Variability in the dual mycorrhizal associations of tea tree, Melaleuca alternifolia

This repository contains eight packed data files.

The quality-filtered otu tables and taxonomic annotation tables for arbuscular mycorrhizal fungi and ectomycorrhizal fungi, as well as the sample metadata sheet, can be used to run the reproducible statistical analysis workflow at GitHub.

Contents:

The

BLAST_best_10.csv

file contains the following information:

OTU_ID: OTU identifier

abundance: total OTU read abundance

reference: UNITE database reference sequence id

kingdom: UNITE kingdom annotation

phylum: UNITE phylum annotation

class: UNITE class annotation

order: UNITE order annotation

family: UNITE family annotation

genus: UNITE genus annotation

species: UNITE species hypothesis annotation

pident: per cent sequence similarity to the reference sequence

length: alignment length of the query to the reference sequence (sequence overlap)

slen: query sequence length

mismatches: number of mismatches to the reference sequence

gapopen: number of gap openings relative to the reference sequence

qstart: first position of alignment of the query sequence to the reference sequence

qend: last position of alignment of the query sequence to the reference sequence

sstart: first position of alignment of the reference sequence

send: last position of alignment of the reference sequence

evalue: e-value of the query sequence to the best-hitting reference sequence

bitscore: score of the blast match of the query sequence to the reference sequence

The

taxa_AM.csv

and

taxa_ECM.csv

files contain the following information (consensus similarity is 66.67% across the five best hits; coverage threshold is 90%; similarity thresholds are defined at level genus for AM fungi and ectomycorrhiza lineage for ECM fungi):

OTU_ID: OTU identifier

kingdom: kingdom annotation based on consensus hit and similarity and coverage thresholds

phylum: phylum annotation based on consensus hit and similarity and coverage thresholds

class: class annotation based on consensus hit and similarity and coverage thresholds

order: order annotation based on consensus hit and similarity and coverage thresholds

family: family annotation based on consensus hit and similarity and coverage thresholds

genus: genus annotation based on consensus hit and similarity and coverage thresholds

species: genus annotation based on consensus hit and similarity and coverage thresholds

taxa_consensus: per cent consensus of BLAST hit across the five best hits

abundance: total OTU read abundance

similarity: per cent sequence similarity to the consensus sequence

coverage: per cent sequence coverage to the consensus sequence

evalue: evalue to the consensus sequence

ectomycorrhiza_exploration_type: inferred lineage of ectomycorrhizal fungi based on the FungalTraits database

ectomycorrhiza_lineage: inferred ectomycorrhiza exploration type based on the FungalTraits database

The

metadata.csv

file contains the following information:

sample: sample ID

ecotype: tea tree ecotype

site: site ID

col_AM: number of arbuscular mycorhizal observations per 60 cm of fine root

col_ECM: number of ectomycorrhizal observations per root tips counted

weight: number of total mycorrhizal observations per sample

latitude: latitude in decimal degrees

longitude: longitude in decimal degrees

MAP: mean annual precipitation (°C)

MAT: mean annual temperatre (mm)

soil_moisture: estimate of site level soil moisture content (%)

pH: estimate of site level soil pH (1:5 water)

C_total: estimate of site level total soil organic carbon (%)

N_total: estimate of site level total soil nitrogen (%)

P_available: estimate of site level soil plant-avalable phosphorus (mg/kg; Colwell extraction method)

ammonium: estimate of site level soil ammonium (mg/kg; KCl extraction)

nitrate: estimate of site level soil nitrate (mg/kg; KCl extraction)