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Published April 1, 2015 | Version v1
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Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China

Authors/Creators

  • 1. Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P.R. China,
  • 2. Natural Products Center, School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, United States of America,
  • 3. 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

Description

Teng, Chao, Zhou, Zhengfu, Molnár, István, Li, Xinna, Tang, Ran, Chen, Ming, Wang, Lin, Su, Shiyou, Zhang, Wei, Lin, Min (2015): Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China. PLoS ONE (e0122254) 10 (4): 1-16, DOI: 10.1371/journal.pone.0122254

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urn:lsid:plazi.org:pub:D6744A22025DFFCBFFEC542DC22BFFE3
URL
http://publication.plazi.org/id/D6744A22025DFFCBFFEC542DC22BFFE3

Cites
Publication: 10.1099/ijs.0.059774-0 (DOI)
Publication: 10.1099/mic.0.033977-0 (DOI)
Publication: 10.1128/JCM.00093-13 (DOI)
Publication: 10.1099/ijs.0.030429-0 (DOI)
Publication: 10.1099/ijs.0.004523-0 (DOI)
Publication: 10.1038/nbt.2478 (DOI)
Publication: 10.1371/journal.pone.0034458 (DOI)
Publication: 10.1371/journal.pone.0076376 (DOI)
Publication: 10.1099/ijs.0.018481-0 (DOI)
Publication: 10.1007/s12275-009-0296-2 (DOI)
Publication: 10.1073/pnas (DOI)
Publication: 10.1111/j.1574-6941.2009 (DOI)
Publication: 10.1128/MMBR.00015-10 (DOI)
Publication: 10.1128/AAC.01382-08 (DOI)
Has part
Taxonomic treatment: 10.5281/zenodo.12630638 (DOI)
Taxonomic treatment: http://treatment.plazi.org/id/2A4D325A0259FFC2FDF956F9C7FCFC8A (URL)
Figure: 10.5281/zenodo.12802692 (DOI)
Dataset: http://table.plazi.org/id/F69BD3C40258FFCEFF8C54E2C6A5FF00 (URL)
Dataset: http://table.plazi.org/id/F69BD3C4025BFFCDFF8C54E2C613FF00 (URL)
Figure: 10.5281/zenodo.12802696 (DOI)
Figure: 10.5281/zenodo.12802700 (DOI)
Figure: 10.5281/zenodo.12820020 (DOI)
Figure: 10.5281/zenodo.12802704 (DOI)
Dataset: http://table.plazi.org/id/F69BD3C40257FFC1FDF9519EC784FA24 (URL)

