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Comparative genomics analysis of five Psychrobacter strains isolated from world-wide habitats reveal high intra-genus variations

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Abstract

Psychrobacter has been regarded as an important genus for bacterial cold adaptation studies. However, members of this genus are highly varied in terms of both cold adaptability and genome content. To get an understanding of the diversity of members of this genus, five Psychrobacter strains (G, K5, 273-4, PAMC21119 and PRwf-1), with publicly available complete/draft genome, were selected and comprehensive comparative genomics analyses were performed among them. The closest phylogenetic relationship, highest average nucleotide identity (96.78%) and best sequence synteny were identified between strains G and K5. These findings suggest they belong to the same species, despite the long geographic distance between them (Antarctic and Siberia). 4542 gene clusters in total were identified from the five genomes, and of which 1424 were shared by all of them. The number of genes unique to strains G, K5, 273-4, PAMC21119 and PRwf-1 are 183, 188, 300, 637 and 665, respectively. COG assignment revealed their differences in gene content related to stress response. The extensive sequence rearrangements and the large number of genes unique to strain PAMC21119 and PRwf-1 suggest they may have experienced a high level of gene exchanges in the permafrost soil and the surface of fish skin.

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Abbreviations

ANI:

Average nucleotide identity

BLAST:

Basic local alignment search tool

BlastN:

Nucleotide BLAST

BRIG:

BLAST ring image generator

COG:

Clusters of orthologous groups

CSP:

Cold shock protein

NCBI:

National center for biotechnology information

ORF:

Open reading frame

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Acknowledgements

This research was funded by the National Natural Science Foundation of China (41176174), awarded to Xuezheng Lin. Weizhi Song was funded by the China Scholarship Council (201508200019).

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Authors and Affiliations

  1. School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia

    Shan Zhang & Weizhi Song

  2. Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, 2052, Australia

    Shan Zhang & Weizhi Song

  3. College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China

    Min Yu

  4. The First Institute of Oceanography, State Oceanic Administration, Qingdao, 266061, China

    Xuezheng Lin

Authors
  1. Shan Zhang
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  2. Weizhi Song
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  3. Min Yu
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Correspondence to Xuezheng Lin.

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Communicated by M. da Costa.

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Zhang, S., Song, W., Yu, M. et al. Comparative genomics analysis of five Psychrobacter strains isolated from world-wide habitats reveal high intra-genus variations. Extremophiles 21, 581–589 (2017). https://doi.org/10.1007/s00792-017-0927-1

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  • DOI: https://doi.org/10.1007/s00792-017-0927-1

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