Phylogenomics of aquatic bacteria
type: Dataset
distribution: Landing page for the dataset
description: Intermediate data files obtained during the work on the manuscript "Phylogenomics of aquatic bacteria reveal molecular mechanisms behind the limits of their adaptation to salinity". The files published here were used at various stages of the analysis (or sum-up the stages) and should allow reproduction of the results as well as expanded investigation of the dataset. These files are: ar_mags_info.txt - information table for collected archeal MAGs. It contains names of the MAGs in format {data source 2-letter code}_{name of the MAG as in ENA}, the biome of origin and taxonomic classification. For the brackish MAGs there is also annotation to the basin (Baltic/Caspian) of origin and additional metadata for the Baltic Sea MAGs. bac_mags_info.txt - information table for collected bacterial MAGs. It contains names of the MAGs in format {data source 2-letter code}_{name of the MAG as in ENA}, the biome of origin and taxonomic classification. For the brackish MAGs there is also annotation to the basin (Baltic/Caspian) of origin and additional metadata for the Baltic Sea MAGs. CheckM_all_MAGs.csv - CheckM results for all the investigated MAGs (completness, contamination, strain heterogeneity). ani_file.txt - average nucleotide indentity between all the pairs of investigated MAGs. MAG-cluster-stats-interbiome-clusters.xlsx - Excel file with a table annotating MAGs to >95% ANI clusters and the represtatives chosen for further analysis marked. Contains also sheets with just the representatives, clusters common between the brackish basins and between the biomes, as well as MSG_table.tsv imported into Excel spreadsheet. The first sheet also contains accession numbers for the bacterial MAGs used in this study. nozero.bifurc.bac.tree.nwk - phylogenetic tree of all the MAGs and GTDB reference genomes. Obtained using GTDB-tk. pruned95.nozero.bifurc.bac.tree.nwk - the phylogenetic tree (nozero.bifurc.bac.tree.nwk) pruned to contain only one represtative for a biome from each >95% ANI …
modified: 2025-02-17T00:00:00Z
issued: 2025-02-17T00:00:00Z
publisher: Royal Institute of Technology
theme: HEAL
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Krzysztof Jurdzinski
    type: Agent
    account: https://orcid.org/0000-0001-9544-5755
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Maliheh Mehrshad
    type: Agent
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Stefan Bertilsson
    type: Agent
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Anders Andersson
    type: Agent
    type: PrivateIndividual(s)
keyword: Biological adaptation
keyword: Biogeography and phylogeography
keyword: Microbial taxonomy
keyword: Phylogeny and comparative analysis
keyword: Freshwater ecology
keyword: Marine and estuarine ecology (incl. marine ichthyology)
keyword: Genomics and transcriptomics
keyword: Computational ecology and phylogenetics

Landing page for the dataset
type: Distribution
title: Landningssida för datasetet @sv
access URL: Phylogenomics of aquatic bacteria
availability: stable

Royal Institute of Technology
type: Agent
name: Kungliga Tekniska högskolan @sv
type: Academia-ScientificOrganisation
source: 026vcq606