Complete genome sequence of Halopiger xanaduensis type strain (SH-6T)

Standards in Genomic Sciences

Volumn 6, Issue 1, 2012, Pages 31-42

  Anderson, Iain ^a   Tindall, Brian J ^b   Rohde, Manfred ^c   Lucas, Susan ^a   Han, James ^a   Lapidus, Alla ^a   Cheng, Jan Fang ^a   Goodwin, Lynne ^a   Pitluck, Sam ^a   Peters, Lin ^a   Pati, Amrita ^a   Mikhailova, Natalia ^a   Pagani, Ioanna ^a   Teshima, Hazuki ^a,d   Han, Cliff ^a,d   Tapia, Roxanne ^a,d   Land, Miriam ^e   Woyke, Tanja ^a   Klenk, Hans Peter ^b   Kyrpides, Nikos ^a   Ivanova, Natalia ^a   more..

^a DOE JOINT GENOME INSTITUTE   (United States)

^b LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^c HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^d LOS ALAMOS NATIONAL LABORATORY   (United States)

^e OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Archaea; Euryarchaeota; Extreme halophile; Halobacteriaceae

Indexed keywords

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; CARBON SOURCE; CELL MOTILITY; ENERGY METABOLISM; GENE SEQUENCE; GENOME ANALYSIS; HALOBACTERIALES; HALOPHILE; HALOPIGER XANADUENSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; SPOROGENESIS;

EURYARCHAEOTA; HALOBACTERIACEAE; HALOPHILIC ARCHAEON;

EID: 84859173462     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.2505605     Document Type: Article

References (41)

