Global population structure in MAST-4 unicellular marine predators

Supplementary material for "Global population structure in MAST-4 unicellular marine predators" This repository contains the supplementary datasets, source data, analytical workflows, and custom scripts associated with the manuscript: Global population structure in MAST-4 unicellular marine predators Francisco Latorre, Olivier Jaillon, Michael E. Sieracki, Corinne Cruaud, Ramon Massana, and Ramiro Logares. Repository contents MAST4_population_genomics_Zenodo│├── Supplementary_Data│ ├── Supplementary_Data_1.xlsx│ ├── Supplementary_Data_2.xlsx│ ├── Supplementary_Data_3.xlsx│ ├── Supplementary_Data_4.xlsx│ ├── Supplementary_Data_5.xlsx│ └── Supplementary_Data_6.xlsx│├── Source_Data│ ├── MAST4.TARA.coverage.95id.80rcov.tsv│ ├── TaraOceans_stations_metadata.txt│ ├── MAST4_genome_size.txt│ ├── NOG_annotations.tsv│ ├── eggNOG_hierarchy.txt│ ││ └── MAST4│ ├── MAST4A.fst.txt│ ├── MAST4A.intradiv.txt│ ├── MAST4A.snpeff.dnds.txt│ ├── MAST4A_dbCAN.tbl│ ├── MAST4A_eggNOG.tbl│ ││ ├── MAST4B.fst.txt│ ├── MAST4B.intradiv.txt│ ├── MAST4B.snpeff.dnds.txt│ ├── MAST4B_dbCAN.tbl│ ├── MAST4B_eggNOG.tbl│ ││ ├── MAST4C.fst.txt│ ├── MAST4C.intradiv.txt│ ├── MAST4C.snpeff.dnds.txt│ ├── MAST4C_dbCAN.tbl│ ├── MAST4C_eggNOG.tbl│ ││ ├── MAST4E.fst.txt│ ├── MAST4E.intradiv.txt│ ├── MAST4E.snpeff.dnds.txt│ ├── MAST4E_dbCAN.tbl│ └── MAST4E_eggNOG.tbl│├── Tutorials│ ├── 01-Mapping.md│ ├── 02-Abundance.md│ ├── 03-SnpEff.md│ ├── 04-Pogenom.md│ └── 05-dNdS.md│└── Scripts │ ├── Figures │ ├── Figure1_code.R │ ├── Figure2_code.R │ ├── Figure3andS2_code.R │ ├── FigureS1_code.R │ └── FigureS3_code.R │ └── Additional_Scripts ├── dNdS.py └── idfilter.pl File description Supplementary_Data This folder contains the supplementary datasets associated with the manuscript. Supplementary_Data_1.xlsxTara Oceans metagenomic samples used in the study. Supplementary_Data_2.xlsxEnvironmental metadata associated with the analyzed samples. Supplementary_Data_3.xlsxFunctional annotation of genes exclusive to MAST-4A genomic populations. Supplementary_Data_4.xlsxFunctional annotation of genes exclusive to MAST-4B genomic populations. Supplementary_Data_5.xlsxFunctional annotation of genes exclusive to MAST-4C genomic populations. Supplementary_Data_6.xlsxFunctional annotation of genes exclusive to MAST-4E genomic populations. Source_Data This folder contains all source data used for analyses and figure generation. Shared files MAST4.TARA.coverage.95id.80rcov.tsvCoverage and abundance estimates for all MAST-4 species across Tara Oceans metagenomic samples. TaraOceans_stations_metadata.txtMetadata associated with Tara Oceans sampling stations. MAST4_genome_size.txtGenome size estimates for the four MAST-4 reference genomes. NOG_annotations.tsvFunctional annotation database used for gene functional assignments. eggNOG_hierarchy.txtHierarchical classification of eggNOG functional categories. Species-specific files (Source_Data/MAST4) For each MAST-4 species (A, B, C and E), the following files are provided: MAST4X.fst.txtPairwise FST estimates among Tara Oceans populations. MAST4X.intradiv.txtWithin-population nucleotide diversity estimates. MAST4X.snpeff.dnds.txtGene-level dN/dS estimates derived from SNP annotations. MAST4X_dbCAN.tblCarbohydrate-active enzyme annotations obtained using dbCAN. MAST4X_eggNOG.tblFunctional annotations obtained using eggNOG. Where X corresponds to species A, B, C or E. Tutorials This folder contains the analytical workflows used to reproduce the population genomics analyses. 01-Mapping.mdMetagenomic read recruitment workflow against MAST-4 reference genomes. 02-Abundance.mdCoverage and abundance estimation workflow. 03-SnpEff.mdSNP annotation workflow using SnpEff. 04-Pogenom.mdPopulation genomics workflow, including SNP filtering and population structure analyses. 05-dNdS.mdPositive selection analysis workflow and dN/dS estimation. Scripts This folder contains custom scripts used to generate the figures presented in the manuscript. Figures Figure1_code.RScripts used to generate Figure 1. Figure2_code.RScripts used to generate Figure 2. Figure3andS2_code.RScripts used to generate Figure 3 and Supplementary Figure 2. FigureS1_code.RScripts used to generate Supplementary Figure 1. FigureS3_code.RScripts used to generate Supplementary Figure 3. Additional scripts dNdS.pyCustom Python script used for dN/dS calculations. idfilter.plPerl script used for sequence identity filtering. Raw sequencing data Raw sequencing data are publicly available through the European Nucleotide Archive (ENA): Single-cell amplified genomes (SAGs): PRJEB6603 Tara Oceans metagenomes: PRJEB4352 Additional genomic resources Genome coassemblies, coding sequence predictions, and amino acid predictions are available in FigShare: https://doi.org/10.6084/m9.figshare.13072322 Reproducibility All analyses presented in the manuscript can be reproduced using the source data, analytical workflows, and custom scripts provided in this repository together with the publicly available sequencing datasets described above. License Data are distributed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. Code and scripts are distributed under the MIT License unless otherwise specified. Citation If you use these data, scripts, or workflows, please cite both the associated manuscript and this Zenodo repository.