Extrafloral nectaries and mite domatia jointly shape the leaf microbiome in Viburnum

Description of the data and file structure This repository contains field data and code neccessary to reproduce the analysis of "Hidden costs and compensatory benefits: Microbial consequences link extrafloral nectaries and mite domatia in Viburnum".In brief, leaf tissue and extrafloral nectary (EFN) tissue was sampled across species of Viburnum that varied in their combination of mite domatia and EFN traits. The tissue samples were then sequenced for the fungal community. Raw sequence data is archived on NCBI's SRA under BioProject PRJNA1479831. Files and variables R coding file File: efntestzone.Rmd Description: An R markdown file containing all analysis for the project, including processing of raw reads. Can be opened in R and R studio statistical software. Analysis was done in R version 4.5.2 and R Studio 2026.01.0 Data and metadata File: EFNfungi_metadata.csv Description: Metadata linking sequencing data to plant information and treatment. Variables: sample-id: Sequence sample unique name number: Unique number for the sequence sample well: Well plate associated with the sequence sample barcode: Unique barcode associated with the sequence sample, used for separating reads into their respective samples full_treatment: Short code to represent the plant and treatment. It is an amalgamation of Plant replicate (I-IV), species name, leaf replicate (1-3), domatia treatment (A [Blocked] or B [Control]), and whether the leaf or EFN was sampled (Suffix of EFN means EFN was sampled) Plant: Plant replicate within species, ranging from I to IV species: Species of Viburnum the sample is from leaf_rep: What leaf replicate the sample is taken from, ranging from 1-3 domatia_treatment: Whether the domatia on that leaf was experimentally blocked with pruning tar (Blocked) or not (Control) Trait_sampled: Whether the sample is from leaf tissue (Leaf) or EFN tissue (EFN) Plant_unique_ID: A code for the unique plant. It is the species with the plant replicate as a suffix Plant_identifier: Unique identifier for the leaf sample. It is an amalgation of Viburnum species, plant replicate (I-IV), leaf replicate (rep1-rep3), and whether the domatia were blocked or control EFN_type: The location of EFNs naturally on the plant Domatia_naturally: Whether the leaf naturally had domatia (Tuft) or not (None) File: efn_mite_CFU.csv Description: Data on fungal and mite abundance for each leaf and EFN sample. Variables: blank first column for row names Plant_identifier: Unique identifier for the leaf sample. It is an amalgation of Viburnum species, plant replicate (I-IV), leaf replicate (rep1-rep3), and whether the domatia were blocked or control full_treatment: Short code to represent the plant and treatment. It is an amalgamation of Plant replicate (I-IV), species name, leaf replicate (1-3), domatia treatment (A [Blocked] or B [Control]), and whether the leaf or EFN was sampled (Suffix of EFN means EFN was sampled) species: Species of Viburnum the sample is from leaf_rep: What leaf replicate the sample is taken from, ranging from 1-3 domatia_treatment: Whether the domatia on that leaf was experimentally blocked with pruning tar (Blocked) or not (Control) Trait_sampled: Whether the sample is from leaf tissue (Leaf) or EFN tissue (EFN) Plant_unique_ID: A code for the unique plant. It is the species with the plant replicate as a suffix EFN_type: The location of EFNs naturally on the plant Domatia_maturally: Whether the leaf naturally had domatia (Tuft) or not (None) sample_id: Sequence sample unique name total.mites_mitecsv: Total mites counted on the leaves, originally from a csv datasheet on mite abundance. These are the values used in the analysis of mite abundance. An 'NA' means this data was not possible to collect or missing for this sample. CFU_per_area_leaf: The number of fungal colony forming units from the leaf sample, standardized by area sampled. An 'NA' means this data was not possible to collect or missing for this sample. Avg_EFN_Cov: ???????? An 'NA' means this data was not possible to collect or missing for this sample. total.mites_cfucsv: Count data of mites originally from the cfu csv file. Preliminary data???- Not used in the analysis of mite abundance. An 'NA' means this data was not possible to collect or missing for this sample. CFU_per_area_EFN: The number of fungal colony forming units from the EFN sample, standardized by area sampled. An 'NA' means this data was not possible to collect or missing for this sample. domatia_functional: Whether there were functional mite domatia on the leaf (Yes or No), accounting both for whether there were domatia and whether they were blocked CFU_raw_leaf: The raw counts of colony forming units from the leaf sample. An 'NA' means this data was not possible to collect or missing for this sample. CFU_raw_EFN: The raw counts of colony forming units from the EFN sample. An 'NA' means this data was not possible to collect or missing for this sample. radius_leaf: The radius of the leaf hole punch sample, in cm. An 'NA' means this data was not possible to collect or missing for this sample. area_leaf: The area in mm^2 of the leaf hole punch sample, in mm. An 'NA' means this data was not possible to collect or missing for this sample. radius_EFN: The radius of the EFN hole punch sample, in mm. An 'NA' means this data was not possible to collect or missing for this sample. EFN_area: The area in mm^2 of the leaf hole punch sample, in cm. An 'NA' means this data was not possible to collect or missing for this sample. File: UNITE_dada2_taxonomy_ASV.csv Description: Taxonomy file linking ASVs with assigned taxonomy (Kingdom; Phylum; Order; Class; Family; Genus; Species) using UNITE ITS dynamic classifying database release sh_general_release_dynamic_19.02.2025.fasta (available at https://dx.doi.org/10.15156/BIO/3301229). Variables: first row contains the unique Amplicon Sequence Variant (ASV) identifier Kingdom: Kingdom of the ASV, with the prefix k__ Phylum: Phylum of the ASV, with the prefix p__. An "NA" means the ASV could not be classified to this taxonomic depth. Class: Class of the ASV, with the prefix c__. An "NA" means the ASV could not be classified to this taxonomic depth. Order: Order of the ASV, with the prefix o__. An "NA" means the ASV could not be classified to this taxonomic depth. Family: Family of the ASV, with the prefix f__. An "NA" means the ASV could not be classified to this taxonomic depth. Genus: Genus of the ASV, with the prefix g__. An "NA" means the ASV could not be classified to this taxonomic depth. Species: Species of the ASV, with the prefix s__. An "NA" means the ASV could not be classified to this taxonomic depth. File: EFN_feature_table_ASV.csv Description: Feature table of sequencing samples, where columns headers are the unique Amplicon Sequence Variant names and rows names are sample IDs (corresponding to EFNfungi_metadata.csv 'sample-id' columns). The numbers in the matrix are read counts after sequencing. File: out.2.t163.f5.mcc.tre Description: This tree (mcc.tre) is the maximum clade credibility (MCC) tree for Viburnum species. See more information at https://github.com/mlandis/vib_div/blob/master/output/out.2.t163.f5.mcc.tre and https://doi.org/10.1093/sysbio/syaa027