#====================================================# # Zinger_et_al_metabar_PP1_filtered_tabs.zip # #====================================================# Data from: Determinants of soil community assembly in a tropical forest By Zinger, Lucie, Taberlet, Pierre, Schimann, Heidy, Bonin, Aurélie, Boyer, Frédéric, De Barba, Marta, Gaucher, Philippe, Gielly, Ludovic, Giguet-Covex, Charline, Iribar, Amaia, Réjou-Méchain, Maxime, Rayé, Gilles, Rioux, Delphine, Schilling, Vincent, Tymen, Blaise, Viers, Jérôme, Zouiten, Cyril, Thuiller, Wilfried, Coissac, Eric, Chave, Jérôme. Contact author: Lucie Zinger (lucie@zinger.fr) This zip file contains 4 txt files (tab delim) of filtered sequencing data (i.e. after sequence clustering and spurious OTUs removal), corresponding each to Archaea, Bacteria, Eukaryota and Plants amplicons. A full description of data curation is provided in the Supplementary Methods of Zinger et al. Determinants of soil community assembly in a tropical forest. Briefly, it consisted in: (i) Removing low quality reads (containing Ns, too short, singletons) (ii) Forming OTUs (Operational Taxonomic Units) using sumatra (https://git.metabarcoding.org/obitools/sumatra/wikis/home) and Infomap (http://www.mapequation.org/code.html) for a dissimilarity threshold of 3 mismatches. (iii) Taxonomic assignments with the ecotag program (part of the OBITools package) using genbank v197 and specific reference databases (see below). (iv) Removing low quality OTUs (putative contaminants, chimeras or degraded). (v) Smoothing of OTUs counts to reduce the impact of tag-switching (Esling et al. 2015). Column headings: - id the OTU id - count OTU abundance (nb reads) in the whole dataset - occurrence OTU occurrence (nb samples where present) - GC_content OTU sequence GC content - seq_length OTU sequence length - best_identity OTU maximum similarity (%) against references in gb_r197 Genbank v197 silva_v119 SILVA v119 (MOTHUR version) nouragues2013 plant database (https://doi.org/10.5061/dryad.1qt12/2) - best_match.* OTU best match in corresponding reference database - db_ok Database selected for taxonomic assignation - [superkingdom, phylum, class, order, family, genus, species]_name_ok OTU taxonomic affiliation at the corresponding taxonomic level - scientific_name_ok OTU finest taxonomic assignment - taxonomic_rank_ok taxonomic rank at which the OTU is assigned - sequence OTU representative sequence (most abundant) - sample.*** OTU abundances (nb reads) in each sample. See information in Zinger_et_al_SBB_extracellular_samples.txt for samples correspondances. #Further details on content #========================== #1/Zinger_et_al_metabar_PP1_Archaea_filtered_tab.txt #----------------------------- Target taxon: Archaea Target region: v8-v9 of the 16S rRNA gene Forward primer: CCTGCTCCTTGCACACAC Reverse primer: CCTACGGCTACCTTGTTAC Sequencing platform: HiSeq 2x100 Specific reference database: silva 16S (MOTHUR version 119) #1/Zinger_et_al_metabar_PP1_Bacteria_filtered_tab.txt #----------------------------- Target taxon: Bacteria Target region: v5-v6 of the 16S rRNA gene Forward primer : GGATTAGATACCCTGGTAGT Reverse primer : CACGACACGAGCTGACG Sequencing platform: MiSeq 2x250 Specific reference database: silva 16S (MOTHUR version 119) #2/Zinger_et_al_metabar_PP1_Eukaryota_filtered_tab.txt #----------------------------- Target taxon: Eukaryota Target region: v7 of the 18S rRNA gene Forward primer: TTTGTCTGSTTAATTSCG Reverse primer: TCACAGACCTGTTATTGC Sequencing platform: HiSeq 2x150 Specific reference database: silva 18S (MOTHUR version 119) #3/Zinger_et_al_metabar_PP1_Plants_filtered_tab.txt #----------------------------- Target taxon: Viridiplantae Target region: trnL P6 loop Forward primer: GGGCAATCCTGAGCCAA Reverse primer: CCATTGAGTCTCTGCACCTATC Sequencing platform: HiSeq 2x100 Specific reference database: Nouragues 2013 database (https://doi.org/10.5061/dryad.1qt12/2). #4/Other information #------------------- Data collection: All authors have collected samples in the field and/or performed DNA extraction Taberlet Pierre, Bonin Aurélie, and Rioux Delphine have conducted PCR amplifications. Viers Jerome and Zouiten Cyril performed the chemical analyses. Chave Jerome, Réjou-Mechain Maxime, and Tymen Blaise provided the LiDAR data. Zinger Lucie and Schilling Vincent performed the bioinformatics analyses. References: Esling, P., Lejzerowicz, F., Pawlowski, J., 2015. Accurate multiplexing and filtering for high-throughput amplicon-sequencing. Nucleic Acids Research 43, 2513-2524.