Data from: The interaction of Saccharomyces paradoxus with its natural competitors on oak bark

ITS_taxonomySix oak bark pieces (~1g) from four oak trees (three pieces from oak 1 and one piece from each of the other trees) in Northern Germany were collected. In addition an infusion (20g oak bark in a sterile tea bag in 300 mL water for 24 hours) for each tree was prepared. DNA was extracted from all samples using the Soil DNA Kit from Omega Bio-Tek. The resulting DNA was sent to LGC Genomics (GmbH, Berlin, Germany) for amplification of the fungal ITS (ITS1, 5.8S and ITS2) sequences using ITS1f (CTTGGTCATTTAGAGGAAGTAA) and ITS4 (TCCTCCGCTTATTGATATGC) primers using the 454 GS FLX+ Titanium Sequencer (Roche). ITS sequences were processed with mothur and subsampled to 4000 sequences per sample. For taxonomic classification the mothur implementation of naive Bayesian classification was used with a threshold bootstrap value of 70% for each taxonomic level. The used fungal database was the “dynamic” mothur release from 08.12.2013 of the UNITE database.ITS.tax.summaryITS_OTUSix oak bark pieces (~1g) from four oak trees (three pieces from oak 1 and one piece from each of the other trees) in Northern Germany were collected. In addition an infusion (20g oak bark in a sterile tea bag in 300 mL water for 24 hours) for each tree was prepared. DNA was extracted from all samples using the Soil DNA Kit from Omega Bio-Tek. The resulting DNA was sent to LGC Genomics (GmbH, Berlin, Germany) for amplification of the fungal ITS (ITS1, 5.8S and ITS2) sequences using ITS1f (CTTGGTCATTTAGAGGAAGTAA) and ITS4 (TCCTCCGCTTATTGATATGC) primers using the 454 GS FLX+ Titanium Sequencer (Roche). We used the “pairwise.seqs” command in mothur for the OTU-based analysis with ignoring the penalization of the sequence ends. The shared file shows the distribution of OTUs in the ten groups at 97% and 95% identity level.16S_taxonomySix oak bark pieces (~1g) from four oak trees (three pieces from oak 1 and one piece from each of the other trees) in Northern Germany were collected. In addition an infusion (20g oak bark in a sterile tea bag in 300 mL water for 24 hours) for each tree was prepared. DNA was extracted from all samples using the Soil DNA Kit from Omega Bio-Tek. The resulting DNA was sent to LGC Genomics (GmbH, Berlin, Germany) for amplification of the bacterial 16S rRNA (V1 to V5) sequences using GM3 (AGAGTTTGATCMTGGC) and 926R (CCGTCAATTCMTTTGAGTTT) primers using the 454 GS FLX+ Titanium Sequencer (Roche). 16S sequences were processed with mother, aligned to the comprehensive seed database from SILVA downloaded on April 29, 2013 and subsampled to 4000 sequences per sample. Sequence classification was performed using the mothur implementation of naive Bayesian classification based on the RDP Classifier version 9, with a threshold bootstrap value of 70% for each taxonomic level.16S.tax.summary16S_OTUSix oak bark pieces (~1g) from four oak trees (three pieces from oak 1 and one piece from each of the other trees) in Northern Germany were collected. In addition an infusion (20g oak bark in a sterile tea bag in 300 mL water for 24 hours) for each tree was prepared. DNA was extracted from all samples using the Soil DNA Kit from Omega Bio-Tek. The resulting DNA was sent to LGC Genomics (GmbH, Berlin, Germany) for amplification of the bacterial 16S rRNA (V1 to V5) sequences using GM3 (AGAGTTTGATCMTGGC) and 926R (CCGTCAATTCMTTTGAGTTT) primers using the 454 GS FLX+ Titanium Sequencer (Roche). 16S sequences were processed with mother, aligned to the comprehensive seed database from SILVA downloaded on April 29, 2013 and subsampled to 4000 sequences per sample. We created a distance matrix of aligned sequences and clustered them into operational taxonomic units (OTUs) using the average neighbor clustering algorithm. The shared file shows the distribution of OTUs in the ten groups at 97% and 95% identity level.

