This repository supports Facultative symbiont virulence determines horizontal transmission rate without host strain specificity in Dictyostelium discoideum social amoebas
It contains two directories:
experiment, which contains
- bonniea_transmission_2023.R - R code used to run statistical analyses using the data files and generate figures
- host_fitness.clean.20220711.txt - Data from host fitness experiment with columns in the following order
- host identity
- symbiont identity
- MOI (multiplicity of infection) of host-symbiont pairing
- date of experiment
- estimated total number of host spores produced by sample
- percent of host spored infected by symbiont in sample
- percent of spores produced by sample relative to mean of uninfected controls
- type of host-symbiont pairing
- symbiont_transmission.clean.20220711.txt - Data from symbiont transmission experiment with columns in the following order
- host identity
- symbiont identity
- MOI of host-symbiont pairing
- date of experiment
- percent of host spores infected by symbiont in sample
- percent of infected spores that were previously uninfected
- type of host-symbiont pairing
genomics, which contains
- GFF files for the three P. bonniea genomes - Predicted intact gene for each symbiont genome
- assembly_to_set_operations.txt - Description and command-line code for how the GFF files were generated including long read assembly, short read polishing, gene annotation, pseudogene prediction, and set operations
- virulence_candidates.faa - Protein sequences for the candidate virulence factors identified in the study