Mothur tutorial

The tutorial have been moved to GitHub.<div><br></div><div>Please go to : https://github.com/vaulot/metabarcodes_tutorials</div

Oceanic picoplankton abundance measured by flow cytometry between1987 and 2004 - Database in Access 2007 format.

This dataset (Access format) encompass a number of cruises from 1985 to about 2004 with depth profiles of photosynthetic picoplankton measure by  flow cytometry.<br><br>Buitenhuis, E.T., Li, W.K.W., Vaulot, D., Lomas, M.W., Landry, M., Partensky, F., Karl, D.M. et al. 2012. Picophytoplankton biomass distribution in the global ocean. Earth Syst. Sci. Data. 4:37–46.<br><br><b>List of cruises :</b><br> <table> <tbody><tr> <th>Cruise</th> <th>Ship</th> <th>Year</th> </tr> <tr> <td>OLIPAC</td> <td>NO Atalante</td> <td>1994</td> </tr> <tr> <td>MINOS</td> <td>NO Suroit</td> <td>1995</td> </tr> <tr> <td>EQPACTT007</td> <td>RV Thomson</td> <td>1992</td> </tr> <tr> <td>EQPACTT008</td> <td>RV Thomson</td> <td>1992</td> </tr> <tr> <td>EQPACTT008D</td> <td>RV Thomson</td> <td>1992</td> </tr> <tr> <td>EQPACTT011</td> <td>RV Thomson</td> <td>1992</td> </tr> <tr> <td>EQPACTT012</td> <td>RV Thomson</td> <td>1992</td> </tr> <tr> <td>CHLOMAX</td> <td>NO Suroit</td> <td>1987</td> </tr> <tr> <td>EROSDISCO89</td> <td>HMS Discovery</td> <td>1989</td> </tr> <tr> <td>EROSBAN</td> <td>Bannock</td> <td>1989</td> </tr> <tr> <td>EROSDISCO93</td> <td>HMS Discovery</td> <td>1993</td> </tr> <tr> <td>Li87022</td> <td><br></td> <td>1987</td> </tr> <tr> <td>Li88026</td> <td>CSS Hudson</td> <td>1988</td> </tr> <tr> <td>Li89003</td> <td><br></td> <td>1989</td> </tr> <tr> <td>Li91001</td> <td><br></td> <td>1991</td> </tr> <tr> <td>POEM91</td> <td><br></td> <td>1991</td> </tr> <tr> <td>Eddy92</td> <td><br></td> <td>1992</td> </tr> <tr> <td>Li92037</td> <td><br></td> <td>1992</td> </tr> <tr> <td>Malaga93</td> <td><br></td> <td>1993</td> </tr> <tr> <td>Li93002</td> <td><br></td> <td>1993</td> </tr> <tr> <td>Delaware95</td> <td><br></td> <td>1995</td> </tr> <tr> <td>Chile95</td> <td><br></td> <td>1995</td> </tr> <tr> <td>Li95016</td> <td><br></td> <td>1995</td> </tr> <tr> <td>Lopez96</td> <td><br></td> <td>1995</td> </tr> <tr> <td>HOT</td> <td>Moana Wave</td> <td>1990-1994</td> </tr> <tr> <td>EROSVALD</td> <td>Valdivia</td> <td>1992</td> </tr> <tr> <td>Surtropac17</td> <td>NO Noroit</td> <td>1992</td> </tr> <tr> <td>Flupac</td> <td>NO Suroit</td> <td>1994</td> </tr> <tr> <td>EUMELI3</td> <td>NO Atalante</td> <td>1991</td> </tr> <tr> <td>EUMELI4</td> <td>NO Atalante</td> <td>1992</td> </tr> <tr> <td>EUMELI5</td> <td>NO Atalante</td> <td>1992</td> </tr> <tr> <td>NOAA93</td> <td>NOAA Malcolm Baldbridge</td> <td>1993</td> </tr> <tr> <td>NOAA95</td> <td>NOAA Malcolm Baldbridge</td> <td>1995</td> </tr> <tr> <td>Palau</td> <td>RV Sohgen-Maru</td> <td>1990</td> </tr> <tr> <td>McManus</td> <td><br></td> <td>1991</td> </tr> <tr> <td>Bermuda</td> <td><br></td> <td>1988-1989</td> </tr> <tr> <td>Endeavour177</td> <td>Endeavour</td> <td>1988</td> </tr> <tr> <td>Oceanus206</td> <td>Oceanus</td> <td>1989</td> </tr> <tr> <td>Meteor87</td> <td>RV Meteor</td> <td>1987</td> </tr> <tr> <td>Aquaba</td> <td><br></td> <td>1992-1993</td> </tr> <tr> <td>NOPACCS</td> <td>RV Hakurei-Maru</td> <td>1990</td> </tr> <tr> <td>NIOZNatl89</td> <td>RV Tyro</td> <td>1989</td> </tr> <tr> <td>NIOZIndian</td> <td><br></td> <td>1992-1993</td> </tr> <tr> <td>Australia</td> <td>RV Sohgen-Maru</td> <td>1990</td> </tr> <tr> <td>SurugaBay</td> <td>Boat</td> <td>1992-1993</td> </tr> <tr> <td>ArabianTTN043</td> <td>RV Thomson</td> <td>1995</td> </tr> <tr> <td>ArabianTTN045</td> <td>RV Thomson</td> <td>1995</td> </tr> <tr> <td>ArabianTTN049</td> <td>RV Thomson</td> <td>1995</td> </tr> <tr> <td>PROSOPE99</td> <td>NO Atalante</td> <td>1999</td> </tr> <tr> <td>ArabianTTN050</td> <td>RV Thomson</td> <td>1995</td> </tr> <tr> <td>ArabianTTN053</td> <td>RV Thomson</td> <td>1995</td> </tr> <tr> <td>ArabianTTN054</td> <td>RV Thomson</td> <td>1995</td> </tr> <tr> <td>Kiwi6</td> <td>RV Revelle</td> <td>1997</td> </tr> <tr> <td>Kiwi7</td> <td>RV Revelle</td> <td>1997</td> </tr> <tr> <td>Kiwi8</td> <td>RV Revelle</td> <td>1998</td> </tr> <tr> <td>Kiwi9</td> <td>RV Revelle</td> <td>1998</td> </tr> <tr> <td>Almo-1</td> <td>NO Atalante</td> <td>1997</td> </tr> <tr> <td>Hesperides</td> <td>Hesperides</td> <td>1995</td> </tr> <tr> <td>Almo-2</td> <td>NO Atalante</td> <td>1998</td> </tr> <tr> <td>AESOPS/NBP97-1</td> <td>R/V Nathaniel B. Palmer</td> <td>1997</td> </tr> <tr> <td>BIOSOPE</td> <td>NO Atalante<br></td> <td><br><br>2004<br><br><br></td> </tr> </tbody></table> <br