ITS_taxonomy
从德国北部的4株栎树中采集了6块栎树皮样品（每块约1g，其中栎树1采集3块，其余3株栎树各采集1块）。此外，为每株栎树制备了浸提液：将20g栎树皮置于无菌茶包中，加入300mL水浸泡24小时。随后使用Omega Bio-Tek公司的土壤DNA提取试剂盒（Soil DNA Kit）对所有样品提取基因组DNA。将提取得到的DNA送至德国柏林的LGC Genomics（GmbH）公司，采用引物ITS1f（CTTGGTCATTTAGAGGAAGTAA）和ITS4（TCCTCCGCTTATTGATATGC）对真菌ITS（包含ITS1、5.8S和ITS2区域）序列进行扩增，随后使用罗氏（Roche）的454 GS FLX+ Titanium测序仪进行测序。使用mothur软件对ITS序列进行分析，并将每个样品的序列数抽平至4000条。分类学注释采用mothur实现的朴素贝叶斯分类器，每个分类学层级的bootstrap阈值设为70%。所用的真菌参考数据库为2013年12月8日发布的UNITE数据库“动态”mothur版。
ITS.tax.summary
ITS_OTU
从德国北部的4株栎树中采集了6块栎树皮样品（每块约1g，其中栎树1采集3块，其余3株栎树各采集1块）。此外，为每株栎树制备了浸提液：将20g栎树皮置于无菌茶包中，加入300mL水浸泡24小时。使用Omega Bio-Tek公司的土壤DNA提取试剂盒对所有样品提取基因组DNA，将提取得到的DNA送至德国柏林的LGC Genomics（GmbH）公司，采用引物ITS1f和ITS4对真菌ITS序列进行扩增，随后使用罗氏454 GS FLX+ Titanium测序仪进行测序。本研究采用mothur软件中的“pairwise.seqs”命令进行基于操作分类单元（operational taxonomic units, OTU）的分析，过程中忽略序列末端的罚分。共享文件展示了10个分组在97%和95%相似度水平下的OTU分布情况。
16S_taxonomy
从德国北部的4株栎树中采集了6块栎树皮样品（每块约1g，其中栎树1采集3块，其余3株栎树各采集1块）。此外，为每株栎树制备了浸提液：将20g栎树皮置于无菌茶包中，加入300mL水浸泡24小时。使用Omega Bio-Tek公司的土壤DNA提取试剂盒对所有样品提取基因组DNA，将提取得到的DNA送至德国柏林的LGC Genomics（GmbH）公司，采用引物GM3（AGAGTTTGATCMTGGC）和926R（CCGTCAATTCMTTTGAGTTT）对细菌16S核糖体RNA（16S rRNA）的V1至V5可变区序列进行扩增，随后使用罗氏454 GS FLX+ Titanium测序仪进行测序。使用mothur软件对16S序列进行处理，将序列与2013年4月29日下载的SILVA综合种子数据库进行比对，并将每个样品的序列数抽平至4000条。序列分类学注释采用基于RDP分类器第9版的mothur实现朴素贝叶斯分类方法，每个分类学层级的bootstrap阈值设为70%。
16S.tax.summary
16S_OTU
从德国北部的4株栎树中采集了6块栎树皮样品（每块约1g，其中栎树1采集3块，其余3株栎树各采集1块）。此外，为每株栎树制备了浸提液：将20g栎树皮置于无菌茶包中，加入300mL水浸泡24小时。使用Omega Bio-Tek公司的土壤DNA提取试剂盒对所有样品提取基因组DNA，将提取得到的DNA送至德国柏林的LGC Genomics（GmbH）公司，采用引物GM3和926R对细菌16S rRNA的V1至V5可变区序列进行扩增，随后使用罗氏454 GS FLX+ Titanium测序仪进行测序。使用mothur软件对16S序列进行处理，将序列与2013年4月29日下载的SILVA综合种子数据库进行比对，并将每个样品的序列数抽平至4000条。本研究构建了比对后序列的距离矩阵，并使用平均邻接聚类算法将序列聚类为操作分类单元（operational taxonomic units, OTU）。共享文件展示了10个分组在97%和95%相似度水平下的OTU分布情况。