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:TheBLAST_best_10.csvfile contains the following information:OTU_ID: OTU identifier abundance: total OTU read abundancereference: UNITE database reference sequence idkingdom: UNITE kingdom annotationphylum: UNITE phylum annotationclass: UNITE class annotationorder: UNITE order annotationfamily: UNITE family annotationgenus: UNITE genus annotationspecies: UNITE species hypothesis annotationpident: per cent sequence similarity to the reference sequencelength: alignment length of the query to the reference sequence (sequence overlap)slen: query sequence lengthmismatches: number of mismatches to the reference sequencegapopen: number of gap openings relative to the reference sequenceqstart: first position of alignment of the query sequence to the reference sequenceqend: last position of alignment of the query sequence to the reference sequencesstart: first position of alignment of the reference sequencesend: last position of alignment of the reference sequenceevalue: e-value of the query sequence to the best-hitting reference sequencebitscore: score of the blast match of the query sequence to the reference sequenceThetaxa_AM.csvandtaxa_ECM.csvfiles 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 thresholdsphylum: phylum annotation based on consensus hit and similarity and coverage thresholdsclass: class annotation based on consensus hit and similarity and coverage thresholdsorder: order annotation based on consensus hit and similarity and coverage thresholdsfamily: family annotation based on consensus hit and similarity and coverage thresholdsgenus: genus annotation based on consensus hit and similarity and coverage thresholdsspecies: genus annotation based on consensus hit and similarity and coverage thresholdstaxa_consensus: per cent consensus of BLAST hit across the five best hitsabundance: total OTU read abundancesimilarity: per cent sequence similarity to the consensus sequencecoverage: per cent sequence coverage to the consensus sequenceevalue: evalue to the consensus sequenceectomycorrhiza_exploration_type: inferred lineage of ectomycorrhizal fungi based on the FungalTraits databaseectomycorrhiza_lineage: inferred ectomycorrhiza exploration type based on the FungalTraits databaseThemetadata.csvfile contains the following information:sample: sample IDecotype: tea tree ecotypesite: site IDcol_AM: number of arbuscular mycorhizal observations per 60 cm of fine rootcol_ECM: number of ectomycorrhizal observations per root tips countedweight: number of total mycorrhizal observations per samplelatitude: latitude in decimal degreeslongitude: longitude in decimal degreesMAP: 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)

本存储库包含八个打包数据文件。经质量过滤的丛枝菌根真菌（arbuscular mycorrhizal fungi）与外生菌根真菌（ectomycorrhizal fungi）的操作分类单元（OTU）表、分类注释表，以及样本元数据表，可用于复现GitHub平台上的可重复统计分析工作流。
文件内容说明如下：
1. `BLAST_best_10.csv` 文件包含以下信息：
- OTU_ID：OTU标识符
- abundance：OTU总读取丰度
- reference：UNITE数据库参考序列ID
- kingdom：UNITE数据库界水平注释
- phylum：UNITE数据库门水平注释
- class：UNITE数据库纲水平注释
- order：UNITE数据库目水平注释
- family：UNITE数据库科水平注释
- genus：UNITE数据库属水平注释
- species：UNITE物种假说注释
- pident：与参考序列的序列相似度百分比
- length：查询序列与参考序列的比对长度（即序列重叠区域）
- slen：查询序列长度
- mismatches：与参考序列的错配碱基数目
- gapopen：相对于参考序列的间隙开放数目
- qstart：查询序列与参考序列比对的起始位置
- qend：查询序列与参考序列比对的终止位置
- sstart：参考序列比对的起始位置
- send：参考序列比对的终止位置
- evalue：查询序列与最佳比对参考序列的e值
- bitscore：查询序列与参考序列的BLAST匹配得分
2. `taxa_AM.csv` 与 `taxa_ECM.csv` 文件包含以下信息（5条最佳比对结果的一致性相似度阈值为66.67%，覆盖度阈值为90%；丛枝菌根真菌的相似度阈值以属水平定义，外生菌根真菌的相似度阈值以进化支水平定义）：
- OTU_ID：OTU标识符
- kingdom：基于一致性比对结果、相似度及覆盖度阈值得到的界水平注释
- phylum：基于一致性比对结果、相似度及覆盖度阈值得到的门水平注释
- class：基于一致性比对结果、相似度及覆盖度阈值得到的纲水平注释
- order：基于一致性比对结果、相似度及覆盖度阈值得到的目水平注释
- family：基于一致性比对结果、相似度及覆盖度阈值得到的科水平注释
- genus：基于一致性比对结果、相似度及覆盖度阈值得到的属水平注释
- species：基于一致性比对结果、相似度及覆盖度阈值得到的属水平注释
- taxa_consensus：5条最佳BLAST比对结果的一致性百分比
- abundance：OTU总读取丰度
- similarity：与一致性序列的序列相似度百分比
- coverage：与一致性序列的序列覆盖度百分比
- evalue：与一致性序列的e值
- ectomycorrhiza_exploration_type：基于FungalTraits数据库推断的外生菌根真菌进化支
- ectomycorrhiza_lineage：基于FungalTraits数据库推断的外生菌根真菌探索型
3. `metadata.csv` 文件包含以下信息：
- sample：样本ID
- ecotype：茶树生态型
- site：样地ID
- col_AM：每60cm细根中丛枝菌根结构观测数
- col_ECM：每计数根尖中外生菌根结构观测数
- weight：单样本总菌根结构观测数
- latitude：十进制纬度
- longitude：十进制经度
- MAP：年平均降水量（°C）
- MAT：年平均气温（mm）
- soil_moisture：样地水平土壤含水率估算值（%）
- pH：样地水平土壤pH值（1:5水土比浸提）
- C_total：样地水平土壤总有机碳估算值（%）
- N_total：样地水平土壤总氮估算值（%）
- P_available：样地水平土壤有效磷估算值（mg/kg；考尔菲尔德提取法）
- ammonium：样地水平土壤铵态氮估算值（mg/kg；氯化钾提取法）
- nitrate：样地水平土壤硝态氮估算值（mg/kg；氯化钾提取法）