signature=b4592c525429ba9ce25bc6de815d8e9e,Genomic taxonomy of vibrios

1.

Colwell RR: Polyphasic taxonomy of the genus vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol. 1970, 104 (1): 410-433.

2.

Wang Q, Garrity GM, Tiedje JM, Cole JR: Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007, 73 (16): 5261-5267. 10.1128/AEM.00062-07.

3.

Woese CR, Fox GE: Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA. 1977, 74 (11): 5088-5090. 10.1073/pnas.74.11.5088.

4.

Stackebrandt E, Goebel BM: A place for DNA-DNA reassociation and 16S ribosomal-RNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol. 1994, 49: 846-849.

5.

Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, et al: Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol. 1987, 37: 463-464.

6.

Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, Peer Van de Y, Vandamme P, Thompson FL, et al: Opinion: Re-evaluating prokaryotic species. Nat Rev Microbiol. 2005, 3 (9): 733-739. 10.1038/nrmicro1236.

7.

Gillis M, Vandamme P, De Vos P, Swings J, Kersters K: Polyphasic taxonomy. Bergey's Manual of Systematic Bacteriology: The Proteobacteria: Introductory Essays. Edited by: Brenner DJ, Krieg NR, Staley JT, Garrity GM. 2005, New york: Springer, 2: 43-48.

8.

Lawrence JG, Retchless AC: The interplay of homologous recombination and horizontal gene transfer in bacterial speciation. Methods Mol Biol. 2009, 532: 29-53. full_text.

9.

Cohan FM, Koeppel AF: The origins of ecological diversity in prokaryotes. Curr Biol. 2008, 18: 1024-1034. 10.1016/j.cub.2008.09.014.

10.

Coenye T, Gevers D, Peer Van de Y, Vandamme P, Swings J: Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev. 2005, 29 (2): 147-167. 10.1016/j.femsre.2004.11.004.

11.

Coenye T, Vandamme P: Extracting phylogenetic information from whole-genome sequencing projects: the lactic acid bacteria as a test case. Microbiology. 2003, 149 (Pt 12): 3507-3517. 10.1099/mic.0.26515-0.

12.

Karlin S, Mrazek J, Campbell AM: Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol. 1997, 179 (12): 3899-3913.

13.

Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, Huq A, Colwell RR, Knight IT, Salzberg SL: Comprehensive DNA signature discovery and validation. PLoS Comput Biol. 2007, 3 (5): e98-10.1371/journal.pcbi.0030098.

14.

van Passel MWJ, Kuramae EE, Luyf ACM, Bart A, Boekhout T: The reach of the genome signature in prokaryotes. BMC Evol Biol. 2006, 6 (84):

15.

Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ: Universal trees based on large combined protein sequence data sets. Nat Genet. 2001, 28 (3): 281-285. 10.1038/90129.

16.

Daubin V, Gouy M, Perriere G: Bacterial molecular phylogeny using supertree approach. Genome Inform. 2001, 12: 155-164.

17.

Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV: Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol. 2001, 1: 8-10.1186/1471-2148-1-8.

18.

Konstantinidis KT, Tiedje JM: Towards a genome-based taxonomy for prokaryotes. J Bacteriol. 2005, 187 (18): 6258-6264. 10.1128/JB.187.18.6258-6264.2005.

19.

Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM: DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol. 2007, 57 (Pt 1): 81-91. 10.1099/ijs.0.64483-0.

20.

Wright F: The 'effective number of codons' used in a gene. Gene. 1990, 87 (1): 23-29. 10.1016/0378-1119(90)90491-9.

21.

Sawabe T, Kita-Tsukamoto K, Thompson FL: Inferring the evolutionary history of vibrios by means of multilocus sequence analysis. J Bacteriol. 2007, 189 (21): 7932-7936. 10.1128/JB.00693-07.

22.

Thompson FL, Gevers D, Thompson CC, Dawyndt P, Naser S, Hoste B, Munn CB, Swings J: Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis. Appl Environ Microbiol. 2005, 71 (9): 5107-5115. 10.1128/AEM.71.9.5107-5115.2005.

23.

Thompson CC, Thompson FL, Vicente AC, Swings J: Phylogenetic analysis of vibrios and related species by means of atpA gene sequences. Int J Syst Evol Microbiol. 2007, 57 (Pt 11): 2480-2484. 10.1099/ijs.0.65223-0.

24.

Thompson FL, Gomez-Gil B, Vasconcelos AT, Sawabe T: Multilocus sequence analysis reveals that Vibrio harveyi and V. campbellii are distinct species. Appl Environ Microbiol. 2007, 73 (13): 4279-4285. 10.1128/AEM.00020-07.

25.

