Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea
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Altschul, 1990, Basic local alignment search tool, J Mol Biol, 215, 403, 10.1016/S0022-2836(05)80360-2
Amaral, 2014, Genotype to phenotype: identification of diagnostic vibrio phenotypes using whole genome sequences, Int J Syst Evol Microbiol, 64, 357, 10.1099/ijs.0.057927-0
Camacho, 2009, blast+: architecture and applications, BMC Bioinformatics, 10, 421, 10.1186/1471-2105-10-421
Camelo-Castillo, 2014, Streptococcus dentisani sp. nov., a new member of the Mitis group, Int J Syst Evol Microbiol, 64, 10.1099/ijs.0.062802-0
Chan, 2012, Defining bacterial species in the genomic era: insights from the genus Acinetobacter, BMC Microbiol, 12, 302, 10.1186/1471-2180-12-302
Chun, 2009, Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae, Proc Natl Acad Sci U S A, 106, 15442, 10.1073/pnas.0907787106
Cole, 2009, The Ribosomal Database Project: improved alignments and new tools for rRNA analysis, Nucleic Acids Res, 37, D141, 10.1093/nar/gkn879
Colwell, 1970, Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species, J Bacteriol, 104, 410, 10.1128/JB.104.1.410-433.1970
Curtis, 2002, Estimating prokaryotic diversity and its limits, Proc Natl Acad Sci U S A, 99, 10494, 10.1073/pnas.142680199
Deloger, 2009, A genomic distance based on MUM indicates discontinuity between most bacterial species and genera, J Bacteriol, 191, 91, 10.1128/JB.01202-08
Eid, 2009, Real-time DNA sequencing from single polymerase molecules, Science, 323, 133, 10.1126/science.1162986
Fleischmann, 1995, Whole-genome random sequencing and assembly of Haemophilus influenzae Rd, Science, 269, 496, 10.1126/science.7542800
Fox, 1992, How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity, Int J Syst Bacteriol, 42, 166, 10.1099/00207713-42-1-166
Goris, 2007, DNA–DNA hybridization values and their relationship to whole-genome sequence similarities, Int J Syst Evol Microbiol, 57, 81, 10.1099/ijs.0.64483-0
Guo, 2008, A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics, Int J Syst Evol Microbiol, 58, 149, 10.1099/ijs.0.65224-0
Haley, 2010, Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae, BMC Microbiol, 10, 154, 10.1186/1471-2180-10-154
Henz, 2005, Whole-genome prokaryotic phylogeny, Bioinformatics, 21, 2329, 10.1093/bioinformatics/bth324
Hofer, 2013, Environmental microbiology: exploring diversity with single-cell genomics, Nat Rev Microbiol, 11, 598, 10.1038/nrmicro3095
Hoffmann, 2012, Vibrio caribbeanicus sp. nov., isolated from the marine sponge Scleritoderma cyanea, Int J Syst Evol Microbiol, 62, 1736, 10.1099/ijs.0.032375-0
Jeon, 2014, EzEditor: a versatile sequence alignment editor for both ribosomal RNA and protein coding genes, Int J Syst Evol Microbiol, 64, 10.1099/ijs.0.059360-0
Jiménez, 2013, Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations, Syst Appl Microbiol, 36, 383, 10.1016/j.syapm.2013.04.008
Johnson, 1968, Deoxyribonucleic acid homology in bacterial taxonomy: effect of incubation temperature on reaction specificity, J Bacteriol, 95, 893, 10.1128/JB.95.3.893-900.1968
Kim, 2012, Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species, Int J Syst Evol Microbiol, 62, 716, 10.1099/ijs.0.038075-0
Kim, 2014a, Towards a taxanomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes, Int J Syst Evol Microbiol, 64, 346, 10.1099/ijs.0.059774-0
Kim, 2014b, Applications of next-generation sequencing to unravelling the evolutionary history of algae, Int J Syst Evol Microbiol, 64, 333, 10.1099/ijs.0.054221-0
Konstantinidis, 2005, Genomic insights that advance the species definition for prokaryotes, Proc Natl Acad Sci U S A, 102, 2567, 10.1073/pnas.0409727102
Koren, 2012, Hybrid error correction and de novo assembly of single-molecule sequencing reads, Nat Biotechnol, 30, 693, 10.1038/nbt.2280
Kurtz, 2004, Versatile and open software for comparing large genomes, Genome Biol, 5, R12, 10.1186/gb-2004-5-2-r12
Kurtzman, 2014, Use of gene sequence analyses and genome comparisons for yeast systematics, Int J Syst Evol Microbiol, 64, 325, 10.1099/ijs.0.054197-0
Lang, 2013, Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices, PLoS ONE, 8, e62510, 10.1371/journal.pone.0062510
