title: Whole-genome optical mapping and finished genome sequence of Sphingobacterium deserti sp. nov., a new species isolated from the Western Desert of China.
abstract: A novel Gram-negative bacterium, designated ZWT, was isolated from a soil sample of the Western Desert of China, and its phenotypic properties and phylogenetic position were investigated using a polyphasic approach. Growth occurred on TGY medium at 5-42°C with an optimum of 30°C, and at pH 7.0-11.0 with an optimum of pH 9.0. The predominant cellular fatty acids were summed feature 3 (C16:1ω7c/C16:1ω6c or C16:1ω6c/C16:1ω7c) (39.22%), iso-C15:0 (27.91%), iso-C17:0 3OH (15.21%), C16:0 (4.98%), iso-C15:0 3OH (3.03%), C16:0 3OH (5.39%) and C14:0 (1.74%). The major polar lipid of strain ZWT is phosphatidylethanolamine. The only menaquinone observed was MK-7. The GC content of the DNA of strain ZWT is 44.9 mol%. rDNA phylogeny, genome relatedness and chemotaxonomic characteristics all indicate that strain ZWT represents a novel species of the genus Sphingobacterium. We propose the name S. deserti sp. nov., with ZWT (= KCTC 32092T = ACCC 05744T) as the type strain. Whole genome optical mapping and next-generation sequencing was used to derive a finished genome sequence for strain ZWT, consisting of a circular chromosome of 4,615,818 bp in size. The genome of strain ZWT features 3,391 protein-encoding and 48 tRNA-encoding genes. Comparison of the predicted proteome of ZWT with those of other sphingobacteria identified 925 species-unique proteins that may contribute to the adaptation of ZWT to its native, extremely arid and inhospitable environment. As the first finished genome sequence for any Sphingobacterium, our work will serve as a useful reference for subsequent sequencing and mapping efforts for additional strains and species within this genus.
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Chao
authors.initials: C
authors.lastname: Teng
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Zhengfu
authors.initials: Z
authors.lastname: Zhou
authors.affiliation: Natural Products Center, School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, United States of America.
authors.forename: István
authors.initials: I
authors.lastname: Molnár
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Xinna
authors.initials: X
authors.lastname: Li
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Ran
authors.initials: R
authors.lastname: Tang
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P.R. China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, P.R. China.
authors.forename: Lin
authors.initials: L
authors.lastname: Wang
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Shiyou
authors.initials: S
authors.lastname: Su
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Min
authors.initials: M
authors.lastname: Lin
mesh_terms: D002681:China; D002874:Chromosome Mapping; D016680:Genome, Bacterial; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D045249:Sphingobacterium / Q000235:genetics* / Q000302:isolation & purification
references.citation: Can J Microbiol. 1995 Jan;41(1):92-8
references.pmid: 7728659
references.citation: Int J Syst Evol Microbiol. 2012 Mar;62(Pt 3):683-7
references.pmid: 21551333
references.citation: Microbiol Mol Biol Rev. 2011 Mar;75(1):133-91
references.pmid: 21372322
references.citation: Int J Syst Evol Microbiol. 2009 Jun;59(Pt 6):1513-7
references.pmid: 19502345
references.citation: Mol Biol Evol. 1987 Jul;4(4):406-25
references.pmid: 3447015
references.citation: Int J Syst Evol Microbiol. 2012 Nov;62(Pt 11):2559-64
references.pmid: 22180612
references.citation: PLoS One. 2012;7(12):e50225
references.pmid: 23226514
references.citation: Int J Syst Evol Microbiol. 2012 Aug;62(Pt 8):1809-13
references.pmid: 21984669
references.citation: FEMS Microbiol Ecol. 2010 Mar;71(3):327-40
references.pmid: 20030718
references.citation: Antonie Van Leeuwenhoek. 2002 Aug;81(1-4):61-72
references.pmid: 12448706
references.citation: Int J Syst Evol Microbiol. 2007 Jan;57(Pt 1):81-91
references.pmid: 17220447
references.citation: PLoS One. 2013 Oct 23;8(10):e76376
references.pmid: 24194836
references.citation: Microbiology. 2007 Jun;153(Pt 6):1720-33
references.pmid: 17526830
references.citation: ISME J. 2008 Apr;2(4):393-403
references.pmid: 18273068
references.citation: Genome Res. 2003 Sep;13(9):2178-89
references.pmid: 12952885
references.citation: Evolution. 1985 Jul;39(4):783-791
references.pmid: 28561359
references.citation: Microbiology. 2006 Apr;152(Pt 4):1041-54
references.pmid: 16549668
references.citation: Int J Syst Evol Microbiol. 2014 Feb;64(Pt 2):346-51
references.pmid: 24505072
references.citation: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references.pmid: 15034147
references.citation: PLoS One. 2011;6(11):e27085
references.pmid: 22132087
references.citation: Int J Syst Evol Microbiol. 2006 Sep;56(Pt 9):2031-6
references.pmid: 16957095
references.citation: Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18296-301
references.pmid: 17114289
references.citation: Appl Environ Microbiol. 1995 Oct;61(10):3592-7
references.pmid: 7486995
references.citation: Int J Syst Evol Microbiol. 2013 Feb;63(Pt 2):755-60
references.pmid: 22561594
references.citation: J Microbiol. 2009 Dec;47(6):693-8
references.pmid: 20127461
references.citation: J Clin Microbiol. 2013 Apr;51(4):1066-70
references.pmid: 23363821
references.citation: FEMS Microbiol Ecol. 2007 Sep;61(3):470-82
references.pmid: 17672851
references.citation: Nat Biotechnol. 2013 Feb;31(2):135-41
references.pmid: 23263233
references.citation: Appl Environ Microbiol. 2000 Nov;66(11):4620-4
references.pmid: 11055902
references.citation: Microbiology. 2010 Jul;156(Pt 7):2124-35
references.pmid: 20378655
references.citation: Nucleic Acids Res. 2007;35(9):3100-8
references.pmid: 17452365
references.citation: Int J Syst Evol Microbiol. 2012 Mar;62(Pt 3):716-21
references.pmid: 22140171
references.citation: Nature. 2003 Jan 23;421(6921):436-40
references.pmid: 12540918
references.citation: Science. 2013 Dec 20;342(6165):1516-7
references.pmid: 24357320
references.citation: Antimicrob Agents Chemother. 2009 May;53(5):1964-73
references.pmid: 19273681
references.citation: J Exp Biol. 2007 Mar;210(Pt 6):946-55
references.pmid: 17337707
references.citation: Int J Syst Evol Microbiol. 2010 Oct;60(Pt 10):2377-81
references.pmid: 19933581
references.citation: PLoS One. 2012;7(3):e34458
references.pmid: 22470573
references.citation: Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19126-31
references.pmid: 19855009
references.citation: Int J Syst Evol Microbiol. 2012 Apr;62(Pt 4):791-4
references.pmid: 21571935
references.citation: Int J Syst Evol Microbiol. 2014 Jan;64(Pt 1):248-53
references.pmid: 24052628
references.citation: Appl Environ Microbiol. 1997 Dec;63(12):4713-20
references.pmid: 9406390
references.citation: Int J Syst Evol Microbiol. 2007 Jul;57(Pt 7):1590-3
references.pmid: 17625199
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W686-9
references.pmid: 15980563
references.citation: Microbiol Rev. 1994 Sep;58(3):563-602
references.pmid: 7968924
references.citation: Int J Syst Evol Microbiol. 2005 Jul;55(Pt 4):1405-6
references.pmid: 16014458