Impact of genomics on the understanding of microbial evolution and classification: The importance of Darwin's views on classification

FEMS Microbiology Reviews

Volumn 40, Issue 4, 2016, Pages 520-553

  Gupta, Radhey S ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

Conserved signature indels and proteins; Darwin's theory of evolution; Genome sequences; Genomes derived molecular signatures; Horizontal gene transfer; Microbial systematics and taxonomy

Indexed keywords

CONSERVED SIGNATURE INDEL; CONSERVED SIGNATURE PROTEIN; MOLECULAR MARKER; UNCLASSIFIED DRUG; GENETIC MARKER; RNA 16S;

ARTICLE; BACTERIAL GENOME; BORRELIA; BORRELIA INFECTION; CHARACTER STATE; CHLAMYDIA; CLADISTICS; CLASSIFICATION; CONVERGENT EVOLUTION; DARWIN THEORY; EVOLUTION; GENE SEQUENCE; GENOMICS; HALOBACTERIALES; HORIZONTAL GENE TRANSFER; HUMAN; LYME DISEASE; MICROBIAL DIVERSITY; MICROBIAL EVOLUTION; MICROBIAL GENOME; MICROBIOLOGICAL PHENOMENA AND FUNCTIONS; MOLECULAR PHYLOGENY; MOLECULAR SYSTEMATICS; NONHUMAN; PHYLOGENOMICS; PHYLUM; PLANCTOMYCETES; PROKARYOTE; SPIROCHETE; SYNAPOMORPHY; THEORY; THERMOTOGAE; VERRUCOMICROBIA; BACTERIUM; GENETIC MARKER; GENETICS; PHYLOGENY; SPECIES DIFFERENTIATION;

BACTERIA; CLASSIFICATION; GENETIC MARKERS; GENETIC SPECIATION; GENOME, BACTERIAL; GENOMICS; PHYLOGENY; RNA, RIBOSOMAL, 16S;

EID: 84977073931     PISSN: 01686445     EISSN: 15746976     Source Type: Journal    
DOI: 10.1093/femsre/fuw011     Document Type: Article

References (410)

