Supporting data and code for: Report of a new resistance to carbendazim in Fusicoccum amygdali, the causal agent of constriction canker of peach and almond trees

Context

The constriction canker of peach and almond trees, caused by Fusicoccum amygdali, is an important disease which is mainly controled using fungicides. In this study, we report a first case of resistance to carbendazim for this pathogen in France. We first screened a set of populations using bioassay. After identifying a population displaying evidence of resistance, isolates were cultivated on medium and tested with a bioassay, confirming the presence of highly resistant phenotypes. A fragment of the beta-tubulin gene were sequenced from isolates displaying resistance or sensitive phenotypes. A mutation leading to the E198K substitution was identified in resistant isolates. The population from which resistant isolates have been identified is located in Corsica Island.

Datasets

There are five data sets used in this study. The files can be found in the "data" folder.

• COM_SHP.RDATA: the first data set contains geographical information to plot the french administrative layer 'commune'

• DEP_SHP.RDATA: the first data set contains geographical information to plot the french administrative layer 'departement'

• REG_SHP.RDATA: the second data set contains geographical information to plot the french administrative layer 'regions'

These three geographical data files were obtained using the data from the IGN website. The version of the data used is the "Edition Novembre 2017". The shapefile were simplified using mapshaper online tool in order to reduce the size of the files.

• fusicodat.txt: The third dataset contains the results of the dose-response bioassays conducted on populations or isolates.

  • strain_ID: the ID of the population or the strain
  • species: species name
  • strain_type: type of biological sample. Possible values are 'population', 'individual' or 'reference' (for the reference strain)
  • active_substance: the tested active substance
  • sampling_year: the year the sample was sampled in the field
  • nb_day: number of day post inoculation on plate with medium
  • dose: the concentration of the active substance in the medium (mg/L)
  • perc_croiss: the ratio between the measured mycelial growth for a given dose and the measured mycelial growth at dose '0 mg/L' (ie without active substance) for individuals OR the ratio between the average elongation of the germ tube for a given dose and the the average elongation of the germ tube at dose '0 mg/L' (ie without active substance)

• fusipopdat.txt: the fourth dataset contains the information to plot the studied populations on the map.

  • pop_ID: the ID of the sampled population
  • carbend_R: the resistance status of the population, at least confirmed by founding a strain resistant to a mycelial growth bioassay
  • sampling_year: the year the population was sampled
  • departement: the french 'departement' which the population was sampled from

R scripts

• load_fusico_data.R: the script to load the different datasets in the R environment.
• fusico_bioassay_pop.R: the script to perform the regression analysis on the populations germination inhibition bioassay results, with carbendazim. It also contains the code for producing Figure 1.
• fusico_bioassay_ind.R: the script to perform the regression analysis on the individuals growth inhibition bioassay results, with both carbendazim and diethofencarb. It also contains the code for producing Figure 3.
• fusico_map.R: the script for producing the map (Figure 2).

Citation

You can cite the related study as follow:

• Fontaine S., Caddoux L., Remuson F. and Barrès B. Report of a new resistance to carbendazim in Fusicoccum amygdali, the causal agent of constriction canker of peach and almond trees. Plant Pathology, 71:785-792, 2022. doi:10.1111/ppa.13525.

If you want to use (some of) the code found on this page or if you want to cite this repository:

• Benoit Barrès. Supporting data and code for: Report of a new resistance to carbendazim in Fusicoccum amygdali, the causal agent of constriction canker of peach and almond trees. Zenodo.