title: Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite.
abstract: 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.
authors.affiliation: Department of Zoology, University of Delhi, New Delhi, 110007, India. anukriti.sharma8@gmail.com.
authors.forename: Anukriti
authors.initials: A
authors.lastname: Sharma
authors.affiliation: Department of Zoology, University of Delhi, New Delhi, 110007, India. nikki1018sangwan@gmail.com.
authors.forename: Naseer
authors.initials: N
authors.lastname: Sangwan
authors.affiliation: Department of Zoology, University of Delhi, New Delhi, 110007, India. viveknegi2006@gmail.com.
authors.forename: Vivek
authors.initials: V
authors.lastname: Negi
authors.affiliation: Department of Zoology, University of Delhi, New Delhi, 110007, India. puneet.k1311@gmail.com.
authors.forename: Puneet
authors.initials: P
authors.lastname: Kohli
authors.affiliation: Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India. khuranaj@genomeindia.org.
authors.forename: Jitendra Paul
authors.initials: JP
authors.lastname: Khurana
authors.affiliation: All India Network Project on Soil Biodiversity and Biofertilizers, Indian Institute of Soil Science, Bhopal, 462038, India. desiraju.rao@gmail.com.
authors.forename: Desiraju Lakshmi Narsimha
authors.initials: DL
authors.lastname: Rao
authors.affiliation: Department of Zoology, University of Delhi, New Delhi, 110007, India. ruplal@gmail.com.
authors.forename: Rup
authors.initials: R
authors.lastname: Lal
mesh_terms: D001483:Base Sequence; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D005838:Genotype; D001556:Hexachlorocyclohexane / Q000737:chemistry / Q000378:metabolism*; D032023:Integrons / Q000235:genetics; D056186:Metagenomics; D010802:Phylogeny; D011549:Pseudomonas / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D014871:Water Microbiology; D014874:Water Pollutants, Chemical / Q000737:chemistry / Q000378:metabolism
chemical_list: D012336:RNA, Ribosomal, 16S; D014874:Water Pollutants, Chemical; D001556:Hexachlorocyclohexane