1. Abby SS, Tannier E, Gouy M et al. Lateral gene transfer as a support for the tree of life 3. P Natl Acad Sci USA 2012;109: 4962-7.
2. Adeolu M, Gupta RS. Phylogenomics and molecular signatures for the order Neisseriales: proposal for division of the order Neisseriales into the emended family Neisseriaceae and Chromobacteriaceae fam. nov. Anton Leeuw 2013;104:1-24.
3. Adeolu M, Gupta RS. A phylogenomic and molecular marker based proposal for the division of the genus Borrelia into two genera: the emended genus Borrelia containing only the members of the relapsing fever Borrelia, and the genus Borreliella gen. nov. containing the members of the Lyme disease Borrelia (Borrelia burgdorferi sensu lato complex). Anton Leeuw 2014;105:1049-72.
4. Ahmod NZ, Gupta RS, Shah HN. Identification of a Bacillus anthracis specific indel in the yeaC gene and development of a rapid pyrosequencing assay for distinguishing B. anthracis from the B. cereus group. J Microbiol Meth 2011;87:278-85.
5. Ajawatanawong P, Baldauf SL. Evolution of protein indels in plants, animals and fungi. BMC Evol Biol 2013;13:140.
6. Akiva E, Itzhaki Z, Margalit H. Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains. P Natl Acad Sci USA 2008;105:13292-7.
7. Amin AG, Goude R, Shi L et al. EmbA is an essential arabinosyltransferase in Mycobacterium tuberculosis. Microbiology 2008;154:240-8.
8. Andam CP, Gogarten JP. Biased gene transfer in microbial evolution. Nat Rev Microbiol 2011;9:543-55.
9. Andersson JO. Lateral gene transfer in eukaryotes 3. Cell Mol Life Sci 2005;62:1182-97.
10. Ang D, Georgopoulos C. The heat-shock-regulated grpE gene of Escherichia coli is required for bacterial growth at all temperatures but is dispensable in certain mutant backgrounds. J Bacteriol 1989;171:2748-55.
11. Arahal D. Whole-genome analyses: average nucleotide identity. Methods Microbiol 2014;41:103-22.
12. Baldauf SL. Phylogeny for the faint of heart: a tutorial. Trends Genet 2003;19:345-51.
13. Baldauf SL, Palmer JD. Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. P Natl Acad Sci USA 1993;90:11558-62.
14. Bapteste E, O'Malley MA, Beiko RG et al. Prokaryotic evolution and the tree of life are two different things 7. Biol Direct 2009;4:34.
15. Bapteste E, Philippe H. The potential value of indels as phylogenetic markers: position of trichomonads as a case study. Mol Biol Evol 2002;19:972-7.
16. Bapteste E, Susko E, Leigh J et al. Do orthologous gene phylogenies really support tree-thinking? BMC Evol Biol 2005; 5:33.
17. Beiko RG. Telling the whole story in a 10 000-genome world. Biol Direct 2011;6:34.
18. Beiko RG, Chan CX, Ragan MA. A word-oriented approach to alignment validation. Bioinformatics 2005;21:2230-9.
19. Beiko RG, Harlow TJ, Ragan MA. Highways of gene sharing in prokaryotes. P Natl Acad Sci USA 2005;102:14332-7.
20. Beiko RG, Ragan MA. Detecting lateral genetic transfer: a phylogenetic approach. Methods Mol Biol 2008;452:457-69.
21. Bentley SD, Parkhill J. Comparative genomic structure of prokaryotes. Annu Rev Genet 2004;38:771-92.
22. Bhandari V, Ahmod NZ, Shah HN et al. Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus. Int J Syst Evol Micr 2013;63:2712-26.
23. Bhandari V, Gupta RS. Molecular signatures for the phylum Synergistetes and some of its subclades. Anton Leeuw 2012;102:517-40.
24. Bhandari V, Gupta RS. Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov., Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov., Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five newcombinations. Anton Leeuw 2014a;105:143-68.
25. Bhandari V, Gupta RS. Phylum thermotogae. The Prokaryotes 2014b;4:989-1015.
26. Bhandari V, Naushad HS, Gupta RS. Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution. Front Cell Infect Microbiol 2012;2:98.
27. Biesiada G, Czepiel J, Lesniak MR et al. Lyme disease: review. Arch Med Sci 2012;8:978-82.
28. Binnewies TT, Motro Y, Hallin PF et al. Ten years of bacterial genome sequencing: comparative-genomics-based discoveries. Funct Integr Genomics 2006;6:165-85.
29. Boto L. Horizontal gene transfer in evolution: facts and challenges. Proc Biol Sci 2010;277:819-27.