Green microalgae in marine coastal waters: The Ocean Sampling Day (OSD) dataset - Supplementary material

Supplementary material to paper published in Scientific Reports. See the pdf file for the description of the supplementary data files

R functions for flow cytometry histogram correction

Correction for flow cytometry histograms when part of the population is in noise.<br><br>This has been published in the following paper :<br><br>Gérikas Ribeiro C, Marie D, Lopes dos Santos A, Pereira Brandini F, Vaulot D. (2016). Estimating microbial populations by flow cytometry: Comparison between instruments. Limnol Oceanogr Methods doi:10.1002/lom3.10135.<br><div><br></div><div>The code has been moved to github : https://github.com/vaulot/R_flow-cytometry-correction</div

Protist Ribosomal Reference database (PR2) - SSU rRNA gene database - old version

The Protist Ribosomal Reference database (PR²) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields.<br><br><div>The database is now available on <b>Github </b>for easier maintenance. <br></div><div><br></div><div><b>Home page : </b>https://github.com/vaulot/pr2_database</div><div><br></div><div><a href="https://github.com/vaulot/pr2_database/releases">Link to latest release</a></div><div><br><div><div><b>DOI: </b><a href="https://doi.org/10.6084/m9.figshare.5913181" rel="nofollow">https://doi.org/10.6084/m9.figshare.5913181</a></div><div><b><br></b></div><div><b>Contact<br><br></b>Daniel VAULOT, Laure GUILLOU and Fabrice NOT<br>DIPO team, Plankton Group, UMR 7144 CNRS-UPMC<br>Station Biologique,<br>Place G. Tessier<br>29680 Roscoff FRANCE<br>email: [email protected]<br><br><b>Please cite</b><br><p>Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. <i>Nucleic Acids Res.</i> 41:D597–604.</p><p><br></p><b>The PhytoRef (16S plastid database) is available here : </b>https://figshare.com/articles/PhytoREF_a_reference_database_of_the_plastidial_16S_rRNA_gene_of_photosynthetic_eukaryotes_with_curated_taxonomy/4689826<br><br></div></div></div

Protist Ribosomal Reference database (PR2) - SSU rRNA gene database

The Protist Ribosomal Reference database (PR²) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields.<br><br><div>The database is now synchronized on <b>Github </b>for easier maintenance.<br></div><div><br></div><div><b>Home page</b></div><div>https://github.com/vaulot/pr2_database</div><div><br></div><div><b>Latest version of files</b></div><div>https://github.com/vaulot/pr2_database/releases</div><div><br></div><div><b>Information</b></div><div>https://github.com/vaulot/pr2_database/wiki<br></div><div><br></div><div><b>Reports problems and bugs</b></div><div>https://github.com/vaulot/pr2_database/issues<br></div><div><br><div><b>Contact<br><br></b>Daniel VAULOT, Laure GUILLOU and Fabrice NOT<br>DIPO team, Plankton Group, UMR 7144 CNRS-UPMC<br>Station Biologique,<br>Place G. Tessier<br>29680 Roscoff FRANCE<br>email: [email protected]<br><br><b>Please cite</b><br><p>Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. <i>Nucleic Acids Res.</i> 41:D597–604.</p><p><br></p><b>The PhytoRef (16S plastid database) is available here : </b>https://figshare.com/articles/PhytoREF_a_reference_database_of_the_plastidial_16S_rRNA_gene_of_photosynthetic_eukaryotes_with_curated_taxonomy/4689826</div></div

Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of 18S rRNA gene with a focus on Chlorophyta

<b>Supplementary data 1</b>. Mothur script for sequence analysis<br><b>Supp. data 2</b>. Fasta file of Chlorophyta OTUs for V4<br><b>Supp. data 3</b>. Fasta file of Chlorophyta OTUs for V9<br><b>Supp. data 4</b>. Chlorophyta OTUs for V4 with assignation and read abundance at the different stations (Excel file).<br><b>Supp. data 5</b>. Chlorophyta OTUs for V9 with assignation and read abundance at the different stations (Excel file).<br><b>Supp. data 6</b>. Top 10 BLAST hits against Genbank nr database for Chlorophyta V4 OTUs. Red lines correspond to OTUs badly assigned to non Chlorophyta and green corresponds to OTUs badly assigned to another Chlorophyta representative.<br><b>Supp. data 7</b>. Top 10 BLAST hits against Genbank nr database for Chlorophyta V9 OTUs. Red lines correspond to OTUs badly assigned to non Chlorophyta and green lines corresponds to OTUs badly assigned to another Chlorophyta representative.<br

Diversity and distribution of haptophytes reavealed by environmental sequencing - a review. Perspectives in Phycology. Supplementary material.

<p><b></b> </p><p><b>7. Fig. S1. </b>Maximum-likelihood tree<b> </b>(RAxML v. 8.026, GTRCAT) based on 971 haptophyte 18S rRNA gene sequences from Table S1, 451 are from cultured strains and 520 from environmental clone libraries. Bootstrap values are marked at the nodes. The colours indicate taxonomic groups.</p> <p><b>8. Table S1. </b>Haptophyte 18S rRNA gene sequence reference database including 971 sequences, 451 from cultures and 520 from environmental clone libraries. See File S1 for description of its construction. Chimeras (32) identified by uchime in mothur and by manual blast are listed on sheet 2.</p> <p><b>9. Table S2</b>. Information on selected, commonly used PCR primers for environmental sequencing and metabarcoding of haptophytes.</p> <p><b>10. File S1.</b> Description of the construction of the Haptophyte 18S rRNA gene reference sequence database, alignment and final RAxML phylogenetic tree.</p> <p><b>11. File S2. </b>Fasta file with accession numbers and 18S rRNA gene sequence of 971 reference sequences for taxonomic assignment in mothur or Qiime. </p> <p><b>12. File S3. </b>Taxonomy file with systematic placement of 971 haptophyte reference sequences for taxonomic assignment in mothur or Qiime. </p> <p><b>13. File S4. </b>Curated haptophyte 18S rRNA gene alignment for Figs 2 and S1.</p

DinoREF: a curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene

<p>Mordret, S., Piredda, R., Vaulot, D., Montresor, M., Kooistra, H. C. F. & Sarno, D. (under revision 2018). DinoREF: a curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene. <i>Molecular Ecology Resources.</i><br></p><p><b><br></b></p><p><b>Supplementary Material</b><b> 1 </b></p><p> </p><p>List of 18S sequences included in DinoREF including annotations extracted from GenBank and literature sources (see “read-me” for details on metadata).</p><p><b>Supplementary Material 2</b></p><p>Fasta file (.fast) of sequences used to build DinoREF including the GenBank Accession number of each sequence.</p><p><b>Supplementary Material 3</b></p><p>DinoREF taxonomy file 1 (.taxonomy) with the taxonomy provided by GenBank for each sequence included in the database. </p><p><b>Supplementary Material 4</b></p><p>DinoREF taxonomy file 2 (.taxonomy) with the 8-level taxonomy for each sequence included in the database. </p><p><b>Supplementary Material 5</b></p><p>DinoREF taxonomy file 3 (.taxonomy) with the classification by Superclades for each sequence included in the database.</p><p><b>Supplementary Material 6</b></p><p>List of V4 unique sequences. When multiple 18S sequences share the same V4 region, the sequences IDs (GenBank # and species name) are reported, one after the other, in the same row.</p><p><b>Supplementary Material 7</b></p><p>List of OTUs_98%. When multiple V4 sequences cluster in the same OTU at 98%, the sequences IDs (GenBank # and species name) are reported, one after the other, in the same row.</p><p><b>Supplementary Material 8</b></p><p> Fasta file (.fasta) of sequences of early branching dinoflagellates.<br></p

Pico and Nanoplankton Abundance and Carbon Stocks along the Brazilian Bight. PeerJ. Supplementary material. Table S1.

<p><b>Table S1.</b>  Raw flow cytometry and environmental data.</p