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Title: Draft genome sequence of Halomonas lutea strain YIM 91125 T (DSM 23508 T) isolated from the alkaline Lake Ebinur in Northwest China

Abstract

Species of the genus Halomonas are halophilic and their flexible adaption to changes of salinity and temperature brings considerable potential biotechnology applications, such as degradation of organic pollutants and enzyme production. The type strain Halomonas lutea YIM 91125 T was isolated from a hypersaline lake in China. The genome of strain YIM 91125 T becomes the twelfth species sequenced in Halomonas, and the thirteenth species sequenced in Halomonadaceae. We described the features of H. lutea YIM 91125 T, together with the high quality draft genome sequence and annotation of its type strain. The 4,533,090 bp long genome of strain YIM 91125 T with its 4,284 protein-coding and 84 RNA genes is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. From the viewpoint of comparative genomics, H. lutea has a larger genome size and more specific genes, which indicated acquisition of function bringing better adaption to its environment. Finally, DDH analysis demonstrated that H. lutea is a distinctive species, and halophilic features and nitrogen metabolism related genes were discovered in its genome.

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [6];  [6];  [6];  [6];  [6];  [6];  [7];  [8];  [6];  [9];  [10];  [11]
  1. Chinese Academy of Sciences (CAS), Urumqi,(China). Xinjiang Institute of Ecology and Geography; Univ. of Chinese Academy of Sciences, Beijing (China)
  2. Yunnan Univ., Kunming (China)
  3. Yunnan Univ., Kunming (China); Qujing Affiliated Hospital of Kunming Medical University, Qujing (China)
  4. Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang (China)
  5. St. Petersburg State Univ., St. Petersburg (Russia). Theodosius Dobzhansky Center for Genome Bionformatics; St. Petersburg Academic Univ., St. Petersburg (Russia)
  6. DOE Joint Genome Institute, Walnut Creek, CA (United States)
  7. Leibniz Inst. DSMZ, Braunschweig (Germany)
  8. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  9. Leibniz Inst. DSMZ, Braunschweig (Germany); Newcastle Univ. Newcastle upon Tyne (United Kingdom)
  10. DOE Joint Genome Institute, Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
  11. Chinese Academy of Sciences (CAS), Urumqi,(China). Xinjiang Institute of Ecology and Geography; Yunnan Univ., Kunming (China)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1256080
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Halomonas lutea; Aerobic; Gram-negative; Chemoorganotrophic; Moderately halophilic; Lake Ebinur

Citation Formats

Gao, Xiao-Yang, Zhi, Xiao-Yang, Li, Hong-Wei, Zhou, Yu, Lapidus, Alla, Han, James, Haynes, Matthew, Lobos, Elizabeth, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N., Mavromatis, Konstantinos, Tindall, Brian J., Markowitz, Victor, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., and Li, Wen-Jun. Draft genome sequence of Halomonas lutea strain YIM 91125T (DSM 23508T) isolated from the alkaline Lake Ebinur in Northwest China. United States: N. p., 2015. Web. doi:10.1186/1944-3277-10-1.
Gao, Xiao-Yang, Zhi, Xiao-Yang, Li, Hong-Wei, Zhou, Yu, Lapidus, Alla, Han, James, Haynes, Matthew, Lobos, Elizabeth, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N., Mavromatis, Konstantinos, Tindall, Brian J., Markowitz, Victor, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., & Li, Wen-Jun. Draft genome sequence of Halomonas lutea strain YIM 91125T (DSM 23508T) isolated from the alkaline Lake Ebinur in Northwest China. United States. doi:10.1186/1944-3277-10-1.
Gao, Xiao-Yang, Zhi, Xiao-Yang, Li, Hong-Wei, Zhou, Yu, Lapidus, Alla, Han, James, Haynes, Matthew, Lobos, Elizabeth, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N., Mavromatis, Konstantinos, Tindall, Brian J., Markowitz, Victor, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., and Li, Wen-Jun. Tue . "Draft genome sequence of Halomonas lutea strain YIM 91125T (DSM 23508T) isolated from the alkaline Lake Ebinur in Northwest China". United States. doi:10.1186/1944-3277-10-1. https://www.osti.gov/servlets/purl/1256080.
@article{osti_1256080,
title = {Draft genome sequence of Halomonas lutea strain YIM 91125T (DSM 23508T) isolated from the alkaline Lake Ebinur in Northwest China},
author = {Gao, Xiao-Yang and Zhi, Xiao-Yang and Li, Hong-Wei and Zhou, Yu and Lapidus, Alla and Han, James and Haynes, Matthew and Lobos, Elizabeth and Huntemann, Marcel and Pati, Amrita and Ivanova, Natalia N. and Mavromatis, Konstantinos and Tindall, Brian J. and Markowitz, Victor and Woyke, Tanja and Klenk, Hans-Peter and Kyrpides, Nikos C. and Li, Wen-Jun},
abstractNote = {Species of the genus Halomonas are halophilic and their flexible adaption to changes of salinity and temperature brings considerable potential biotechnology applications, such as degradation of organic pollutants and enzyme production. The type strain Halomonas lutea YIM 91125T was isolated from a hypersaline lake in China. The genome of strain YIM 91125T becomes the twelfth species sequenced in Halomonas, and the thirteenth species sequenced in Halomonadaceae. We described the features of H. lutea YIM 91125T, together with the high quality draft genome sequence and annotation of its type strain. The 4,533,090 bp long genome of strain YIM 91125T with its 4,284 protein-coding and 84 RNA genes is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. From the viewpoint of comparative genomics, H. lutea has a larger genome size and more specific genes, which indicated acquisition of function bringing better adaption to its environment. Finally, DDH analysis demonstrated that H. lutea is a distinctive species, and halophilic features and nitrogen metabolism related genes were discovered in its genome.},
doi = {10.1186/1944-3277-10-1},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 10,
place = {United States},
year = {Tue Jan 20 00:00:00 EST 2015},
month = {Tue Jan 20 00:00:00 EST 2015}
}

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