Unifying the known and unknown microbial coding sequence space

Description

Data availability

We used public data as described in the Methods section and Appendix 1-table 5. The code used for the analyses in the manuscript is available at https://github.com/functional-dark-side/functional-dark-side.github.io/tree/master/scripts, (copy archived at swh:1:rev:86968509e38902580b04a25786c5a58ba2777b21). A list with the program versions can be found in https://github.com/functional-dark-side/functional-dark-side.github.io/blob/master/programs_and_versions.txt. The code to create the figures is available at https://github.com/functional-dark-side/vanni_et_al-figures, (copy archived at swh:1:rev:4c8f60e761bcac0dd02f17d2fdbb65dcaf75707a), and the data for the figure can be downloaded from https://doi.org/10.6084/m9.figshare.12738476.v2. A reproducible version of the workflow is available at https://github.com/functional-dark-side/agnostos-wf, (copy archived at swh:1:rev:5f9e23e8ac524a533f81c57e500a60b56191b1f5). The data is publicly available at https://doi.org/10.6084/m9.figshare.12459056.

The following data sets were generated:

Vanni C Fernandez-Guerra A (2020) figshare agnostosDB_dbf02445-20200519. https://doi.org/10.6084/m9.figshare.12459056

The following previously published data sets were used:

O'Gara F Jackson S Orlic S Steinke M Busch J Duarte B Caçador I Bobrova O Marteinsson V Reynisson E Loureiro C Luna G Quero GM Löscher CR Kremp A DeLorenzo ME Øvreås L Tolman J LaRoche J Penna A Frischer M Davis T Katherine B Meyer C Ramos S Magalhães C Jude-Lemeilleur F Aguirre-Macedo ML Wang S Poulton N Jones S Collin R Fuhrman JA Conan P Alonso C Stambler N Goodwin K Yakimov MM Baltar F Bodrossy L Kamp JV Frampton DMF Ostrowski M Ruth PV Malthouse P Claus S Deneudt K Mortelmans J Pitois S Wallom D Salter I Costa R Schroeder DC Kandil MM Amaral V Biancalana F Santana R Pedrotti ML Yoshida T Ogata H Ingleton T Munnik K Rodriguez-Ezpeleta N Berteaux-Lecellier V Wecker P Cancio I Vaulot D Bienhold C Ghazal H Chaouni B Essayeh S Ettamimi S Zaid EH Boukhatem N Bouali A Chahboune R Barrijal S Timinouni M Otmani F Bennani M Mea M Todorova N Karamfilov V Hoopen P Cochrane G L'Haridon S Bizsel K CVezzi A Lauro FM Martin P Jensen RM Hinks J Gebbels S Rosselli R Pascale FD Schiavon R Santos A Villar E Pesant S Cataletto B Malfatti F Edirisinghe R (2015) OSD ID ERS667653. Ocean Sampling Day. https://github.com/MicroB3-IS/osd-analysis/wiki/Guide-to-OSD-2014-data

Sunagawa A (2015) EBI European Nucleotide Archive ID PRJEB402. TARA Oceans. https://www.ebi.ac.uk/ena/browser/view/PRJEB402

Rusch DB Halpern AL Sutton G Heidelberg KB Williamson S Yooseph S Wu D Eisen JA Hoffman JM Remington K Beeson K Tran B Smith H Baden-Tillson H Stewart C Thorpe J Freeman J Andrews-Pfannkoch C Venter JE Li K Kravitz S Heidelberg JF Utterback T Rogers Y Falcón LI Souza V Bonilla-Rosso G Eguiarte LE Karl DM Sathyendranath S Platt T Bermingham E Gallardo V Tamayo-Castillo G Ferrari MR Strausberg RL Nealson K Friedman R Frazier M Venter JC (2007) NCBI BioProject ID PRJNA13694. Global Ocean Sampling. https://www.ncbi.nlm.nih.gov/bioproject?cmd=PRJNA13694

Mendler K Chen H PArks DH Lobb B Hug LA Doxey AC (2019) Annotree-Genome Taxonomy Database ID GTDB_r86. Annotree-GTDB_r86. https://data.ace.uq.edu.au/public/misc_downloads/annotree/r86/

Lloyd-Price JMahurkar ARahnavard GCrabtree JOrvis JHall ABBrady ACreasy HHMcCracken CGiglio MGMcDonald DFranzosa EAKnight RWhite OHuttenhower C (2017) Human Microbiome Project ID HMP. HMP (phase I and II). http://hmpdacc.org/