Lee, 2013, Flavobacterium limnosediminis sp. nov., isolated from sediment of a freshwater lake, Int J Syst Evol Microbiol, 63, 4784, 10.1099/ijs.0.055566-0
Löffler, 2013, Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi, Int J Syst Evol Microbiol, 63, 625, 10.1099/ijs.0.034926-0
Lucena, 2012, Vibrio aestivus sp. nov. and Vibrio quintilis sp. nov., related to Marisflavi and Gazogenes clades, respectively, Syst Appl Microbiol, 35, 427, 10.1016/j.syapm.2012.08.002
Maiden, 1998, Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms, Proc Natl Acad Sci U S A, 95, 3140, 10.1073/pnas.95.6.3140
Margulies, 2005, Genome sequencing in microfabricated high-density picolitre reactors, Nature, 437, 376, 10.1038/nature03959
Marrero, 2013, Phylogeny and classification of Dickeya based on multilocus sequence analysis, Int J Syst Evol Microbiol, 63, 3524, 10.1099/ijs.0.046490-0
Martens, 2007, Multilocus sequence analysis of Ensifer and related taxa, Int J Syst Evol Microbiol, 57, 489, 10.1099/ijs.0.64344-0
Meier-Kolthoff, 2013, Genome sequence-based species delimitation with confidence intervals and improved distance functions, BMC Bioinformatics, 14, 60, 10.1186/1471-2105-14-60
Meier-Kolthoff, 2014, Taxanomic use of DNA G+C content and DNA-DNA hybridization in the genomic age, Int J Syst Evol Microbiol, 64, 352, 10.1099/ijs.0.056994-0
Mende, 2013, Accurate and universal delineation of prokaryotic species, Nat Methods, 10, 881, 10.1038/nmeth.2575
Naushad, 2014, Conserved signature indels and signature proteins as novel tools for understanding microbioal phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria, Int J Syst Evol Microbiol, 64, 366, 10.1099/ijs.0.054213-0
Oren, 2010, Molecular Phylogeny of Microorganisms
Ramasamy, 2014, A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species, Int J Syst Evol Microbiol, 64, 384, 10.1099/ijs.0.057091-0
Richter, 2009, Shifting the genomic gold standard for the prokaryotic species definition, Proc Natl Acad Sci U S A, 106, 19126, 10.1073/pnas.0906412106
Rinke, 2013, Insights into the phylogeny and coding potential of microbial dark matter, Nature, 499, 431, 10.1038/nature12352
Rosselló-Mora, 2006, DNA-DNA reassociation methods applied to microbial taxonomy and their critical evaluation, Molecular Identification, Systematics and Population Structure of Prokaryotes, 23, 10.1007/978-3-540-31292-5_2
Rosselló-Mora, 2001, The species concept for prokaryotes, FEMS Microbiol Rev, 25, 39, 10.1016/S0168-6445(00)00040-1
Ruvira, 2013, Marinifilum flexuosum sp. nov., a new Bacteroidetes isolated from coastal Mediterranean Sea water and emended description of the genus Marinifilum Na et al., 2009, Syst Appl Microbiol, 36, 155, 10.1016/j.syapm.2012.12.003
Sokal, 1963, Principles of Numerical Taxonomy
Stackebrandt, 2006, Taxonomic parameters revisited: tarnished gold standards, Microbiol Today, 33, 152
Stackebrandt, 1994, Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology, Int J Syst Bacteriol, 44, 846, 10.1099/00207713-44-4-846
Stackebrandt, 2002, Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology, Int J Syst Evol Microbiol, 52, 1043
Sullivan, 2005, Multilocus sequence typing: data analysis in clinical microbiology and public health, Mol Biotechnol, 29, 245, 10.1385/MB:29:3:245
Swan, 2013, Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean, Proc Natl Acad Sci U S A, 110, 11463, 10.1073/pnas.1304246110
Tindall, 2010, Notes on the characterization of prokaryote strains for taxonomic purposes, Int J Syst Evol Microbiol, 60, 249, 10.1099/ijs.0.016949-0
Vanlaere, 2009, Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov., Int J Syst Evol Microbiol, 59, 102, 10.1099/ijs.0.001123-0
Wayne, 1987, Report of the ad hoc committee on reconciliation of approaches to bacterial systematics, Int J Syst Bacteriol, 37, 463, 10.1099/00207713-37-4-463
Whitman, 1998, Prokaryotes: the unseen majority, Proc Natl Acad Sci U S A, 95, 6578, 10.1073/pnas.95.12.6578
Wu, 2009, A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea, Nature, 462, 1056, 10.1038/nature08656
Yarza, 2013, Sequencing orphan species initiative (SOS): filling the gaps in the 16S rRNA gene sequence database for all species with validly published names, Syst Appl Microbiol, 36, 69, 10.1016/j.syapm.2012.12.006