30. Boucher Y, Douady CJ, Papke RT et al. Lateral gene transfer and the origins of prokaryotic groups. Annu Rev Genet 2003;37:283-328.
31. Boussau B, Daubin V. Genomes as documents of evolutionary history. Trends Ecol Evol 2010;25:224-32.
32. Brenner DJ, Staley JT, Krieg NR. Classification of Procaryotic Organisms and the Concept of Bacterial Speciation. In: Brenner DJ, Krieg NR, Staley JT (eds). Bergey's Manual of Systematic Bacteriology, Volume 2, Part C, Introductory Essays. Springer: New York, 2005, 27-32.
33. Brown JR, Douady CJ, Italia MJ et al. Universal trees based on large combined protein sequence data sets. Nat Genet 2001;28: 281-5.
34. Buchanan RE. General Systematic Bacteriology. Baltimore:Williams and Wilkins, 1925.
35. Buchanan RE, Gibbons NE. Bergey's Manual of Deteminative Bacteriology. Baltimore: Williams and Wilkins, 1974.
36. Bukau B, Horwich AL. The Hsp70 and Hsp60 chaperone machines. Cell 1998;92:351-66.
37. Bush RM, Everett KDE. Molecular evolution of the Chlamydiaceae. Int J Syst Bacteriol 2001;51:203-20.
38. Campbell C, Adeolu M, Gupta RS. Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov., Veillonellales ord. nov. Int J Syst Evol Micr 2015;65:3203-15.
39. Capes MD, DasSarma P, DasSarma S. The core and unique proteins of haloarchaea. BMC Genomics 2012;13:39.
40. Chaconas G, Kobryn K. Structure, function, and evolution of linear replicons in Borrelia. Annu Rev Microbiol 2010;64: 185-202.
41. Chan EC, McLaughlin R. Taxonomy and virulence of oral spirochetes. Oral Microbiol Immunol 2000;15:1-9.
42. Chandra G, Chater KF. Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences. FEMS Microbiol Rev 2014;38:345-79.
43. Chatton E. Titres et travaux scientifiques (1906-1937) de Edouard Chatton. Sete, France: E.Sottano, 1937.
44. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Micr 2014;64:316-24.
45. Ciccarelli FD, Doerks T, von Mering C et al. Toward automatic reconstruction of a highly resolved tree of life. Science 2006;311:1283-7.
46. Coenye T, Gevers D, Van de PY et al. Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev 2005;29:147-67.
47. Cohn F. Untersuchungen über Bakterien. II. Beitr Biol Pflanz 1875;3:141-208.
48. Cole JR, Wang Q, Fish JA et al. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 2014;42:D633-42.
49. Colewell RR. Polyphasic taxonomy of bacteria. In: Iizuka H, Hasegawa T (eds). Culture Collections of Microorganisms. Tokyo: University of Tokyo Press, 1970, 421-36.
50. Crick FHC. The biological replication of macromolecules. Symp Soc Exp Biol 1958;12:138-63.
51. Cutino-Jimenez AM, Martins-Pinheiro M, Lima WC et al. Evolutionary placement of Xanthomonadales based on conserved protein signature sequences. Mol Phylogenet Evol 2010;54: 524-34.
52. Dagan T. Phylogenomic networks. Trends Microbiol 2011;19: 483-91.
53. Dagan T, Artzy-Randrup Y, Martin W. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. P Natl Acad Sci USA 2008;105:10039-44.
54. Dagan T, Martin W. The tree of one percent. Genome Biol 2006;7:118.
55. Danchin A. From protein sequence to function. Curr Opin Struct Biol 1999;9:363-7.
56. Danchin A. The Delphic Boat: What Genomes Tell Us. Cambridge, MA: Harvard University Press, 2002.
57. Danchin A. Genomes and evolution. Curr Issues Mol Biol 2003;5:37-42.
58. Danchin A, Fang G, Noria S. The extant core bacterial proteome is an archive of the origin of life. Proteomics 2007;7:875-89.
59. Darwin C. The Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. London: John Murray, 1859.
60. Darwin FE. The Life and Letters of Charles Darwin. London: John Murray, 1887.
61. Daubin V, Ochman H. Bacterial genomes as newgene homes: the genealogy of ORFans in E. coli. Genome Res 2004;14:1036-42.
62. de Queiroz K, Gauthier J. Phylogenetic taxonomy. Ann Rev Ecol Syst 1992;23:449-80.
63. Dean D. Chlamydia trachomatis today: treatment, detection, immunogenetics and the need for a greater global understanding of chlamydial disease pathogenesis. Drugs Today 2009;45 (Suppl B):25-31.
64. Dean D, Kandel RP, Adhikari HK et al. Multiple Chlamydiaceae species in trachoma: implications for disease pathogenesis and control. PLoS Med 2008;5:e14.
