Variability in the dual mycorrhizal associations of tea tree, <i>Melaleuca alternifolia</i>

<p dir="ltr">This repository contains eight packed data files.</p><p dir="ltr">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 <a href="https://github.com/LukeLikesDirt/TeaTreeMycorrhizas" target="_blank">GitHub</a>.</p><p dir="ltr">Contents:</p><p dir="ltr">The</p><p dir="ltr"><b>BLAST_best_10.csv</b></p><p dir="ltr">file contains the following information:</p><p dir="ltr">OTU_ID: OTU identifier </p><p dir="ltr">abundance: total OTU read abundance</p><p dir="ltr">reference: UNITE database reference sequence id</p><p dir="ltr">kingdom: UNITE kingdom annotation</p><p dir="ltr">phylum: UNITE phylum annotation</p><p dir="ltr">class: UNITE class annotation</p><p dir="ltr">order: UNITE order annotation</p><p dir="ltr">family: UNITE family annotation</p><p dir="ltr">genus: UNITE genus annotation</p><p dir="ltr">species: UNITE species hypothesis annotation</p><p dir="ltr">pident: per cent sequence similarity to the reference sequence</p><p dir="ltr">length: alignment length of the query to the reference sequence (sequence overlap)</p><p dir="ltr">slen: query sequence length</p><p dir="ltr">mismatches: number of mismatches to the reference sequence</p><p dir="ltr">gapopen: number of gap openings relative to the reference sequence</p><p dir="ltr">qstart: first position of alignment of the query sequence to the reference sequence</p><p dir="ltr">qend: last position of alignment of the query sequence to the reference sequence</p><p dir="ltr">sstart: first position of alignment of the reference sequence</p><p dir="ltr">send: last position of alignment of the reference sequence</p><p dir="ltr">evalue: e-value of the query sequence to the best-hitting reference sequence</p><p dir="ltr">bitscore: score of the blast match of the query sequence to the reference sequence</p><pre></pre><p dir="ltr">The</p><p dir="ltr"><b>taxa_AM.csv</b></p><p dir="ltr">and</p><p dir="ltr"><b>taxa_ECM.csv</b></p><p dir="ltr">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):</p><p><br></p><p dir="ltr">OTU_ID: OTU identifier </p><p dir="ltr">kingdom: kingdom annotation based on consensus hit and similarity and coverage thresholds</p><p dir="ltr">phylum: phylum annotation based on consensus hit and similarity and coverage thresholds</p><p dir="ltr">class: class annotation based on consensus hit and similarity and coverage thresholds</p><p dir="ltr">order: order annotation based on consensus hit and similarity and coverage thresholds</p><p dir="ltr">family: family annotation based on consensus hit and similarity and coverage thresholds</p><p dir="ltr">genus: genus annotation based on consensus hit and similarity and coverage thresholds</p><p dir="ltr">species: genus annotation based on consensus hit and similarity and coverage thresholds</p><p dir="ltr">taxa_consensus: per cent consensus of BLAST hit across the five best hits</p><p dir="ltr">abundance: total OTU read abundance</p><p dir="ltr">similarity: per cent sequence similarity to the consensus sequence</p><p dir="ltr">coverage: per cent sequence coverage to the consensus sequence</p><p dir="ltr">evalue: evalue to the consensus sequence</p><p dir="ltr">ectomycorrhiza_exploration_type: inferred lineage of ectomycorrhizal fungi based on the FungalTraits database</p><p dir="ltr">ectomycorrhiza_lineage: inferred ectomycorrhiza exploration type based on the FungalTraits database</p><p dir="ltr">The</p><p dir="ltr"><b>metadata.csv</b></p><p dir="ltr">file contains the following information:</p><p dir="ltr">sample: sample ID</p><p dir="ltr">ecotype: tea tree ecotype</p><p dir="ltr">site: site ID</p><p dir="ltr">col_AM: number of arbuscular mycorhizal observations per 60 cm of fine root</p><p dir="ltr">col_ECM: number of ectomycorrhizal observations per root tips counted</p><p dir="ltr">weight: number of total mycorrhizal observations per sample</p><p dir="ltr">latitude: latitude in decimal degrees</p><p dir="ltr">longitude: longitude in decimal degrees</p><p dir="ltr">MAP: mean annual precipitation (°C)</p><p dir="ltr">MAT: mean annual temperatre (mm)</p><p dir="ltr">soil_moisture: estimate of site level soil moisture content (%)</p><p dir="ltr">pH: estimate of site level soil pH (1:5 water)</p><p dir="ltr">C_total: estimate of site level total soil organic carbon (%)</p><p dir="ltr">N_total: estimate of site level total soil nitrogen (%)</p><p dir="ltr">P_available: estimate of site level soil plant-avalable phosphorus (mg/kg; Colwell extraction method)</p><p dir="ltr">ammonium: estimate of site level soil ammonium (mg/kg; KCl extraction)</p><p dir="ltr">nitrate: estimate of site level soil nitrate (mg/kg; KCl extraction)</p>