Geographic divergence of “Sulfolobus islandicus” strains assessed by genomic analyses including electronic DNA hybridization confirms they are geovars
Ten well-annotated genomes of “Sulfolobus islandicus” strains from different geographic locations have been released at the NCBI database. Whole genome based composition vector trees indicate that these strains show the same branching patterns as originally reported by multi-locus sequence analysis....
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ftpubmed:oai:pubmedcentral.nih.gov:3893479 2023-05-15T16:50:51+02:00 Geographic divergence of “Sulfolobus islandicus” strains assessed by genomic analyses including electronic DNA hybridization confirms they are geovars Zuo, Guanghong Hao, Bailin Staley, James T. 2013-12-04 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893479 http://www.ncbi.nlm.nih.gov/pubmed/24301254 https://doi.org/10.1007/s10482-013-0081-4 en eng Springer Netherlands http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893479 http://www.ncbi.nlm.nih.gov/pubmed/24301254 http://dx.doi.org/10.1007/s10482-013-0081-4 © The Author(s) 2013 Open AccessThis article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited. CC-BY Short Communication Text 2013 ftpubmed https://doi.org/10.1007/s10482-013-0081-4 2014-01-26T01:38:09Z Ten well-annotated genomes of “Sulfolobus islandicus” strains from different geographic locations have been released at the NCBI database. Whole genome based composition vector trees indicate that these strains show the same branching patterns as originally reported by multi-locus sequence analysis. To determine whether the ten strains meet the criteria for separate species, DNA–DNA hybridization (DDH) was performed in silico. DDH values of strains from the same geographic location, i.e., Iceland, Kamchatka and North America, ranged from 82.4 to 95.4 %, clearly qualifying them as members of the same species. The lowest DDH values found between locations ranged from 75.5 to 76.6 %, which exceed the 70 % DDH threshold for a species thereby indicating they are all members of the same species based on the currently accepted definition. The clear divergences of strains from the different geographic locations are sufficiently great to consider them as separate geovars. “S. islandicus” has not yet been validly named and a type strain has not been deposited in culture collections. We urgently recommend that those who study the organism fulfill the criteria of the International Code of Nomenclature of Bacteria in order to designate a type strain and to identify and deposit related strains of this species to make them available to the broader scientific community. Text Iceland Kamchatka PubMed Central (PMC) Antonie van Leeuwenhoek 105 2 431 435 |
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Short Communication |
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Short Communication Zuo, Guanghong Hao, Bailin Staley, James T. Geographic divergence of “Sulfolobus islandicus” strains assessed by genomic analyses including electronic DNA hybridization confirms they are geovars |
topic_facet |
Short Communication |
description |
Ten well-annotated genomes of “Sulfolobus islandicus” strains from different geographic locations have been released at the NCBI database. Whole genome based composition vector trees indicate that these strains show the same branching patterns as originally reported by multi-locus sequence analysis. To determine whether the ten strains meet the criteria for separate species, DNA–DNA hybridization (DDH) was performed in silico. DDH values of strains from the same geographic location, i.e., Iceland, Kamchatka and North America, ranged from 82.4 to 95.4 %, clearly qualifying them as members of the same species. The lowest DDH values found between locations ranged from 75.5 to 76.6 %, which exceed the 70 % DDH threshold for a species thereby indicating they are all members of the same species based on the currently accepted definition. The clear divergences of strains from the different geographic locations are sufficiently great to consider them as separate geovars. “S. islandicus” has not yet been validly named and a type strain has not been deposited in culture collections. We urgently recommend that those who study the organism fulfill the criteria of the International Code of Nomenclature of Bacteria in order to designate a type strain and to identify and deposit related strains of this species to make them available to the broader scientific community. |
format |
Text |
author |
Zuo, Guanghong Hao, Bailin Staley, James T. |
author_facet |
Zuo, Guanghong Hao, Bailin Staley, James T. |
author_sort |
Zuo, Guanghong |
title |
Geographic divergence of “Sulfolobus islandicus” strains assessed by genomic analyses including electronic DNA hybridization confirms they are geovars |
title_short |
Geographic divergence of “Sulfolobus islandicus” strains assessed by genomic analyses including electronic DNA hybridization confirms they are geovars |
title_full |
Geographic divergence of “Sulfolobus islandicus” strains assessed by genomic analyses including electronic DNA hybridization confirms they are geovars |
title_fullStr |
Geographic divergence of “Sulfolobus islandicus” strains assessed by genomic analyses including electronic DNA hybridization confirms they are geovars |
title_full_unstemmed |
Geographic divergence of “Sulfolobus islandicus” strains assessed by genomic analyses including electronic DNA hybridization confirms they are geovars |
title_sort |
geographic divergence of “sulfolobus islandicus” strains assessed by genomic analyses including electronic dna hybridization confirms they are geovars |
publisher |
Springer Netherlands |
publishDate |
2013 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893479 http://www.ncbi.nlm.nih.gov/pubmed/24301254 https://doi.org/10.1007/s10482-013-0081-4 |
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Iceland Kamchatka |
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Iceland Kamchatka |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893479 http://www.ncbi.nlm.nih.gov/pubmed/24301254 http://dx.doi.org/10.1007/s10482-013-0081-4 |
op_rights |
© The Author(s) 2013 Open AccessThis article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited. |
op_rightsnorm |
CC-BY |
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https://doi.org/10.1007/s10482-013-0081-4 |
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Antonie van Leeuwenhoek |
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105 |
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2 |
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431 |
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435 |
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