Thompson CC, Thompson FL, Vicente AC: Identification of vibrio cholerae and vibrio mimicus by multilocus sequence analysis (MLSA). Int J Syst Evol Microbiol. 2008, 58 (Pt 3): 617-621. 10.1099/ijs.0.65461-0.

26.

Thompson FL, Austin B, Swings J: The biology of vibrios. 2006, Washington: ASM

27.

Payne GW, Vandamme P, Morgan SH, Lipuma JJ, Coenye T, Weightman AJ, Jones TH, Mahenthiralingam E: Development of a recA gene-based identification approach for the entire Burkholderia genus. Appl Environ Microbiol. 2005, 71 (7): 3917-3927. 10.1128/AEM.71.7.3917-3927.2005.

28.

Andersson AF, Lindberg M, Jakobsson H, Backhed F, Nyren P, Engstrand L: Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE. 2008, 3 (7): e2836-10.1371/journal.pone.0002836.

29.

Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, et al: Real-time DNA sequencing from single polymerase molecules. Science. 2009, 323 (5910): 133-138. 10.1126/science.1162986.

30.

Mahenthiralingam E, Baldwin A, Drevinek P, Vanlaere E, Vandamme P, LiPuma JJ, Dowson CG: Multilocus sequence typing breathes life into a microbial metagenome. PLoS ONE. 2006, 1: e17-10.1371/journal.pone.0000017.

31.

Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, Polz MF: Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science. 2008, 320 (5879): 1081-1085. 10.1126/science.1157890.

32.

Thompson FL, Klose KE: Vibrio the First International Conference on the Biology of Vibrios. J Bacteriol. 2005, 188 (13): 4592-4596. 10.1128/JB.00141-06.

33.

Farmer JJ, Janda M, Brenner FW, Cameron DN, Birkhead KM: Genus I. Vibrio Pacini 1854. Bergey's Manual of Systematic Bacteriology: The Proteobacteria: The Gamma-Proteobacteria. Edited by: Brenner DJ, Krieg NR, Staley JT, Garrity GM. 2005, New York: Springer, 2: 494-545.

34.

Thompson FL, Iida T, Swings J: Biodiversity of vibrios. Microbiol Mol Biol Rev. 2004, 68 (3): 403-431. 10.1128/MMBR.68.3.403-431.2004. table of contents

35.

Urbanczyk H, Ast JC, Higgins MJ, Carson J, Dunlap PV: Reclassification of Vibrio fischeri, Vibrio logei, Vibrio salmonicida and Vibrio wodanis as Aliivibrio fischeri gen. nov., comb. nov., Aliivibrio logei comb. nov., Aliivibrio salmonicida comb. nov. and Aliivibrio wodanis comb. nov. Int J Syst Evol Microbiol. 2007, 57 (Pt 12): 2823-2829. 10.1099/ijs.0.65081-0.

36.

Pitcher DG, Saunders NA, Owen RJ: Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol. 1989, 8: 151-156. 10.1111/j.1472-765X.1989.tb00262.x.

37.

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 (7057): 376-380.

38.

Almeida LG, Paixao R, Souza RC, Costa GC, Barrientos FJ, Santos MT, Almeida DF, Vasconcelos AT: A System for Automated Bacterial (genome) Integrated Annotation--SABIA. Bioinformatics. 2004, 20 (16): 2832-2833. 10.1093/bioinformatics/bth273.

39.

Tamura K, Dudley J, Nei M, Kumar S: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007, 24 (8): 1596-1599. 10.1093/molbev/msm092.

40.

Hallin PF, Binnewies TT, Ussery DW: The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology. Mol Biosyst. 2008, 4 (5): 363-371. 10.1039/b717118h.

41.

Pedersen AG, Jensen LJ, Brunak S, Staerfeldt HH, Ussery DW: A DNA structural atlas for Escherichia coli. J Mol Biol. 2000, 299 (4): 907-930. 10.1006/jmbi.2000.3787.

42.

Ussery DW, Borini S, Wassenaar T: Computing for comparative genomics: bioinformatics for microbiologists. 2009, London: Spring-verlag

43.

Swofford DL, Olsen GJ, Waddell PJ, Hillis DM: Phylogentic inference. Molecular Systematics. Edited by: Hillis DM, Moritz C, Mable BK. 1996, Sunderland: Sinauer, 407-514.

44.

Saitou N, Nei M: The Neighbor-Joining Method - a New Method for Reconstructing Phylogenetic Trees. Japanese Journal of Genetics. 1986, 61 (6): 611-611.

45.

Jukes TH, Cantor CR: Evolution of protein molecules. Mammalian protein metabolism. Edited by: Munro HN. 1996, New York: Academic Press, 21-132.

46.

Felsenstein J: Confidence limits on phylogenies: An approach using the bootstrap. Evolution. 1985, 39: 783-791. 10.2307/2408678.

