Gao et al. Standards in Genomic Sciences 2015, 10:1
http://www.standardsingenomics.com/content/10/1/1
SHORT GENOME REPORT
Open Access
Draft genome sequence of Halomonas lutea strain
YIM 91125T (DSM 23508T) isolated from the
alkaline Lake Ebinur in Northwest China
Xiao-Yang Gao1,11, Xiao-Yang Zhi2, Hong-Wei Li2,9, Yu Zhou10, Alla Lapidus3,4, James Han5, Matthew Haynes5,
Elizabeth Lobos5, Marcel Huntemann5, Amrita Pati5, Natalia N Ivanova5, Konstantinos Mavromatis5, Brian J Tindall7,
Victor Markowitz6, Tanja Woyke5, Hans-Peter Klenk7,12, Nikos C Kyrpides5,8 and Wen-Jun Li1,2*
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 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. DDH
analysis demonstrated that H. lutea is a distinctive species, and halophilic features and nitrogen metabolism related
genes were discovered in its genome.
Keywords: Halomonas lutea, Aerobic, Gram-negative, Chemoorganotrophic, Moderately halophilic, Lake Ebinur
Introduction
Strain YIM 91125T (= DSM 23508T = KCTC 12847T =
CCTCC AB 206093T) is the type strain of Halomonas
lutea [1]. Currently, there are 83 validly named species in
the genus Halomonas on the basis of most recent released
from LPSN [2] and EzTaxon-e [3]. Halomonadaceae
comprises the largest number of halophilic and halotolerant bacteria described to date, and Halomonas is the
largest genus in this family. However, most of the taxa
in Halomonadaceae have been reclassified in the past due
to their heterogeneous features [4-7]. In Halomonas, a
small group of species has been formally re-located to
* Correspondence: liwenjun@ms.xjb.ac.cn
1
Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang
Institute of Ecology and Geography, Chinese Academy of Sciences,
Urumqi, China
2
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
Full list of author information is available at the end of the article
Chromohalobacter, Cobetia and Kushneria by further
taxonomic studies. Members of the genus Halomonas
were usually isolated from saline environments [8-12].
Strain YIM 91125T was originally isolated from soil sample of Ebinur Lake, which has been a long-term target for
the studies of element cycling and microbial biota under
extremely high-saline conditions in Xinjiang, Northwest
China. As a type strain, it’s the original isolate used in species description, which exhibits the relevant phenotypic
and genotypic properties cited in the original published
taxonomic circumscriptions [13]. This organism grows
well across a wide range of salinity and temperature and
also participates in nitrogen reduction. In this context,
strain YIM 91125T has been sequenced as a halophilic
representative, and becomes a part of Genomic Encylopedia of Type Strains, Phase I: the one thousand microbial
genomes project.
Here, we present a summary classification and a set of
features for H. lutea strain YIM 91125T, together with the
description of the genomic sequencing and annotation,
© 2015 Gao et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative
Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly credited. 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.
Gao et al. Standards in Genomic Sciences 2015, 10:1
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and provide brief findings of its genome sequence as
compared to genomes of other Halomonas species. The
genomic data will provide insights into its new biotechnological applications, such as sewage treatment. The
comprehensive genomes of this genus will facilitate our
understanding of the ecological roles that Halomonas
species play in those hypersaline habitats and their
relationships with other halophilic and nonhalophilic
microorganisms.
Page 2 of 9
Table 1 Classification and general features of H. lutea
YIM 91125T [18]
MIGS ID
Property
Term
Evidence
codea
Classification
Domain Bacteria
TAS [19]
Phylum Proteobacteria
TAS [20]
Class
Gammaproteobacteria
TAS [21,22]
Classification and features
T
H. lutea YIM 91125 is a Gram-negative-staining, motile,
aerobic and moderately halophilic bacterium, which
can reduce nitrate (Table 1). Cells of the strain are
short rods, 0.4 to 0.7 μm in diameter and 0.6 to 1.0 μm
in length (Figure 1). They are motile by means of single
polar flagellum and their colonies are orange, flat, opaque
and mucoid with slightly irregular edges (Figure 1). The
predominant respiratory quinone found in H. lutea YIM
91125T is Q-9, similar to other members of the genus
Halomonas. The predominant fatty acids are C18:1 ω7c
(25.1%), C16:0 (17.0%), C19:0 cyclo ω8c (13.6%), C12:0 3-OH
(10.7%), C12:0 (7.9%), C10:0 (6.0%) and C17:0 cyclo (4.6%) [1].