References

  • 1. Yabuuchi E, Kaneko T, Yano I, Moss CW, Miyoshi N. Sphingobacterium gen. nov., Sphingobacterium spiritivorum comb.nov., Sphingobacterium multivorum comb. nov., Sphingobacterium mizutae sp. nov., and Flavobacterium indologenes sp. nov.: Glucose-Nonfermenting Gram-Negative Rods in CDC Groups IIK-2 and IIb. International Journal of Systematic Bacteriology. 1983; 33(3):580-98.
  • 2. Lee DH, Hur JS, Kahng HY. Sphingobacterium cladoniae sp. nov., isolated from lichen, Cladonia sp., and emended description of Sphingobacterium siyangense.International journal of systematic and evolutionary microbiology. 2013; 63(Pt 2):755-60.
  • 3. Yoo SH, Weon HY, Jang HB, Kim BY, Kwon SW, Go SJ, et al. Sphingobacterium composti sp. nov., isolated from cotton-waste composts. International journal of systematic and evolutionary microbiology. 2007; 57(7):1590-3. PMID: 17625199
  • 4. Zhang J, Zheng JW, Cho BC, Hwang CY, Fang CX, He J, et al. Sphingobacterium wenxiniae sp. nov., a cypermethrin-degrading species from activated sludge. International journal of systematic and evolutionary microbiology. 2012; 62(Pt 3):683-7.
  • 5. Holmes B, Owen R, Hollis D. Flavobacterium spiritivorum, a new species isolated from human clinical specimens. International Journal of Systematic Bacteriology. 1982; 32(2):157-65.
  • 6. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. International journal of systematic and evolutionary microbiology. 2014; 64(Pt 2):346-51. doi: 10.1099/ijs.0.059774-0 PMID: 24505072
  • 7. Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, et al. Assembly and Validation of the Genome of the Nonmodel Basal Angiosperm Amborella. Science. 2013; 342(6165):1516-7. doi: 10. 1126/science.1241130 PMID: 24357320
  • 9. Chen Q, Savarino SJ, Venkatesan MM. Subtractive hybridization and optical mapping of the enterotoxigenic Escherichia coli H10407 chromosome: isolation of unique sequences and demonstration of significant similarity to the chromosome of E. coli K-12. Microbiology. 2006; 152(4):1041-54. PMID: 16549668
  • 10. Schwan WR, Briska A, Stahl B, Wagner TK, Zentz E, Henkhaus J, et al. Use of optical mapping to sort uropathogenic Escherichia coli strains into distinct subgroups. Microbiology. 2010; 156(7):2124-35. doi: 10.1099/mic.0.033977-0 PMID: 20378655
  • 11. Kotewicz ML, Jackson SA, LeClerc JE, Cebula TA. Optical maps distinguish individual strains of Escherichia coli O157: H7. Microbiology. 2007; 153(6):1720-33. PMID: 17526830
  • 12. Miller JM. Whole-genome mapping: a new paradigm in strain-typing technology. Journal of clinical microbiology. 2013; 51(4):1066-70. doi: 10.1128/JCM.00093-13 PMID: 23363821
  • 13. Jiang S, Chen M, Su S, Yang M, Li A, Zhang C, et al. Sphingobacterium arenae sp. nov., isolated from sandy soil. International journal of systematic and evolutionary microbiology. 2014; 64(Pt 1):248-53.
  • 14. Cowan ST, Steel KJ, Barrow G, Feltham R. Cowan and Steel's manual for the identification of medical bacteria: Cambridge university press; 2003.
  • 15. Sorokin DY. Is there a limit for high-pH life? International journal of systematic and evolutionary microbiology. 2005; 55(4):1405-6. PMID: 16014458
  • 16. Zhou Z, Yuan M, Tang R, Chen M, Lin M, Zhang W. Corynebacterium deserti sp. nov., isolated from desert sand. International journal of systematic and evolutionary microbiology. 2012; 62(Pt 4):791-4. doi: 10.1099/ijs.0.030429-0 PMID: 21571935
  • 17. Yabuuchi E, TANIMURA E, OHYAMA A, YANO I, YAMAMOTO A. Flavobacterium devorans ATCC 10829: A strain of Pseudomonas paucimobilis. The Journal of General and Applied Microbiology. 1979; 25(2):95-107.
  • 18. Zhu H, Guo J, Chen M, Feng G, Yao Q. Burkholderia dabaoshanensis sp. nov., a heavy-metal-tolerant bacteria isolated from Dabaoshan mining area soil in China. PloS one. 2012; 7(12):e50225. doi: 10. 1371/journal.pone.0050225 PMID: 23226514
  • 19. Yuan M, Zhang W, Dai S, Wu J, Wang Y, Tao T, et al. Deinococcus gobiensis sp. nov., an extremely radiation-resistant bacterium. International journal of systematic and evolutionary microbiology. 2009; 59 (6):1513-7. doi: 10.1099/ijs.0.004523-0 PMID: 19502345
  • 20. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular biology and evolution. 1987; 4(4):406-25. PMID: 3447015
  • 21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985:783-91.
  • 22. Dong Y, Xie M, Jiang Y, Xiao N, Du X, Zhang W, et al. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nature biotechnology. 2013; 31(2):135- 41. doi: 10.1038/nbt.2478 PMID: 23263233
  • 23. Yuan M, Chen M, Zhang W, Lu W, Wang J, Yang M, et al. Genome sequence and transcriptome analysis of the radioresistant bacterium Deinococcus gobiensis: insights into the extreme environmental adaptations. PloS one. 2012; 7(3):e34458. doi: 10.1371/journal.pone.0034458 PMID: 22470573
  • 24. Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic acids research. 2005; 33(suppl 2):W686-W9.
  • 25. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic acids research. 2007; 35(9):3100-8. PMID: 17452365
  • 26. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome research. 2003; 13(9):2178-89. PMID: 12952885
  • 27. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research. 2004; 32(5):1792-7. PMID: 15034147
  • 28. Saw JH, Schatz M, Brown MV, Kunkel DD, Foster JS, Shick H, et al. Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kilauea Caldera, Hawai'i. PloS one. 2013; 8(10):e76376. doi: 10.1371/journal.pone.0076376 PMID: 24194836
