ROBINSON, LINDSEY - Mississippi State University; WILLIS, EMMA - Mississippi State University; Kumpatla, Siva Prasad; Smith, Barbara

Submitted to: Ag Data Commons
Publication Type: Database / Dataset
Publication Acceptance Date: 8/18/2025
Publication Date: 9/8/2025
Citation: Copes, W.E., Leep, K.R., Lu, S., Read, Q.D., Robinson, L., Willis, E., Kumpatla, S., Smith, B.J. 2025. Data and code from: Distribution of Pseudomonas amygdali pv. loropetali in the twig phylloplane of Loropetalum chinense shrubs in ornamental plant nurseries. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/29647553.
DOI: https://doi.org/10.15482/USDA.ADC/29647553

Interpretive Summary: Nurseries that raise the ornamental shrub loropetalum have reported damage to their plants caused by the bacterium PAL, a pathogen that does not have a reliable method of control. In the associated manuscript, we present results from a survey of PAL across six nurseries. We developed a method to reliably determine how abundant PAL is by counting how many gene copies are present on the bark of the shrub. We looked at the presence of galls caused by PAL and used the gene-counting method to determine abundance on twigs at base, middle, and new growth levels of the plant. Our statistical models showed significant differences in abundance between nurseries, between heights on the plant, and between plants with and without galls. This dataset includes all the raw data and statistical software code needed to do all the data analysis and create all the graphs and tables presented in the associated manuscript.

Technical Abstract: This dataset contains all raw data and R statistical software code needed to reproduce the data processing, statistical model fitting, and data/model visualizations presented in the associated manuscript, titled “Distribution of Pseudomonas amygdali pv. loropetali in the twig phylloplane of Loropetalum chinense shrubs in ornamental plant nurseries.” The manuscript describes a survey done across six ornamental plant nurseries to assess the prevalence of galling symptoms in loropetalum plants caused by the bacterium Pseudomonas amygdali pv. loropetali (PAL), and the abundance of the PAL bacterium. The presence of symptoms was assessed, and the abundance of PAL estimated with a PAL-specific qPCR method, on twigs at three height strata on each plant. In the associated analysis notebook, we present a spatial analysis of the symptom prevalence (Moran’s I and logistic regression), and a Gamma generalized linear mixed model comparing PAL abundance across nurseries, height strata, and galled versus gall-free plants. Significant differences in PAL number were found between nurseries, between strata, and between galled and gall-free plants. The raw data are provided here in .csv format, and the R statistical software code in an RMarkdown notebook, with .Rmd source code and rendered .html output.