1. Gutiérrez MC, Castillo AM, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A. Halopiger xanaduensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from saline Lake Shangmatala in Inner Mongolia, China. Int J Syst Evol Microbiol 2007; 57:1402-1407.[doi:10.1099/ijs.0.65001-0] [pmid:17625165]
2. Hezayen FF, Gutiérrez MC, Steinbüchel A, Tindall BJ, Rehm BHA. Halopiger aswanensis sp. nov., a polymer-producing and extremely halophilic archaeon isolated from hypersaline soil. Int J Syst Evol Microbiol 2010; 60:633-637.[doi:10.1099/ijs.0.013078-0] [pmid:19654343]
3. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009; 37(Database issue):D141-D145.[doi:10.1093/nar/gkn879] [pmid:19004872]
4. Bruno WJ, Socci ND, Halpern AL. Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol Biol Evol 2000; 17:189-197.[pmid:10666718]
5. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547.[doi:10.1038/nbt1360] [pmid:18464787]
6. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea,Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579.[doi:10.1073/pnas.87.12.4576] [pmid:2112744]
7. Garrity GM, Holt JG. Phylum AII. Euryarchaeota phy. nov. In: Bergey's Manual of Systematic Bacteriology, vol. 1, 2nd ed. Edited by: Garrity GM, Boone DR, and Castenholz RW. Springer, New York; 2001:211-355.
8. List Editor. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Validation List no. 85. Int J Syst Evol Microbiol 2002; 52:685-690.[doi:10.1099/ijs.0.02358-0] [pmid:12054225]
9. Grant WD, Kamekura M, McGenity TJ, Ventosa A. Class III. Halobacteria class. nov. In: Bergey's Manual of Systematic Bacteriology, vol. 1, 2nd ed. Edited by: Garrity GM, Boone DR, and Castenholz RW. Springer, New York; 2001:294.
10. Grant WD, Larsen H. Extremely halophilic archaebacteria, order Halobacteriales ord. nov. In: Bergey's Manual of Systematic Bacteriology, vol. 3, 1st ed. Edited by: Staley JT, Bryant MP, Pfennig N, and Holt JG. Williams & Wilkins, Baltimore, MD 1989:2216-2228.
11. Validation List no. 31. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol 1989; 39:495-497.[doi:10.1099/00207713-39-4-495]
12. Judicial Commission of the International Committee on Systematics of Prokaryotes. The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79. Int J Syst Evol Microbiol 2005; 55:517-518.[doi:10.1099/ijs.0.63548-0] [pmid:15653928]
13. Gibbons NE. Family V. Halobacteriaceae fam. nov. In: Bergey's Manual of Determinative Bacteriology, 8th ed. Edited by: Buchanan RE and Gibbons NE. Williams & Wilkins, Baltimore, MD 1974:269-273.
14. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420.[doi:10.1099/00207713-30-1-225]
15. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25-29.[doi:10.1038/75556] [pmid:10802651]
16. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38(Database Issue):D346-D354.[doi:10.1093/nar/gkp848] [pmid:19914934]
17. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php
18. Bennett S. Solexa Ltd. Pharmacogenomics 2004; 5:433-438.[doi:10.1517/14622416.5.4.433] [pmid:15165179]
19. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437:376-380.[pmid:16056220]
20. DOE Joint Genome Institute. http://www.jgi.doe.gov
21. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829.[doi:10.1101/gr.074492.107] [pmid:18349386]
22. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998; 8:175-185.[pmid:9521921]
23. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998; 8:186-194.[pmid:9521922]
24. Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res 1998; 8:195-202.[pmid:9521923]
25. Han C, Chain P. Finishing repeat regions automatically with Dupfinisher. In Proceedings of the 2006 international conference on bioinformatics and computational biology, ed. Arabnia HR, Valafar H. CSREA Press, 2006:141-146.
26. Hyatt D, Chen GL, Lacascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119.[doi:10.1186/1471-2105-11-119] [pmid:20211023]
27. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455-457. [doi:10.1038/nmeth.1457] [pmid:20436475]
28. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955-964.[doi:10.1093/nar/25.5.955] [pmid:9023104]
29. INFERNAL. Inference of RNA alignments. http://infernal.janelia.org
30. Integrated Microbial Genomes (IMG). http://img.jgi.doe.gov
31. Markowitz VM, Mavromatis K, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271-2278.[doi:10.1093/bioinformatics/btp393] [pmid:19561336]
32. Carbohydrate-Active enZYmes Database. http://www.cazy.org
33. Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, et al. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS ONE 2010; 5:e9605.[doi:10.1371/journal.pone.0009605] [pmid:20333302]
34. Holmes ML, Dyall-Smith ML. Sequence and expression of a halobacterial beta-galactosidase gene. Mol Microbiol 2000; 36:114-122.[doi:10.1046/j.1365-2958.2000.01832.x] [pmid:10760168]
35. Li N, Shi P, Yang P, Wang Y, Luo H, Bai Y, Zhou Z, Yao B. Cloning, expression, and characterization of a new Streptomyces sp. S27 xylanase for which xylobiose is the main hydrolysis product. Appl Biochem Biotechnol 2009; 159:521-531.[doi:10.1007/s12010-008-8411-0] [pmid:19002659]
36. Ochiai A, Itoh T, Kawamata A, Hashimoto W, Murata K. Plant cell wall degradation by saprophytic Bacillus subtilis strains: gene clusters responsible for rhamnogalacturonan depolymerization. Appl Environ Microbiol 2007; 73:3803-3813.[doi:10.1128/AEM.00147-07] [pmid:17449691]
37. Falb M, Müller K, Königsmaier L, Oberwinkler T, Horn P, von Gronau S, Gonzalez O, Pfeiffer F, Bornberg-Bauer E, Oesterhelt D. Metabolism of halophilic archaea. Extremophiles 2008; 12:177-196.[doi:10.1007/s00792-008-0138-x] [pmid:18278431]
38. Johnsen U, Dambeck M, Zaiss H, Fuhrer T, Soppa J, Sauer U, Schönheit P. D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii. J Biol Chem 2009; 284:27290-27303.[doi:10.1074/jbc.M109.003814] [pmid:19584053]
39. Offner S, Hofacker A, Wanner G, Pfeifer F. Eight of fourteen gvp genes are sufficient for formation of gas vesicles in halophilic archaea. J Bacteriol 2000; 182:4328-4336.[doi:10.1128/JB.182.15.4328-4336.2000] [pmid:10894744]
40. Sukupolvi-Petty S, Grass S, St Geme JW. The Haemophilus influenzae type b hcsA and hcsB gene products facilitate transport of capsular polysaccharide across the outer membrane and are essential for virulence. J Bacteriol 2006; 188:3870-3877.[doi:10.1128/JB.01968-05] [pmid:16707679]
41. Liu F, Tanner ME. PseG of pseudaminic acid biosynthesis: a UDP-sugar hydrolase as a masked glycosyltransferase. J Biol Chem 2006; 281:20902-20909.[doi:10.1074/jbc.M602972200] [pmid:16728396]