The profile of major fatty acids in strain YIM 91125T is also
similar to other members of the genus Halomonas [14-17].
16S rRNA gene sequence of strain YIM 91125T was
compared with the newly released database from the
Greengenes [26], using NCBI BLAST [27,28] under
default settings (e.g., considering only HSPs from the
best 250 hits) and the relative frequencies of taxa were
determined, weighted by BLAST scores. The most
frequently occurring genera were Halomonas (71.4%),
Chromohalobacter (17.8%), Bacillus (3.6%), Haererehalobacter (3.6%) and Modicisalibacter (3.6%) (228 hits in
total). Regarding 186 hits to sequences from members of
the genus Halomonas, the average identity within HSPs
was 95.5%, whereas the average coverage by HSPs was
98.3%. Among all other species, the one yielding the
highest score was Halomonas xinjiangensis, which corresponded to identity of 99.9% and HSP coverage of
98.0%. (Note that the Greengenes database uses the
INSDC (=EMBL/NCBI/DDBJ) annotation, which is not
an authoritative source for nomenclature or classification.) The highest scoring environmental sequences were
EF157249 and EF157230 (Greengenes short name ‘tar
pits clone 101–11 k’ and ‘tar pits clone 101–120 k’),
which showed identity of 96.3% and an HSP coverage of
99.6%. The most frequently occurring keywords within
the labels of all environmental samples which yielded hits
were soil like ‘soil’, ‘seafloor’, ‘drilling deep-earth’; water
like ‘groundwater’, ‘aquatic’, ‘lake’, ‘marine’; oil and plant.
Environmental samples yielded hits of a higher score
than the highest scoring species were not found.
Gram stain
Order Oceanospirillales
TAS [21,23]
Family Halomonadaceae
TAS [4]
Genus Halomonas
TAS [24]
Species Halomonas lutea
TAS [1]
Type strain YIM 91125T
TAS [1]
negative
TAS [1]
Cell shape
short rods
TAS [1]
Motility
motile
TAS [1]
Sporulation
non-sporulating
TAS [1]
Temperature range
4-45°C
TAS [1]
Optimum
temperature
37°C
TAS [1]
pH range; Optimum
5.0-9.0
TAS [1]
Carbon source
mono- and polysaccarides
TAS [1]
MIGS-6
Habitat
aquatic, fresh water,
lake, salinewater
TAS [1]
MIGS-6.3
Salinity
1-20% NaCl (w/v)
TAS [1]
MIGS-22
Oxygen requirement
aerobe
TAS [1]
MIGS-15
Biotic relationship
free living
TAS [1]
MIGS-14
Pathogenicity
none
NAS
MIGS-4
Geographic location
Ebinur Lake (China)
TAS [1]
MIGS-5
Sample collection
2008 or before
NAS
MIGS-4.1
Latitude
45.05
TAS [1]
MIGS-4.2
Longitude
82.977
TAS [1]
MIGS-4.4
Altitude
not reported
a
Evidence codes – TAS: Traceable Author Statement (i.e., a direct report exists in the
literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the
living, isolated sample, but based on a generally accepted property for the species,
or anecdotal evidence). These evidence codes are from the Gene Ontology
project [25].
Phylogenetic analyses were carried out with two different
algorithms, i.e., neighbor-joining (NJ) and maximumlikelihood (ML). The phylogenetic tree was shown in
Figure 2 and Additional file 1: Figure S1, which provides
an interesting insight into the nomenclature and classification of members of the genus Halomonas, and also
indicates the phylogenetic neighborhood of H. lutea.
The phylogenetic relationships indicate that H. lutea
YIM 91125T is most closely to H. xianhensis A-1T with
99% similarity and the sequence of the sole 16S rRNA
gene in the genome differs by 10 nucleotides from the
previously published 16S rRNA sequence (EF674852).
Gao et al. Standards in Genomic Sciences 2015, 10:1
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Figure 1 Transmission electron micrograph of H. lutea YIM 91125T.
Figure 2 Phylogenetic tree highlighting the position of H. lutea relative to the type strains of the other species within Halomonas.
