DOI: 10.5061/dryad.nd154
title: Data from: Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite

description: Background: Phylogenetic heterogeneity across Pseudomonas genus is
 complemented by its diverse genome architecture enriched by accessory
 genetic elements (plasmids, transposons, and integrons) conferring
 resistance across this genus. Here, we sequenced a stress tolerant
 genotype i.e. Pseudomonas sp. strain RL isolated from a
 hexachlorocyclohexane (HCH) contaminated pond (45 mg of total HCH g−1
 sediment) and further compared its gene repertoire with 17 reference
 ecotypes belonging to P. stutzeri, P. mendocina, P. aeruginosa, P.
 psychrotolerans and P. denitrificans, representing metabolically diverse
 ecosystems (i.e. marine, clinical, and soil/sludge). Metagenomic data from
 HCH contaminated pond sediment and similar HCH contaminated sites were
 further used to analyze the pan-genome dynamics of Pseudomonas genotypes
 enriched across increasing HCH gradient. Results: Although strain RL
 demonstrated clear species demarcation (ANI ≤ 80.03%) from the rest of its
 phylogenetic relatives, it was found to be closest to P. stutzeri clade
 which was further complemented functionally. Comparative functional
 analysis elucidated strain specific enrichment of metabolic pathways like
 α-linoleic acid degradation and carbazole degradation in Pseudomonas sp.
 strain RL and P. stutzeri XLDN-R, respectively. Composition based methods
 (%codon bias and %G + C difference) further highlighted the significance
 of horizontal gene transfer (HGT) in evolution of nitrogen metabolism,
 two-component system (TCS) and methionine metabolism across the
 Pseudomonas genomes used in this study. An intact mobile class-I integron
 (3,552 bp) with a captured gene cassette encoding for dihydrofolate
 reductase (dhfra1) was detected in strain RL, distinctly demarcated from
 other integron harboring species (i.e. P. aeruginosa, P. stutzeri, and P.
 putida). Mobility of this integron was confirmed by its association with
 Tnp21-like transposon (95% identity) suggesting stress specific
 mobilization across HCH contaminated sites. Metagenomics data from pond
 sediment and recently surveyed HCH adulterated soils revealed the in situ
 enrichment of integron associated transposase gene (TnpA6100) across
 increasing HCH contamination (0.7 to 450 mg HCH g−1 of soil). Conclusions:
 Unlocking the potential of comparative genomics supplemented with
 metagenomics, we have attempted to resolve the environment and strain
 specific demarcations across 18 Pseudomonas gene complements. Pan-genome
 analyses of these strains indicate at astoundingly diverse metabolic
 strategies and provide genetic basis for the cosmopolitan existence of
 this taxon.
description: Maximum Likelihood Tree
 (Newick Format) for 51 Pseudomonas Genomes using Azotobacter vinelandii CA
 as outgroup.Conserved genes (400)
 based phylogenetic tree of strain RL and representative Pseudomonas
 genotypes constructed at 1000 bootstrap with Azotobacter vinelandii CA as
 an out-group. Branch lengths are drawn to scale, with scale bar indicating
 the number of amino acid substitutions. Numbers on branches are the
 bootstrap values of the clusters on the right.tree_treebase.nwkMaximum Likelihood Tree (Nexus Format) for 51 Pseudomonas Genomes using Azotobacter vinelandii CA as outgroup.Conserved genes (400) based phylogenetic tree of strain RL and representative Pseudomonas genotypes constructed at 1000 bootstrap with Azotobacter vinelandii CA as an out-group. Branch lengths are drawn to scale, with scale bar indicating the number of amino acid substitutions. Numbers on branches are the bootstrap values of the clusters on the right.tree_treebase.nwk.nexAlignment Files for protein coding sequences of bacterial conserved marker genes (n=400) for 51 representative Pseudomonas genomes.Phylogenetic status of strain RL was determined using 400 conserved bacterial marker genes and representative whole genome sequences from 40 diverse Pseudomonas species as available in NCBI database (http://www.ncbi.nlm.nih.gov/genome/browse/representative/). A phylogenetic tree was hence constructed using maximum likelihood (ML) methodology on the basis of protein coding bacterial conserved gene (400) sequences [39] determined for Pseudomonas sp. RL and 50 other Pseudomonas strains with Azotobacter vinelandii being the outgroup.Alignment Files.zip