65. Deloger M, El Karoui M, Petit MA. A genomic distance based on MUMindicates discontinuity between most bacterial species and genera. J Bacteriol 2009;191:91-99.
66. Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 2005;6:361-75.
67. Delwiche CF, Kuhsel M, Palmer JD. Phylogenetic analysis of tufA sequences indicates a cyanobacterial origin of all plastids. Mol Phylogenet Evol 1995;4:110-28.
68. den Bakker HC, Cummings CA, Ferreira V et al. Comparative genomics of the bacterial genus Listeria: genome evolution is characterized by limited gene acquisition and limited gene loss. BMC Genomics 2010;11:688.
69. Dobzhansky T. Genetics and the Origin of Species. New York: Columbia University Press, 1937.
70. Doolittle WF. Uprooting the tree of life. Sci Am 2000;282:90-95.
71. Doolittle WF. If the Tree of Life fell, would we recognize the sound? In: Sapp J (ed.). Microbial Phylogeny and Evolution. Oxford: Oxford University Press, 2005, 119-33.
72. Doolittle F. The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them. Philos T Roy Soc B 2009;364:2221-8.
73. Doolittle WF, Akam M. Genomes and evolution. Curr Opin Genet Dev 1998;8:613-5.
74. Doolittle WF, Bapteste E. Pattern pluralism and the tree of life hypothesis. P Natl Acad Sci USA 2007;104:2043-9.
75. Doolittle WF, Brunet TD. What is the tree of life? PLoS Genet 2016;12:e1005912.
76. Dowson CG, Hutchison A, Brannigan JA et al. Horizontal transfer of penicillin-binding protein genes in penicillin-resistant clinical isolates of Streptococcus pneumoniae. P Natl Acad Sci USA 1989;86:8842-6.
77. Dutilh BE, Huynen MA, Bruno WJ et al. The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. J Mol Evol 2004;58:527-39.
78. Dutilh BE, Snel B, Ettema TJ et al. Signature genes as a phylogenomic tool. Mol Biol Evol 2008;25:1659-67.
79. Eck RV, DayhoffMO. Atlas of Protein Sequences and Structure. Silver Spring, MD: National Biomedical Research Foundation, 1966. Ellis RJ, van der Vies SM. Molecular chaperones. Annu Rev Biochem 1991;60:321-47.
80. Estabrook GF, Johnson CS, Jr, McMorris FR. A mathematical foundation for the analysis of cladistic character compatibility. Math Biosci 1976;29:181-7.
81. Everett KD. Chlamydia and Chlamydiales: more than meets the eye. Vet Microbiol 2000;75:109-26.
82. Everett KD, Bush RM, Andersen AA. Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov., Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms. Int J Syst Bacteriol 1999;49 (Pt 2):415-40.
83. EZGenome. Chun Labwebsite. 2015, http://www.ezbiocloud.net/ ezgenome (2 June 2016, date last accessed). Fang G, Rocha E, Danchin A. How essential are nonessential genes? Mol Biol Evol 2005;22:2147-56.
84. Fang G, Rocha EP, Danchin A. Persistence drives gene clustering in bacterial genomes. BMC Genomics 2008;9:4.
85. Fayet O, Ziegelhoffer T, Georgopoulos C. The groES and groEL heat shock gene products of Escherichia coli are essential for bacterial growth at all temperatures. J Bacteriol 1989;171:1379-85.
86. Felsenstein J. Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 1988;22:521-65.
87. Felsenstein J. Inferring Phylogenies. Sunderland, MA: Sinauer Associates, Inc., 2004.
88. Fields PI, Barnes RC. The genus Chlamydia. In: Balows A, Trüper HG, Dworkin M et al. (eds). The Prokaryotes. New York: Springer, 1992, 3691-709.
89. Fisher RA. The Genetical Theory of Natural Selection. Oxford: Clarendon Press, 1930.
90. Fitch WM, Margoliash E. Construction of phylogentic trees: a method based on mutational distances as estimated from cytochrome c sequences is of general applicability. Science 1967;155:279-84.
91. Fleischmann RD, Adams MD,White O et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995;269:496-512.
92. Forterre P. Darwin's goldmine is still open: variation and selection run the world. Front Cell Infect Microbiol 2012;2:106.
93. Fox GE, Stackebrandt E, Hespell RB et al. The phylogeny of prokaryotes. Science 1980;209:457-63.
94. Frock AD, Gray SR, Kelly RM. Hyperthermophilic Thermotoga species differ with respect to specific carbohydrate transporters and glycoside hydrolases. Appl Environ Microb 2012;78:1978-86.