According to the most recent release of the EzTaxon-e database, all the 16S rRNA gene sequences of the type strains within genus Halomonas
were retained. The tree was inferred from 1,383 aligned bases [29] under the neighbor-joining (NJ) [30] and maximum-likelihood (ML) [31]
methods with 1,000 randomly selected bootstrap replicates using MEGA version 5.2 [32]. The branches are scaled in terms of the expected
number of substitutions per site. Numbers adjacent to the branches are support values from 1,000 NJ bootstrap (left) and from 1,000 ML bootstrap
(right) replicates [33] if they are larger than 50%. Lineages with type strain genome sequencing projects registered in Genomes OnLine Database
(GOLD) [34] are labeled with one asterisk, and those have available genomic data are labeled with two asterisks. Non-type strain LS21of H. campaniensis
and H. elongata DSM 2581T listed ‘Complete and Published’ are also labeled with two asterisks.
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Genome sequencing and annotation
Genome sequencing and assembly
Genome project history
This organism was selected for sequencing on the basis
of its phylogenetic position and biological application
importance [35,36], and for a better understand the
mechanism of its halophilic adaptation. Sequencing of
H. lutea YIM 91125T is part of Genomic Encyclopedia of
Type Strains, Phase I: the one thousand microbial
genomes (KMG-I) project [37], a follow-up of the GEBA
project [38], which aims for increasing the sequencing
coverage of key reference microbial genomes. The genome
project is deposited in the Genomes OnLine Database
(GOLD), and the high quality draft genome sequence is
deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE JGI using state of the art
sequencing technology [39]. A summary of the project
information is shown in Table 2. It presents the project
information and in compliance with MIGS version 2.0
compliance [18].
The draft genome of strain YIM 91125T was generated
at JGI using Illumina technology [42]. An Illumina standard shotgun library was constructed and sequenced
using the Illumina HiSeq 2000 platform which generated
9,251,032 reads totaling 1,387.7 Mb. All general aspects
of library construction and sequencing performed at the
JGI. All raw Illumina sequence data was passed through
DUK, a filtering program developed at JGI, which removes
known Illumina sequencing and library preparation artifacts. The following steps were then performed for assembly: (1) filtered Illumina reads were assembled using Velvet
version 1.1.04 [43]; (2) 1–3 Kb simulated paired end reads
were created from Velvet contigs using Wgsim [44]; (3)
Illumina reads were assembled with simulated read pairs
using Allpaths-LG [45]. The final draft assembly contained
49 contigs in 42 scaffolds. The total size of the genome is
4.5 Mbp and the final assembly is based on 538.9 Mbp of
Illumina data, which provides an average 119.0 × coverage
of the genome.
Growth conditions and DNA isolation
Genome annotation
H. lutea strain YIM 91125T (DSM 23508T), was grown in
DSMZ medium 514b (Medium 514 plus additional salt) at
37°C [40]. DNA was isolated from 0.5-1.0 g of cell pasted
using Jetflex Genomic DNA Purification Kit (Qiagen,
Hilden, Germany), following the standard protocol as
recommended by the manufacturer, but with an additional
incubation (60 min, 37°C) with 50 μl proteinase K and
finally adding 200 μl protein precipitation buffer (PPT).
DNA is available through the DNA Bank Network [41].
Table 2 Project information
MIGS ID
Property
Term
MIGS-31
Finishing quality
Improved-High-Quality Draft
MIGS-28
Libraries used
Illumina standard shotgun library
MIGS-29
Sequencing platforms Illumina HiSeq 2000
MIGS-31.2 Fold coverage
119 ×
MIGS-30
Assemblers
Velvet v. 1.1.04; ALLPATHS v. r41043
MIGS-32
Gene calling method
Prodigal 1.4
Locus Tag
NZ_ARKK01000000
MIGS-13
Genbank ID
ARKK00000000
Genbank Date
of Release
April 23, 2013
GOLD ID
Gi11553
BIOPROJECT
PRJNA199405
Project relevance
Genomic Encyclopedia of Type Strains,
Phase I: the one thousand microbial
genomes (KMG-I) project
Source Material
Identifier
Halomonas lutea DSM 23508
Genes were identified using Prodigal [46] as part of the
DOE JGI genome annotation pipeline [47], following by
a round of manual curation using the JGI GenePRIMP
pipeline [48]. The predicted CDSs were translated and
used to search the NCBI non-redundant database,
UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and
InterPro database. These data sources were combined
to assert a product description for each predicted protein.
