phyllosphere-priority-effects-metadata-scripts

Metadata and R scripts from the article "Priority effects influence bacterial community assembly on temperate deciduous tree leaves" by Z. Wang, VJ Javaran, J Lauzon, J-B Leducq, and SW Kembel.

Contents

• 16S_rRNA_DADA2.R — R code to identify ASVs for 16S rRNA amplicon data using DADA2
• rpoB_DADA2.R — R code to identify ASVs for rpoB amplicon data using DADA2
• R_analysis_code.R — R code to carry out all analyses described in the article
• metadata.tsv — A tab-delimited text file containing information on sample metadata. Columns:
  • sample_id - unique sample identifier
  • raw_prefix - FASTQ filename prefix for this sample
  • sample_type - sample type - inoculation control, inoculated, or PCR negative control
  • Treatment - control (C) or strain ID of inoculated strain
  • inoculum_id - inoculated strain ID
  • Plant - host plant species
  • site - site (plot) number
  • tree - tree ID
  • branch - branch ID
  • host_tree_block - full specification of host tree species, plot, tree ID for the sample
  • branch_id - full specification of host tree species, plot, tree ID, branch ID for the sample
  • timepoint_label - sampling date (MONTH_DAY)
  • sampling_stage - sampling stage (end-season or two-week sampling)
  • inoctime - inoculation time (control, earlyseason, lateseason)
  • design_window - full specification of inoculation time, sampling stage, sampling date, inoculation treatment for the sample