We report draft genome sequence of Stenotrophomonas sp. strain SAM8, isolated from environmental water. The draft genome size is 3,665,538 bp with a G + C content of 67.2% and contains 6 rRNA sequence (single copies of 5S, 16S & 23S rRNA). The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LDAV00000000

Nashwa Hagagy

Samy Selim

Sherif Hassan

PubMed

AbstractWe report draft genome sequence of Stenotrophomonas sp. strain SAM8, isolated from environmental water. The draft genome size is 3,665,538bp with a G+C content of 67.2% and contains 6 rRNA sequence (single copies of 5S, 16S & 23S rRNA). The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LDAV00000000

Selim, Samy

Hassan, Sherif

Hagagy, Nashwa

Elsevier - Publisher Connector 

Genomics Data 6 (2015) 25–26
Contents lists available at ScienceDirect
Genomics Data
j ou rna l homepage: ht tp : / /www. journa ls .e lsev ie r .com/genomics-data /Data in BriefGenome sequencing and annotation of Stenotrophomonas sp. SAM8Samy Selim a,b,⁎, Sherif Hassan a,c, Nashwa Hagagy b
a Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Aljouf University, Sakaka, P.O. Box 2014, Saudi Arabia
b Microbiology and Botany Department, Faculty of Science, Suez Canal University, Ismailia, P.O. Box 41522, Egypt
c Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef 62511, EgyptO
St
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D
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C
⁎ Corresponding author at. Department of Clinical L
Applied Medical Sciences, Aljouf University, Sakaka, P.
966535268405; fax: + 966046248173.
E-mail address: sadomm2003@yahoo.com (S. Selim).
http://dx.doi.org/10.1016/j.gdata.2015.07.028
2213-5960/© 2015 The Authors. Published by Elsevier Inca b s t r a c ta r t i c l e i n f oArticle history:
Received 29 July 2015
Accepted 31 July 2015
Available online 1 August 2015
Keywords:
Water springs
Stenotrophomonas
Secondary metabolites
Heavy metals resistance
Whole genome sequencingWe report draft genome sequence of Stenotrophomonas sp. strain SAM8, isolated from environmental water. The
draft genome size is 3,665,538 bp with a G + C content of 67.2% and contains 6 rRNA sequence (single copies of
5S, 16S & 23S rRNA). The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no.
LDAV00000000.
© 2015 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license
(http://creativecommons.org/licenses/by-nc-nd/4.0/).Speciﬁcationsrganism/cell line/tissue Stenotrophomonas sp.
rain(s) SAM8
quencer or array type Sequencer; Roche 454
ata format Processed
xperimental factors Microbial strains
xperimental features Draft genome sequence of Stenotrophomonas sp.
SAM8 assembly and annotation
onsent N/A
mple source location Water spring in Aljouf, Saudi ArabiaSa1. Direct link to deposited data
http://www.ncbi.nlm.nih.gov/bioproject/?term=LDAV00000000.
2. Experimental design, materials and methods
Stenotrophomonas sp. stain SAM8 is a Gram-negative obligate aerobe
that is rod shaped and motile with a few polar ﬂagella. The isolate is an
environmental bacterium found in aqueous habitats, including plant
rhizospheres, animals, foods, and water sources [1]. In addition, the iso-
late is an increasingly relevant humanopportunistic pathogen that is in-
volved in infections at hospitals and in patients with cystic ﬁbrosis
[1–2].The isolate is major opportunistic waterborne pathogens causingaboratory Sciences, College of
O. 2014, Saudi Arabia. Tel.: +
. This is an open access article underhospital-acquired infections [3]. Genomic DNA was extracted from
pure culture of bacterial strain and subsequently sequenced using
Roche 454 GS (FLX Titanium) pyrosequencing. All of the reads were as-
sembled using GS De Novo Assembler version 2.8 (454 life science),
which generated 529 contigs with N50 12,907 bp. The G + C content
was calculated using the draft genome sequence. The G + C content
for the draft genome is 67.2%. The genome contains 58 tRNA genes
and 6 rRNA genes (5S–23S–16S) predicted by the NCBI Prokaryotic Ge-
nome Annotation Pipeline (PGAP).
A total of 3448 protein coding sequences in 355 subsystems were
functionally annotated byRapid Annotation using the Subsystems Tech-