95. Frock AD, Notey JS, Kelly RM. The genus Thermotoga: recent developments. Environ Technol 2010;31:1169-81.
96. Fuerst JA. Intracellular compartmentation in planctomycetes. Annu Rev Microbiol 2005;59:299-328.
97. Fuerst JA. The PVC superphylum: exceptions to the bacterial definition? Anton Leeuw 2013;104:451-66.
98. Galperin MY. Conserved 'hypothetical' proteins: new hints and new puzzles. Comp Funct Genomics 2001;2:14-18.
99. Galperin MY, Koonin EV. 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res 2004;32:5452-63.
100. Galtier N. A model of horizontal gene transfer and the bacterial phylogeny problem. Syst Biol 2007;56:633-42.
101. GaltierN, Daubin V. Dealing with incongruence in phylogenomic analyses 1. Philos T Roy Soc B 2008;363:4023-9.
102. Gao B, Gupta RS. Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria. Int J Syst Evol Micr 2005;55:2401-12.
103. Gao B, Gupta RS. Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis. BMC Genomics 2007;8:86.
104. Gao B, Gupta RS. Microbial systematics in the post-genomics era. Anton Leeuw 2012a;101:45-54.
105. Gao B, Gupta RS. Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria. Microbiol Mol Biol R 2012b;76:66-112.
106. Gao B, Mohan R, Gupta RS. Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria. Int J Syst Evol Micr 2009;59:234-47.
107. Gao B, Parmanathan R, Gupta RS. Signature proteins that are distinctive characteristics of Actinobacteria and their subgroups. Anton Leeuw 2006;90:69-91.
108. Gao B, Sugiman-Marangos S, Junop MS et al. Structural and phylogenetic analysis of a conserved actinobacteria-specific protein (ASP1; SCO1997) from Streptomyces coelicolor. BMC Struct Biol 2009;9:40.
109. Garrity GM. Preface to the second edition of Bergey's manual of systematic bacteriology. In: Boone DR, Castenholz RW, Garrity GM (eds). Bergey's Manual of Systematic Bacteriology. New York: Springer, 2001.
110. Garrity GM, Oren A. Response to Gribaldo and Brochier-Armanet: time for order in microbial systematics 2. Trends Microbiol 2012;20:353-4.
111. Ge F, Wang LS, Kim J. The cobweb of life revealed by genomescale estimates of horizontal gene transfer 4. PLoS Biol 2005;3:e316.
112. Georgiades K, Raoult D. How microbiology helps define the rhizome of life 1. Front Cell Infect Microbiol 2012;2:60.
113. Glockner J, KubeM, Shrestha PMet al. Phylogenetic diversity and metagenomics of candidate division OP3. Environ Microbiol 2010;12:1218-29.
114. Gogarten JP. Gene transfer: gene swapping craze reaches eukaryotes. Curr Biol 2003;13:R53-4.
115. Gogarten JP, Doolittle WF, Lawrence JG. Prokaryotic evolution in light of gene transfer. Mol Biol Evol 2002;19:2226-38.
116. Gogarten JP, Townsend JP. Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 2005;3:679-87.
117. Golding GB, Gupta RS. Protein-based phylogenies support a chimeric origin for the eukaryotic genome. Mol Biol Evol 1995;12:1-6.
118. Goris J, Konstantinidis KT, Klappenbach JA et al. DNA-DNA hybridization values and their relationship to wholegenome sequence similarities. Int J Syst Evol Micr 2007;57: 81-91.
119. Grant WD, Kamekura M, McGenity TJ et al. Class III. Halobacteria class nov. In: Boone DR, Castenholz RW, Garrity GM (eds). Bergey's Manual of Systematic Bacteriology. New York: Springer, 2001a, 294.
120. Grant WD, Kamekura M, McGenity TJ et al. Order I. Halobacteriales Grant and Larsen 1989b, 495VP (Effective Publication: Grant and Larsen 1989a, 2216). In: Boon ED, Castenholz RW, Garrity GM (eds). Bergey's Manual of Systematic Bacteriology. New York: Springer, 2001b, 294-9.
121. Gray MW, Doolittle WF. Has the endosymbiont hypothesis been proven? Microbiol Rev 1982;46:1-42.
122. Grazziotin AL, Vidal NM, Venancio TM. Uncovering major genomic features of essential genes in Bacteria and a methanogenic Archaea. FEBS J 2015;282:3395-411.
123. Greub G, Raoult D. Parachlamydiaceae: potential emerging pathogens. Emerg Infect Dis 2002;8:625-30.
124. Gribaldo S, Brochier C. Phylogeny of prokaryotes: does it exist and why should we care? Res Microbiol 2009;160:513-21.
125. Gribaldo S, Brochier-Armanet C. Time for order in microbial systematics 1. Trends Microbiol 2012;20:209-10.
