DOI: 10.5281/zenodo.7551744
title: Tara Oceans (2009-2013) rDNA 16S V4V5 ASV table (dada2)

description: This repository contains a rDNA 16S V4V5 ASV table (TARA-Oceans_16S-V4V5_dada2_table.tsv.gz) for Tara Oceans (2009-2013).


In the file TARA-Oceans_16S-V4V5_dada2_table.tsv.gz, each ASV, one per row, is described by the following fields: amplicon = ASV identifier; taxonomy = taxonomic path assigned to the ASV using IDTAXA; confidence = IDTAXA confidence scores for each taxonomic rank; total = total number of reads for the entire dataset; spread = number of samples in which the ASV is detected; sequence = ASV nucleic acid sequence; TARA_XXXXXXXXXX = number of reads in each of the 1,134 Tara Oceans samples.


Detailed information about DNA extraction, PCR amplification and Illumina sequencing of metabarcodes, as well as subsequent sequence data cleaning and taxonomic assignment can be found in (Alberti et al. 2017). Briefly, DNA samples were amplified by PCR targeting the hypervariable region V4V5 (primer pair: 15F-Y 5′- GTGYCAGCMGCCGCGGTAA-3′ and 926R 5′- CCGYCAATTYMTTTRAGTTT-3′ 16S primers; (Parada et al. 2016)) of the 16S rRNA marker gene followed by the high-throughput sequencing of the amplicons. The details of PCR mixes, thermocycling and sequencing conditions are provided in Alberti et al. (2017).


Resulting paired-end reads were mixed-oriented meaning that both R1 and R2 files are composed by a mix of forward and reverse reads. Paired-end reads were trimmed to remove PCR primer sequences using Cutadapt v2.7 (Martin, 2011) and dispatched into four files, 2 files for the classical orientation (forward reads in R1 and reverse reads in R2) and 2 others for the other orientation (reverse reads in R1 and forward reads in R2). Paired-end reads without both primers were filtered out using the option --discard-untrimmed. Forward and reverse reads were trimmed at position 215 and 190 for R1 and R2 files respectively. Reads with ambiguous nucleotides or with a maximum number of expected errors (maxEE) superior to 2 were filtered out using the function filterAndTrim() from the R package dada2 (Callahan et al., 2016). For each run and read orientation, error rates were defined using the function learnErrors() and denoised using the dada() function with pool = TRUE before being merged using mergePairs() with default parameters. Mixed orientated reads from the same sample and sequencing replicates were summed together. Remaining chimeras were removed using the function removeBimeraDenovo(). Scripts producing the ASV table are publicly available here: https://gitlab.univ-nantes.fr/combi-ls2n/taradada.


ASVs were taxonomically assigned using IDTAXA (50% confidence threshold) (Murali, Bhargava, and Wright 2018) with SILVA v138.


Alberti, A., Poulain, J., Engelen, S., Labadie, K., Romac, S., Ferrera, I., Albini, G., Aury, J.-M., Belser, C., Bertrand, A., Cruaud, C., Da Silva, C., Dossat, C., Gavory, F., Gas, S., Guy, J., Haquelle, M., Jacoby, E., Jaillon, O., Lemainque, A., Pelletier, E., Samson, G., Wessner, M., Genoscope Technical Team, Bazire, P., Beluche, O., Bertrand, L., Besnard-Gonnet, M., Bordelais, I., Boutard, M., Dubois, M., Dumont, C., Ettedgui, E., Fernandez, P., Garcia, E., Aiach, N.G., Guerin, T., Hamon, C., Brun, E., Lebled, S., Lenoble, P., Louesse, C., Mahieu, E., Mairey, B., Martins, N., Megret, C., Milani, C., Muanga, J., Orvain, C., Payen, E., Perroud, P., Petit, E., Robert, D., Ronsin, M., Vacherie, B., Acinas, S.G., Royo-Llonch, M., Cornejo-Castillo, F.M., Logares, R., Fernández-Gómez, B., Bowler, C., Cochrane, G., Amid, C., Hoopen, P.T., De Vargas, C., Grimsley, N., Desgranges, E., Kandels-Lewis, S., Ogata, H., Poulton, N., Sieracki, M.E., Stepanauskas, R., Sullivan, M.B., Brum, J.R., Duhaime, M.B., Poulos, B.T., Hurwitz, B.L., Tara Oceans Consortium Coordinators, Acinas, S.G., Bork, P., Boss, E., Bowler, C., De Vargas, C., Follows, M., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Jaillon, O., Kandels-Lewis, S., Karp-Boss, L., Karsenti, E., Not, F., Ogata, H., Pesant, S., Raes, J., Sardet, C., Sieracki, M.E., Speich, S., Stemmann, L., Sullivan, M.B., Sunagawa, S., Wincker, P., Pesant, S., Karsenti, E., Wincker, P., 2017. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Sci Data 4, 170093. https://doi.org/10.1038/sdata.2017.93


Callahan, B.J., McMurdie, P.J., Rosen, M.J., Han, A.W., Johnson, A.J.A., Holmes, S.P., 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13, 581–583. https://doi.org/10.1038/nmeth.3869


Martin, M., 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet j. 17, 10. https://doi.org/10.14806/ej.17.1.200


Murali, A., Bhargava, A., Wright, E.S., 2018. IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences. Microbiome 6, 140. https://doi.org/10.1186/s40168-018-0521-5