Additional gene prediction analysis and functional annotation were performed within the Integrated Microbial
Genomes-Expert Review (IMG-ER) platform [49].
Genome properties
The assembly of the draft genome sequence consists of
42 scaffolds (Figure 3) amounting to 4,533,090 bp, and
G+C content is 59.1%. The majority of the protein-coding
genes (83.0%) were assigned a putative function while the
remaining ones were annotated as hypothetical proteins.
3,325 protein coding genes belong to 422 paralogous families in this genome. The properties and the statistics of
the genome are summarized in Table 3. The distribution
of genes into COGs functional categories is presented in
Table 4.
Insights from the genome sequence
The genomic sequences of twelve Halomonas species
are available, including H. lutea YIM 91125T. Genome
properties of those Halomonas species are shown in
Table 5, but only H. elongate and H. campaniensis have
complete genome sequences. These Halomonas genome
sequences exhibit dramatic interspecies variations in
size, ranging from 5.34 Mb (H. titanicae) to 2.85 Mb
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Figure 3 Graphical map of the largest scaffold in Halomonas lutea YIM 91125T. From bottom to the top: Genes on forward strand (colored
by COG categories), Genes on reverse strand (colored by COG catergories), RNA genes (tRNA green, rRNA red, other RNAs black), GC content, GC
skew (purpele/olive).
(H. jeotgali); and the size of H. lutea is larger than the
average size, suggesting acquisition of functions may allow
better adaption to its environment, e.g., genes coding for
tripartite ATP-independent periplasmic (TRAP) transporters for substrate uptake or nitrate degradation [50].
Also, GC contents of those species vary from 52.65%
(H. campaniensis) to 67.86% (H. smyrnensis), and of H.
lutea (59.05%) is around the average GC content, close
to H. anticariensis (58.54%). In addition, the distribution
of genes into COG categories was not entirely similar in
all twelve compared genomes (Figure 4). And H. lutea has
more specific genes, since proteins with COG only
account for 71.18% which is lower than other members.
Compared with other Halomonas species, the proportions
of genes with signal peptide and transmembrane helices of
H. lutea are respectively 7.46% and 23.65%, close to the
corresponding averages. The abundance of transmembrane
Table 3 Genome statistics
Table 4 Number of genes associated with general COG
functional categories
Code
Value
% age
Description
J
183
4.66
Translation, ribosomal structure and biogenesis
A
1
0.03
RNA processing and modification
K
278
7.08
Transcription
L
168
4.28
Replication, recombination and repair
B
6
0.15
Chromatin structure and dynamics
D
37
0.94
Cell cycle control, Cell division,
chromosome partitioning
V
36
0.92
Defense mechanisms
T
208
5.30
Signal transduction mechanisms
M
210
5.35
Cell wall/membrane biogenesis
N
92
2.34
Cell motility
U
80
2.04
Intracellular trafficking and secretion
O
158
4.02
Posttranslational modification, protein
turnover, chaperones
Attribute
Value
Genome size (bp)
4,533,090
DNA coding (bp)
3.982.279
DNA G + C (bp)
2.676.712
C
291
7.41
Energy production and conversion
DNA scaffolds
42
G
273
6.95
Carbohydrate transport and metabolism
Total genes
4,368
E
352
8.96
Amino acid transport and metabolism
Protein-coding genes
4,284
F
85
2.16
Nucleotide transport and metabolism
RNA genes
84
H
186
4.74
Coenzyme transport and metabolism
Pseudo genes
51
I
133
3.39
Lipid transport and metabolism
Genes in internal clusters
3,325
P
218
5.55
Inorganic ion transport and metabolism
Genes with function prediction
3,625
Q
126
3.21
Genes assigned to COGs
3,497
Secondary metabolites biosynthesis,
transport and catabolism
Genes with Pfam domains
3,674
R
467
11.89
General function prediction only
Genes with signal peptides
326
S
339
8.63
Function unknown
Genes with transmembrane helices
1,033
-
871
19.94
Not in COGs
CRISPR repeats
1
The total is based on the total number of protein-coding genes in the
annotated genome.
