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High quality draft genome sequence of an extremely halophilic archaeon Natrinema altunense strain AJ2(T)
Natrinema altunense strain AJ2(T), a halophilic archaeal strain, was isolated from a high-altitude (3884 m) salt lake in Xinjiang, China. This strain requires at least 1.7 M NaCl to grow and can grow anaerobically in the presence of nitrate. To understand the genetics underlying its extreme phenotyp...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333441/ https://www.ncbi.nlm.nih.gov/pubmed/28265340 http://dx.doi.org/10.1186/s40793-017-0237-3 |
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author | Cheng, Hong Huo, Ying-Yi Hu, Jing Xu, Xue-Wei Wu, Min |
author_facet | Cheng, Hong Huo, Ying-Yi Hu, Jing Xu, Xue-Wei Wu, Min |
author_sort | Cheng, Hong |
collection | PubMed |
description | Natrinema altunense strain AJ2(T), a halophilic archaeal strain, was isolated from a high-altitude (3884 m) salt lake in Xinjiang, China. This strain requires at least 1.7 M NaCl to grow and can grow anaerobically in the presence of nitrate. To understand the genetics underlying its extreme phenotype, we de novo assembled the entire genome sequence of AJ2(T) (=CGMCC 1.3731(T)=JCM 12890(T)). We assembled 3,774,135 bp of a total of 4.4 Mb genome in only 20 contigs and noted its high GC content (64.6%). Subsequently we predicted the gene content and generated genome annotation to identify the relationship between the epigenetic characteristics and genomic features. The genome sequence contains 52 tRNA genes, 3 rRNA genes and 4,462 protein-coding genes, 3792 assigned as functional or hypothetical proteins in nr database. This Whole Genome Shotgun project was deposited in DDBJ/EMBL/GenBank under the accession JNCS00000000. We performed a Bayesian (Maximum-Likelihood) phylogenetic analysis using 16S rRNA sequence and obtained its relationship to other strains in the Natrinema and Haloterrigena genera. We also confirmed the ANI value between every two species of Natrinema and Haloterrigena genera. In conclusion, our analysis furthered our understanding of the extreme-environment adapted strain AJ2(T) by characterizing its genome structure, gene content and phylogenetic placement. Our detailed case study will contribute to our overall understanding of why Natrinema strains can survive in such a high-altitude salt lake. |
format | Online Article Text |
id | pubmed-5333441 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-53334412017-03-06 High quality draft genome sequence of an extremely halophilic archaeon Natrinema altunense strain AJ2(T) Cheng, Hong Huo, Ying-Yi Hu, Jing Xu, Xue-Wei Wu, Min Stand Genomic Sci Short Report Natrinema altunense strain AJ2(T), a halophilic archaeal strain, was isolated from a high-altitude (3884 m) salt lake in Xinjiang, China. This strain requires at least 1.7 M NaCl to grow and can grow anaerobically in the presence of nitrate. To understand the genetics underlying its extreme phenotype, we de novo assembled the entire genome sequence of AJ2(T) (=CGMCC 1.3731(T)=JCM 12890(T)). We assembled 3,774,135 bp of a total of 4.4 Mb genome in only 20 contigs and noted its high GC content (64.6%). Subsequently we predicted the gene content and generated genome annotation to identify the relationship between the epigenetic characteristics and genomic features. The genome sequence contains 52 tRNA genes, 3 rRNA genes and 4,462 protein-coding genes, 3792 assigned as functional or hypothetical proteins in nr database. This Whole Genome Shotgun project was deposited in DDBJ/EMBL/GenBank under the accession JNCS00000000. We performed a Bayesian (Maximum-Likelihood) phylogenetic analysis using 16S rRNA sequence and obtained its relationship to other strains in the Natrinema and Haloterrigena genera. We also confirmed the ANI value between every two species of Natrinema and Haloterrigena genera. In conclusion, our analysis furthered our understanding of the extreme-environment adapted strain AJ2(T) by characterizing its genome structure, gene content and phylogenetic placement. Our detailed case study will contribute to our overall understanding of why Natrinema strains can survive in such a high-altitude salt lake. BioMed Central 2017-03-01 /pmc/articles/PMC5333441/ /pubmed/28265340 http://dx.doi.org/10.1186/s40793-017-0237-3 Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Short Report Cheng, Hong Huo, Ying-Yi Hu, Jing Xu, Xue-Wei Wu, Min High quality draft genome sequence of an extremely halophilic archaeon Natrinema altunense strain AJ2(T) |
title | High quality draft genome sequence of an extremely halophilic archaeon Natrinema altunense strain AJ2(T) |
title_full | High quality draft genome sequence of an extremely halophilic archaeon Natrinema altunense strain AJ2(T) |
title_fullStr | High quality draft genome sequence of an extremely halophilic archaeon Natrinema altunense strain AJ2(T) |
title_full_unstemmed | High quality draft genome sequence of an extremely halophilic archaeon Natrinema altunense strain AJ2(T) |
title_short | High quality draft genome sequence of an extremely halophilic archaeon Natrinema altunense strain AJ2(T) |
title_sort | high quality draft genome sequence of an extremely halophilic archaeon natrinema altunense strain aj2(t) |
topic | Short Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333441/ https://www.ncbi.nlm.nih.gov/pubmed/28265340 http://dx.doi.org/10.1186/s40793-017-0237-3 |
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