47.

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25 (17): 3389-3402. 10.1093/nar/25.17.3389.

48.

Rost B: Twilight zone of protein sequence alignments. Protein Eng. 1999, 12 (2): 85-94. 10.1093/protein/12.2.85.

49.

Karlin S: Global dinucleotide signatures and analysis of genomic heterogeneity. Curr Opin Microbiol. 1998, 1 (5): 598-610. 10.1016/S1369-5274(98)80095-7.

50.

Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, et al: DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature. 2000, 406 (6795): 477-483. 10.1038/35020000.

51.

Gonzalez-Escalona N, Martinez-Urtaza J, Romero J, Espejo RT, Jaykus LA, DePaola A: Determination of molecular phylogenetics of Vibrio parahaemolyticus strains by multilocus sequence typing. J Bacteriol. 2008, 190 (8): 2831-2840. 10.1128/JB.01808-07.

52.

Thompson FL, Hoste B, Vandemeulebroecke K, Swings J: Genomic diversity amongst Vibrio isolates from different sources determined by fluorescent amplified fragment length polymorphism. Syst Appl Microbiol. 2001, 24 (4): 520-538. 10.1078/0723-2020-00067.

53.

Bansal AK, Meyer TE: Evolutionary analysis by whole-genome comparisons. J Bacteriol. 2002, 184 (8): 2260-2272. 10.1128/JB.184.8.2260-2272.2002.

54.

Snel B, Bork P, Huynen MA: Genome phylogeny based on gene content. Nat Genet. 1999, 21 (1): 108-110. 10.1038/5052.

55.

Mrazek J: Phylogenetic Signals in DNA Composition: Limitations and Prospects. Mol Biol Evol. 2009, 26 (5): 1163-1169. 10.1093/molbev/msp032.

56.

Foerstner KU, von Mering C, Hooper SD, Bork P: Environments shape the nucleotide composition of genomes. EMBO Rep. 2005, 6 (12): 1208-1213. 10.1038/sj.embor.7400538.

57.

Vetsigian K, Goldenfeld N: Genome rhetoric and the emergence of compositional bias. Proc Natl Acad Sci USA. 2009, 106 (1): 215-220. 10.1073/pnas.0810122106.

58.

Paz A, Kirzhner V, Nevo E, Korol A: Coevolution of DNA-interacting proteins and genome "dialect". Mol Biol Evol. 2006, 23 (1): 56-64. 10.1093/molbev/msj007.

59.

Xia X, Wei T, Xie Z, Danchin A: Genomic changes in nucleotide and dinucleotide frequencies in Pasteurella multocida cultured under high temperature. Genetics. 2002, 161 (4): 1385-1394.

60.

Horst JP, Fritz HJ: Counteracting the mutagenic effect of hydrolytic deamination of DNA 5-methylcytosine residues at high temperature: DNA mismatch N-glycosylase Mig.Mth of the thermophilic archaeon Methanobacterium thermoautotrophicum THF. EMBO J. 1996, 15 (19): 5459-5469.

61.

Lindahl T: Instability and decay of the primary structure of DNA. Nature. 1993, 362 (6422): 709-715. 10.1038/362709a0.

62.

Wang RF, Campbell W, Cao WW, Summage C, Steele RS, Cerniglia CE: Detection of Pasteurella pneumotropica in laboratory mice and rats by polymerase chain reaction. Lab Anim Sci. 1996, 46 (1): 81-85.

63.

Meibom KL, Blokesch M, Dolganov NA, Wu CY, Schoolnik GK: Chitin induces natural competence in Vibrio cholerae. Science. 2005, 310 (5755): 1824-1827. 10.1126/science.1120096.

64.

Vidgen M, Carson J, Higgins M, Owens L: Changes to the phenotypic profile of Vibrio harveyi when infected with the Vibrio harveyi myovirus-like (VHML) bacteriophage. J Appl Microbiol. 2006, 100 (3): 481-487. 10.1111/j.1365-2672.2005.02829.x.

65.

Mazel D: Integrons: agents of bacterial evolution. Nat Rev Microbiol. 2006, 4 (8): 608-620. 10.1038/nrmicro1462.

66.

Mandel MJ, Wollenberg MS, Stabb EV, Visick KL, Ruby EG: A single regulatory gene is sufficient to alter bacterial host range. Nature. 2009, 458 (7235): 215-218. 10.1038/nature07660.

67.

Reichelt JL, Baumann P, Baumann L: Study of genetic relationships among marine species of the genera Beneckea and Photobacterium by means of in vitro DNA/DNA hybridization. Arch Microbiol. 1976, 110 (1): 101-120. 10.1007/BF00416975.

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