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Table 5 Comparison of genome features of Halomonas
species
Species
Genome
size (Mb)
GC content (%)
Gene
count
5.07
58.54
4817
H. boliviensis LC1
4.14
54.68
3915
H. campaniensis LS21
4.07
52.65
3665
H. elongata DSM 2581
4.06
63.61
3556
H. halocynthiae
DSM 14573T
2.88
53.80
2773
H. halodenitrificans
DSM 735T
3.47
63.95
3256
H. jeotgali HwaT
2.85
62.92
2636
H. lutea YIM 91125T
4.53
59.05
4368
T
H. smyrnensis AAD6
3.56
67.86
3326
H. stevensiss S18214T
3.69
60.25
3523
H. titanicae BH1
5.34
54.58
2908
H. zhanjiangensis DSM 21076T
4.06
54.48
3739
H. anticariensis FP35T
T
T
T
helices related genes indicates the important role in
metabolism process of Halomonas.
DNA-DNA hybridization is considered as a goldstandard of distinguishing species [51]. Digital DDH
similarities between genome of H. lutea and those of
other Halomonas species were calculated using GGDC
web server version 2.0 under recommend setting [52,53].
The probabilities of DDH value > 70% assessed via logistic
regression under three formulae indicate that H. lutea is
different from other species of the genus (Table 6). The
inter-genome distances under formula 2 between H. lutea
and H. anticariensis, H. boliviensi, H. campaniensis, H.
elongata, H. halocynthiae, H. halodenitrificans, H. jeotgali,
H. smyrnensis, H. stevensii, H. titanicae and H. zhanjiangensis are about 0.22, the corresponding DDH estimates
below the 70% threshold under formula 2 are: 19.5%
(± 2.29), 20.2% (± 2.31), 21.1% (± 2.33), 20.1% (± 2.31),
19.2% (± 2.29), 19.4% (± 2.29), 19.9% (± 2.30), 20.3%
(± 2.32), 20.4% (± 2.32), 20.5% (± 2.32), 18.9% (± 2.28),
respectively. The standard deviations indicate the
Figure 4 Distribution of functional classes of predicted genes in Halomonas species chromosomes according to the clusters of
orthologous groups of proteins.
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Table 6 Digital DDH similarities between H. lutea DSM
23529T and the other Halomonas species
Reference species
Formula 1
Formula 2
Formula 3
H. anticariensis
14.9 ± 3.14
19.5 ± 2.29
15.0 ± 2.67
H. boliviensis
13.0 ± 2.99
20.2 ± 2.31
13.4 ± 2.56
H. campaniensis
13.0 ± 2.99
21.1 ± 2.33
13.3 ± 2.56
H. elongata
15.6 ± 3.19
20.1 ± 2.31
15.6 ± 2.70
H. halocynthiae
13.0 ± 2.99
19.2 ± 2.29
13.3 ± 2.56
H. halodenitrificans
14.5 ± 3.11
19.4 ± 2.29
14.6 ± 2.65
H. jeotgali
13.5 ± 3.03
19.9 ± 2.30
13.8 ± 2.59
H. smyrnensis
15.5 ± 3.18
20.3 ± 2.32
15.5 ± 2.70
H. stevensiss
13.5 ± 3.04
20.4 ± 2.32
13.8 ± 2.59
H. titanicae
13.0 ± 2.99
20.5 ± 2.32
13.3 ± 2.56
H. zhanjiangensis
13.2 ± 3.01
18.9 ± 2.28
13.5 ± 2.57
GenBank accession numbers for the reference genomes: H. anticariensis
(NZ_ASTJ00000000), H. boliviensi (NZ_AGQZ00000000), H. campaniensis
(CP007757), H. elongata (NC_014532), H. halocynthiae (AUDZ00000000),
H. halodenitrificans (JHVH00000000), H. jeotgali (NZ_AMQY00000000),
H. smyrnensis (NZ_AJKS00000000), H. stevensii (NZ_AJTS00000000),
H. titanicae (NZ_AOPO00000000), H. zhanjiangensis (NZ_ARIT00000000).
inherent uncertainty in estimating DDH values from
intergenomic distances based on models derived from
empirical test data sets. Given that the low degree of
DNA-DNA similarity among Halomonas species, it
appears justified to assume that these strains represent
different species. For better understanding of the relationships between H. lutea and other Halomonas members,
availability of more genome sequences of representatives
are needed to implement phylogenomic inference.