  • 29. Hallam SJ, Konstantinidis KT, Putnam N, Schleper C, Watanabe Y, Sugahara J, et al. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proceedings of the National Academy of Sciences. 2006; 103(48):18296-301. PMID: 17114289
  • 30. He X, Xiao T, Kuang H, Lan X, Tudahong M, Osman G, et al. Sphingobacterium shayense sp. nov., isolated from forest soil. International journal of systematic and evolutionary microbiology. 2010; 60 (10):2377-81. doi: 10.1099/ijs.0.018481-0 PMID: 19933581
  • 31. Liu J, Yang LL, Xu CK, Xi JQ, Yang FX, Zhou F, et al. Sphingobacterium nematocida sp. nov., a nematicidal endophytic bacterium isolated from tobacco. International journal of systematic and evolutionary microbiology. 2012; 62(Pt 8):1809-13.
  • 32. Duan S, Liu Z, Feng X, Zheng K, Cheng L. Sphingobacterium bambusae sp. nov., isolated from soil of bamboo plantation. The Journal of Microbiology. 2009; 47(6):693-8. doi: 10.1007/s12275-009-0296-2 PMID: 20127461
  • 33. Kim KH, Ten LN, Liu QM, Im WT, Lee ST. Sphingobacterium daejeonense sp. nov., isolated from a compost sample. International journal of systematic and evolutionary microbiology. 2006; 56(9):2031- 6. PMID: 16957095
  • 34. Choi HA, Lee SS. Sphingobacterium kyonggiense sp. nov., isolated from chloroethene-contaminated soil, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium mizutaii. International journal of systematic and evolutionary microbiology. 2012; 62(Pt 11):2559-64. doi: 10.1099/ ijs.0.024737-0 PMID: 22180612
  • 35. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. International journal of systematic and evolutionary microbiology. 2012; 62(Pt 3):716-21.
  • 36. Stackebrandt E, Goebel B. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. International Journal of Systematic Bacteriology. 1994; 44(4):846-9.
  • 37. Wayne L, Brenner D, Colwell R, Grimont P, Kandler O, Krichevsky M, et al. Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics. International Journal of Systematic Bacteriology. 1987; 37(4):463-4.
  • 38. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. DNA -DNA hybridization values and their relationship to whole-genome sequence similarities. International journal of systematic and evolutionary microbiology. 2007; 57(1):81-91. PMID: 17220447
  • 39. Richter M, Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proceedings of the National Academy of Sciences. 2009; 106(45):19126-31. doi: 10.1073/pnas. 0906412106 PMID: 19855009
  • 40. Vanderlinde EM, Harrison JJ, Muszynski A, Carlson RW, Turner RJ, Yost CK. Identification of a novel ABC transporter required for desiccation tolerance, and biofilm formation in Rhizobium leguminosarum bv. viciae 3841. FEMS microbiology ecology. 2010; 71(3):327-40. doi: 10.1111/j.1574-6941.2009. 00824.x PMID: 20030718
  • 41. Warren Rhodes KA, Boyle LN, Pointing SB, Chen Y, Liu S, Zhuo P, et al. Cyanobacterial ecology across environmental gradients and spatial scales in China's hot and cold deserts. FEMS microbiology ecology. 2007; 61(3):470-82. PMID: 17672851
  • 42. Slade D, Radman M. Oxidative stress resistance in Deinococcus radiodurans. Microbiology and Molecular Biology Reviews. 2011; 75(1):133-91. doi: 10.1128/MMBR.00015-10 PMID: 21372322
  • 43. Friedberg EC. DNA damage and repair. Nature. 2003; 421(6921):436-40. PMID: 12540918
  • 44. Fredrickson JK, Shu mei WL, Gaidamakova EK, Matrosova VY, Zhai M, Sulloway HM, et al. Protein oxidation: key to bacterial desiccation resistance? The ISME journal. 2008; 2(4):393-403. doi: 10.1038/ ismej.2007.116 PMID: 18273068
  • 45. Lorenz MG, Wackernagel W. Bacterial gene transfer by natural genetic transformation in the environment. Microbiological reviews. 1994; 58(3):563. PMID: 7968924
  • 46. Konings WN, Albers SV, Koning S, Driessen AJ. The cell membrane plays a crucial role in survival of bacteria and archaea in extreme environments. Antonie Van Leeuwenhoek. 2002; 81(1-4):61-72. PMID: 12530416
  • 47. Leslie SB, Israeli E, Lighthart B, Crowe JH, Crowe LM. Trehalose and sucrose protect both membranes and proteins in intact bacteria during drying. Applied and environmental microbiology. 1995; 61 (10):3592-7. PMID: 7486995
  • 48. Kim YH, Kwon TK, Park S, Seo HS, Cheong JJ, Kim CH, et al. Trehalose synthesis by sequential reactions of recombinant maltooligosyltrehalose synthase and maltooligosyltrehalose trehalohydrolase from Brevibacterium helvolum. Applied and environmental microbiology. 2000; 66(11):4620-4. PMID: 11055902
  • 49. Suprenant KA, Bloom N, Fang J, Lushington G. The major vault protein is related to the toxic anion resistance protein (TelA) family. Journal of Experimental Biology. 2007; 210(6):946-55. PMID: 17337707
  • 50. O'Gara JP, Gomelsky M, Kaplan S. Identification and molecular genetic analysis of multiple loci contributing to high-level tellurite resistance in Rhodobacter sphaeroides 2.4. 1. Applied and environmental microbiology. 1997; 63(12):4713-20. PMID: 9406390
  • 51. Turner RJ, Weiner JH, Taylor DE. Neither reduced uptake nor increased efflux is encoded by tellurite resistance determinants expressed in Escherichia coli. Canadian journal of microbiology. 1995; 41 (1):92-8. PMID: 7728659
  • 52. Sun Z, Zhong J, Liang X, Liu J, Chen X, Huan L. Novel mechanism for nisin resistance via proteolytic degradation of nisin by the nisin resistance protein NSR. Antimicrobial agents and chemotherapy. 2009; 53(5):1964-73. doi: 10.1128/AAC.01382-08 PMID: 19273681
  • 53. Kawai Y, Saito T. Bacteriocins: Remarks Studies. Lactic Acid Bacteria and Bifidobacteria: Current Progress in Advanced Research. 2011: 205.