Comparative genomics analysis of five Psychrobacter strains isolated from world-wide habitats reveal high intra-genus variations
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, 2...
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ftunivsthongkong:oai:repository.hkust.edu.hk:1783.1-133105 2024-01-28T10:00:58+01:00 Comparative genomics analysis of five Psychrobacter strains isolated from world-wide habitats reveal high intra-genus variations Zhang, Shan Song, Weizhi Yu, Min Lin, Xuezheng 2017 https://repository.hkust.edu.hk/ir/Record/1783.1-133105 https://doi.org/10.1007/s00792-017-0927-1 http://lbdiscover.ust.hk/uresolver?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rfr_id=info:sid/HKUST:SPI&rft.genre=article&rft.issn=1431-0651&rft.volume=21&rft.issue=3&rft.date=2017&rft.spage=581&rft.aulast=Zhang&rft.aufirst=Shan&rft.atitle=Comparative+genomics+analysis+of+five+Psychrobacter+strains+isolated+from+world-wide+habitats+reveal+high+intra-genus+variations&rft.title=Extremophiles http://www.scopus.com/record/display.url?eid=2-s2.0-85015660113&origin=inward http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=LinksAMR&SrcApp=PARTNER_APP&DestLinkType=FullRecord&DestApp=WOS&KeyUT=000400233700014 English eng Springer Tokyo https://repository.hkust.edu.hk/ir/Record/1783.1-133105 Extremophiles, v. 21, (3), March 2017, p. 581-589 1431-0651 1433-4909 https://doi.org/10.1007/s00792-017-0927-1 http://lbdiscover.ust.hk/uresolver?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rfr_id=info:sid/HKUST:SPI&rft.genre=article&rft.issn=1431-0651&rft.volume=21&rft.issue=3&rft.date=2017&rft.spage=581&rft.aulast=Zhang&rft.aufirst=Shan&rft.atitle=Comparative+genomics+analysis+of+five+Psychrobacter+strains+isolated+from+world-wide+habitats+reveal+high+intra-genus+variations&rft.title=Extremophiles http://www.scopus.com/record/display.url?eid=2-s2.0-85015660113&origin=inward http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=LinksAMR&SrcApp=PARTNER_APP&DestLinkType=FullRecord&DestApp=WOS&KeyUT=000400233700014 Comparative genomics Intra-genus variation Psychrobacter Article 2017 ftunivsthongkong https://doi.org/10.1007/s00792-017-0927-1 2023-12-29T01:13:32Z 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. Article in Journal/Newspaper Antarc* Antarctic permafrost Siberia The Hong Kong University of Science and Technology: HKUST Institutional Repository Antarctic K5 ENVELOPE(24.794,24.794,67.805,67.805) Extremophiles 21 3 581 589 |
institution |
Open Polar |
collection |
The Hong Kong University of Science and Technology: HKUST Institutional Repository |
op_collection_id |
ftunivsthongkong |
language |
English |
topic |
Comparative genomics Intra-genus variation Psychrobacter |
spellingShingle |
Comparative genomics Intra-genus variation Psychrobacter Zhang, Shan Song, Weizhi Yu, Min Lin, Xuezheng Comparative genomics analysis of five Psychrobacter strains isolated from world-wide habitats reveal high intra-genus variations |
topic_facet |
Comparative genomics Intra-genus variation Psychrobacter |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Zhang, Shan Song, Weizhi Yu, Min Lin, Xuezheng |
author_facet |
Zhang, Shan Song, Weizhi Yu, Min Lin, Xuezheng |
author_sort |
Zhang, Shan |
title |
Comparative genomics analysis of five Psychrobacter strains isolated from world-wide habitats reveal high intra-genus variations |
title_short |
Comparative genomics analysis of five Psychrobacter strains isolated from world-wide habitats reveal high intra-genus variations |
title_full |
Comparative genomics analysis of five Psychrobacter strains isolated from world-wide habitats reveal high intra-genus variations |
title_fullStr |
Comparative genomics analysis of five Psychrobacter strains isolated from world-wide habitats reveal high intra-genus variations |
title_full_unstemmed |
Comparative genomics analysis of five Psychrobacter strains isolated from world-wide habitats reveal high intra-genus variations |
title_sort |
comparative genomics analysis of five psychrobacter strains isolated from world-wide habitats reveal high intra-genus variations |
publisher |
Springer Tokyo |
publishDate |
2017 |
url |
https://repository.hkust.edu.hk/ir/Record/1783.1-133105 https://doi.org/10.1007/s00792-017-0927-1 http://lbdiscover.ust.hk/uresolver?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rfr_id=info:sid/HKUST:SPI&rft.genre=article&rft.issn=1431-0651&rft.volume=21&rft.issue=3&rft.date=2017&rft.spage=581&rft.aulast=Zhang&rft.aufirst=Shan&rft.atitle=Comparative+genomics+analysis+of+five+Psychrobacter+strains+isolated+from+world-wide+habitats+reveal+high+intra-genus+variations&rft.title=Extremophiles http://www.scopus.com/record/display.url?eid=2-s2.0-85015660113&origin=inward http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=LinksAMR&SrcApp=PARTNER_APP&DestLinkType=FullRecord&DestApp=WOS&KeyUT=000400233700014 |
long_lat |
ENVELOPE(24.794,24.794,67.805,67.805) |
geographic |
Antarctic K5 |
geographic_facet |
Antarctic K5 |
genre |
Antarc* Antarctic permafrost Siberia |
genre_facet |
Antarc* Antarctic permafrost Siberia |
op_relation |
https://repository.hkust.edu.hk/ir/Record/1783.1-133105 Extremophiles, v. 21, (3), March 2017, p. 581-589 1431-0651 1433-4909 https://doi.org/10.1007/s00792-017-0927-1 http://lbdiscover.ust.hk/uresolver?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rfr_id=info:sid/HKUST:SPI&rft.genre=article&rft.issn=1431-0651&rft.volume=21&rft.issue=3&rft.date=2017&rft.spage=581&rft.aulast=Zhang&rft.aufirst=Shan&rft.atitle=Comparative+genomics+analysis+of+five+Psychrobacter+strains+isolated+from+world-wide+habitats+reveal+high+intra-genus+variations&rft.title=Extremophiles http://www.scopus.com/record/display.url?eid=2-s2.0-85015660113&origin=inward http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=LinksAMR&SrcApp=PARTNER_APP&DestLinkType=FullRecord&DestApp=WOS&KeyUT=000400233700014 |
op_doi |
https://doi.org/10.1007/s00792-017-0927-1 |
container_title |
Extremophiles |
container_volume |
21 |
container_issue |
3 |
container_start_page |
581 |
op_container_end_page |
589 |
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1789325623363108864 |