nology (RAST) [4] server (Fig. 1). Genome analysis revealed that the ge-
nome of Stenotrophomonas sp. stain SAM8 contains various gene
clusters for biosynthesis of secondary metabolites and antimicrobial
peptides. The genome information displays several antibiotic resistance
genes encoding methicillin, efﬂux pumps, quinolone, fosmidomycin
and acriﬂavine resistance protein [5].There also exist in the genome
multiple genes encoding chitinase, xylanase, esterase and lipase en-
zymes. Overall, the strain demonstrates the potential for resistance to
a wide range of antimicrobial and heavy metals.
Functional comparison of genome sequences in the RAST server
revealed the closest neighbors of Stenotrophomonas maltophilia
K279a (score 513) followed by Stenotrophomonas sp. SKA14 (score
513), S. maltophilia R551-3 (score 506), S. maltophilia D457 (score
339) and Xanthomonas campestris pv. campestris ATCC 33913 (score
333). On the other hand, the analysis of the complete 16S rRNA se-
quence in EzTaxon server (http://www.ezbiocloud.net/eztaxon;
[6]) under default settings (with matches only against culturedthe CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Fig. 1. Subsystem distribution of Stenotrophomonas strain SAM8 (based on RAST annotation server).
26 S. Selim et al. / Genomics Data 6 (2015) 25–26strains) identiﬁed S. maltophilia. Overall, the various in silico results
conﬁrmed that the present environmental isolate is a member of the
genus Stenotrophomonas, though further characterization work is re-
quired to determine its species.
3. Nucleotide sequence accession number
The Stenotrophomonas sp. SAM8 whole genome shotgun project
has been deposited in DDBJ/EMBL/GenBank under the accession no
LDAV00000000.
Conﬂict of interest
The authors declare that there is no conﬂict of interests on the work
published in this paper.
Acknowledgments
This work was funded by the Deanship of Scientiﬁc Research
(DSR), Aljouf University, Aljouf, KSA, under grant no. 34/155,
2014.The authors, therefore, acknowledgewith thanks DSR technical
and ﬁnancial support. We also would like to acknowledge ArrayGen
Technologies, Pune, India for contributing to data analysis and bioin-
formatics support.References
[1] J.S. Brooke, Stenotrophomonas maltophilia: an emerging global opportunistic patho-
gen. Clin. Microbiol. Rev. 25 (2012) (2012) 2–41.
[2] M.C. Turrientes, M.R. Baquero, M.B. Sánchez, S. Valdezate, E. Escudero, G. Berg, R.
Cantón, F. Baquero, J.C. Galán, J.L. Martínez, Polymorphic mutation frequencies of
clinical and environmental Stenotrophomonas maltophilia populations. Appl. Environ.
Microbiol. 76 (2010) 1746–1758.
[3] C.C. Adjidé, A. De Meyer, M. Weyer, O. Obin, F. Lamory, C. Lesueur, L. Trouillet, M.
Biendo, F. Eb, O. Ganry, Stenotrophomonas maltophilia and Pseudomonas aeruginosa
water associated microbiologic risk assessment in Amiens' University Centre. Pathol.
Biol. 58 (2010) e1–e5.
[4] R.K. Aziz, D. Bartels, A.A. Best, M. DeJongh, T. Disz, R.A. Edwards, K. Formsma, S.
Gerdes, E.M. Glass, M. Kubal, F. Meyer, G.J. Olsen, R. Olson, A.L. Osterman, R.A.
Overbeek, L.K. McNeil, D. Paarmann, T. Paczian, B. Parrello, G.D. Pusch, C. Reich, R.
Stevens, O. Vassieva, V. Vonstein, A. Wilke, O. Zagnitko, The RAST Server: rapid anno-
tations using subsystems technology. BMC Genomics 9 (2008) 75.
[5] L.C. Crossman, V.C. Gould, J.M. Dow, G.S. Vernikos, A. Okazaki, M. Sebaihia, D.
Saunders, C. Arrowsmith, T. Carver, N. Peters, E. Adlem, A. Kerhornou, A. Lord, L.
Murphy, K. Seeger, R. Squares, S. Rutter, M.A. Quail, M.A. Rajandream, D. Harris, C.
Churcher, S.D. Bentley, J. Parkhill, N.R. Thomson, M.B. Avison, The complete genome,
comparative and functional analysis of Stenotrophomonas maltophilia reveals an or-
ganismheavily shielded by drug resistance determinants. Genome Biol. 9 (2008) R74.
[6] O.S. Kim, Y.J. Cho, K. Lee, S.H. Yoon, M. Kim, H. Na, S.C. Park, Y.S. Jeon, J.H. Lee, H. Yi, S.
Won, J. Chun, Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence data-
base with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbiol.
62 (2012) 716–721.


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