High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169(T) (DSM 21076(T)) from a sea urchin in southern China

Yu Zhou; Rui Li; Xiao-Yang Gao; Alla Lapidus; James Han; Matthew Haynes; Elizabeth Lobos; Marcel Huntemann; Amrita Pati; Natalia N Ivanova; Manfred Rohde; Konstantinos Mavromatis; Brian J Tindall; Victor Markowitz; Tanja Woyke; Hans-Peter Klenk; Nikos C Kyrpides; Wen-Jun Li

doi:10.4056/sigs.5449586

High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169(T) (DSM 21076(T)) from a sea urchin in southern China

Stand Genomic Sci. 2014 Apr 11;9(3):1020-30. doi: 10.4056/sigs.5449586. eCollection 2014 Jun 15.

Authors

Yu Zhou¹, Rui Li², Xiao-Yang Gao³, Alla Lapidus⁴, James Han⁵, Matthew Haynes⁵, Elizabeth Lobos⁵, Marcel Huntemann⁵, Amrita Pati⁵, Natalia N Ivanova⁵, Manfred Rohde⁶, Konstantinos Mavromatis⁵, Brian J Tindall⁷, Victor Markowitz⁸, Tanja Woyke⁵, Hans-Peter Klenk⁷, Nikos C Kyrpides⁹, Wen-Jun Li¹⁰

Affiliations

¹ Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China ; State Key Laboratory Breeding Base for Zhejiang Sustainable Plant Pest Control; Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.
² State Key Laboratory Breeding Base for Zhejiang Sustainable Plant Pest Control; Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.
³ Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China ; University of Chinese Academy of Sciences, Beijing, China.
⁴ Theodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia.
⁵ DOE Joint Genome Institute, Walnut Creek, California, USA.
⁶ HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany.
⁷ Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
⁸ Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
⁹ DOE Joint Genome Institute, Walnut Creek, California, USA ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
¹⁰ Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China ; Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China.

Abstract

Halomonas zhanjiangensis Chen et al. 2009 is a member of the genus Halomonas, family Halomonadaceae, class Gammaproteobacteria. Representatives of the genus Halomonas are a group of halophilic bacteria often isolated from salty environments. The type strain H. zhanjiangensis JSM 078169(T) was isolated from a sea urchin (Hemicentrotus pulcherrimus) collected from the South China Sea. The genome of strain JSM 078169(T) is the fourteenth sequenced genome in the genus Halomonas and the fifteenth in the family Halomonadaceae. The other thirteen genomes from the genus Halomonas are H. halocynthiae, H. venusta, H. alkaliphila, H. lutea, H. anticariensis, H. jeotgali, H. titanicae, H. desiderata, H. smyrnensis, H. salifodinae, H. boliviensis, H. elongata and H stevensii. Here, we describe the features of strain JSM 078169(T), together with the complete genome sequence and annotation from a culture of DSM 21076(T). The 4,060,520 bp long draft genome consists of 17 scaffolds with the 3,659 protein-coding and 80 RNA genes and is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

Keywords: Halomonadaceae; chemoorganotrophic; motile Gram-negative; slightly halophilic; strictly aerobic.