As a halophilic bacterium, the genome of H. lutea
also shows properties related to solute and ion transport,
203 genes related ion transport and metablism, 60 genes
related TRAP-type C4-dicarboxylate transport system
which is a crucial family of solute transporters. Moreover,
nitrate reduction was tested using API 20NE system and
57 genes were predicted to participate in the nitrogen
metabolism. PTS IIA-like nitrogen-regulatory protein,
nitrate and sulfonate transport systems related genes
were also detected in its genome.
Conclusions
The genome sequence and annotation of H. lutea YIM
91125T were presented. The genome comprises 42 scaffolds
which together represent the organism of approximately
4.53 Mb. It encodes for key genes and pathways involved
in the compatible solutes production and nitrogen degradation. This provides clues to discover novel genes and
functions, and leads to an improved understanding of
halophilic microbial evolution and function in the
extremely salty conditions. YIM 91125T participates in
nitrogen cycling, although the process of reducing nitrogen needs further studies to fully understand the related
pathways. The genome sequencing of H. lutea marks an
important step toward a comprehensive genomic catalog
and the metabolic diversity of halophilic bacteria. It
may contribute to further studies on important process
for Halomonas, such as quorum-sensing regulatory and
osmoadaption. Combining with genomes of other members
in Halomonas, will make an important advance in understanding of the ecological roles that Halomonas species play
in those hypersaline environments and their relationships
with other halophilic and nonhalophilic microorganisms.
Additional file
Additional file 1: Figure S1. Phylogenetic tree of the genus Halomonas.
Abbreviations
DDH: DNA-DNA hybridization; HSP: High-scoring segment pair.
Competing interests
The authors declare that they have no competing interests.
Authors’ contributions
WJL and HPK conducted the study. XYG performed the data analyses,
genome comparison, and wrote the manuscript. XYZ, HWL, YZ, AL, HPK,NCK
and WJL participated in writing the manuscript. JH, MH, EL, MH, AP, NNI, KM,
BJT, VM and TW performed genome sequencing, assembly and annotation.
All authors read and approved the final manuscript.
Acknowledgements
Susanne Schneider is gratefully acknowledged the assistance for growing
H. lutea cultures. We also thank Evelyne-Marie Brambilla for DNA extraction
and quality control (both at the DSMZ). This work was performed under the
auspices of the US Department of Energy's Office of Science, Biological and
Environmental Research Program, and by the University of California, Lawrence
Berkeley National Laboratory under Contract No. DE-AC02-05CH11231, Lawrence
Livermore National Laboratory under Contract No. DE-AC52-07NA27344.
A. L. was supported in part by Russian Ministry of Science Mega-grant no. 11.
G34.31.0068 (Dr. Stephen J O'Brien Principal Investigator). W.-J. Li was supported
by ‘Hundred Talents Program’ of the Chinese Academy of Sciences.
Author details
Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang
Institute of Ecology and Geography, Chinese Academy of Sciences,
Urumqi, China. 2Key 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. 3Theodosius Dobzhansky Center for Genome Bionformatics,
St. Petersburg State University, St. Petersburg, Russia. 4Algorithmic Biology
Lab, St. Petersburg Academic University, St. Petersburg, Russia. 5DOE Joint
Genome Institute, Walnut Creek, California, USA. 6Biological Data
Management and Technology Center, Lawrence Berkeley National
Laboratory, Berkeley, California, USA. 7Leibniz-Institute DSMZ - German
Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
8
Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi
Arabia. 9The First Hospital of Qujing City, Qujing Affiliated Hospital of
Kunming Medical University, Qujing, China. 10State 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. 11University of Chinese Academy of Sciences,
Beijing, China. 12School of Biology, Newcastle University, Newcastle upon
Tyne, UK.
1
Received: 28 July 2014 Accepted: 6 November 2014
Published: 20 January 2015
Gao et al. Standards in Genomic Sciences 2015, 10:1
http://www.standardsingenomics.com/content/10/1/1
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doi:10.1186/1944-3277-10-1
Cite this article as: Gao et al.: Draft genome sequence of Halomonas
lutea strain YIM 91125T (DSM 23508T) isolated from the alkaline Lake
Ebinur in Northwest China. Standards in Genomic Sciences 2015 10:1.
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