126. Griffiths E, Gupta RS. The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that Fibrobacter diverged at a similar time to Chlamydia and the Cytophaga-Flavobacterium-Bacteroides division. Microbiology 2001;147:2611-22.
127. Griffiths E, Gupta RS. Protein signatures distinctive of chlamydial species: horizontal transfer of cell wall biosynthesis genes glmU from Archaebacteria to Chlamydiae, and murA between Chlamydiae and Streptomyces. Microbiology 2002;148:2541-9.
128. Griffiths E, Gupta RS. Distinctive protein signatures provide molecular markers and evidence for the monophyletic nature of the Deinococcus-Thermus phylum. J Bacteriol 2004a;186:3097-107.
129. Griffiths E, Gupta RS. Signature sequences in diverse proteins provide evidence for the late divergence of the order Aquificales. Int Microbiol 2004b;7:41-52.
130. Griffiths E, Gupta RS. Lateral transfers of serine hydroxymethyl transferase (glyA) and UDP-N-acetylglucosamine enolpyruvyl transferase (murA) genes from free-living Actinobacteria to the parasitic chlamydiae. J Mol Evol 2006a;63:283-96.
131. Griffiths E, Gupta RS. Molecular signatures in protein sequences that are characteristics of the Phylum Aquificales. Int J Syst Evol Micr 2006b;56:99-107.
132. Griffiths E, Gupta RS. Identification of signature proteins that are distinctive of the Deinococcus-Thermus phylum. IntMicrobiol 2007a;10:201-8.
133. Griffiths E, Gupta RS. Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae. Microbiology 2007b;153:2648-54.
134. Griffiths E, Petrich A, Gupta RS. Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification. Microbiology 2005;151:2647-57.
135. Griffiths E, Ventresca MS, Gupta RS. BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species. BMC Genomics 2006;7:14.
136. Gupta RS. Evolution of the chaperonin families (Hsp60, Hsp10 and Tcp-1) of proteins and the origin of eukaryotic cells. Mol Microbiol 1995;15:1-11.
137. Gupta RS. Protein phylogenies and signature sequences: evolutionary relationships within prokaryotes and between prokaryotes and eukaryotes. Anton Leeuw 1997;72: 49-61.
138. Gupta RS. Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol R 1998a;62:1435-91.
139. Gupta RS. What are archaebacteria: life's third domain or monoderm prokaryotes related to Gram-positive bacteria? a new proposal for the classification of prokaryotic organisms. Mol Microbiol 1998b;29:695-708.
140. Gupta RS. The natural evolutionary relationships among Prokaryotes. Crit Rev Microbiol 2000a;26:111-31.
141. Gupta RS. The phylogeny of Proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev 2000b;24:367-402.
142. Gupta RS. The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins. Int Microbiol 2001;4:187-202.
143. Gupta RS. Evolutionary relationships among photosynthetic bacteria. Photosynth Res 2003;76:173-83.
144. Gupta RS. The phylogeny and signature sequences characteristics of Fibrobacters, Chlorobi and Bacteroidetes. Crit Rev Microbiol 2004;30:123-43.
145. Gupta RS. Molecular sequences and the early history of life. In: Sapp J (ed.). Microbial Phylogeny and Evolution: Concepts and Controversies. New York: Oxford University Press, 2005, 160-83.
146. Gupta RS. Molecular signatures (unique proteins and conserved Indels) that are specific for the epsilon proteobacteria (Campylobacterales). BMC Genomics 2006;7:167.
147. Gupta RS. Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades. Int J Syst Evol Micr 2009;59:2510-26.
148. Gupta RS. Applications of conserved indels for understanding microbial phylogeny. In: Oren A, Papke RT (eds). Molecular Phylogeny of Microorganisms. Norfolk, UK: Caister Academic Press, 2010a, 135-50.
149. Gupta RS. Microbial phylogeny and evolution based on protein sequences (The change from targeted genes to proteins). In: Shah HN, Gharbia SE (eds). Mass Spectrometry for Microbial Proteomics. Chichester, UK: Wiley, 2010b, 35-53.
150. Gupta RS. Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups. Photosynth Res 2010c;104:357-72.
151. Gupta RS. Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes. Anton Leeuw 2011;100:171-82.
152. Gupta RS. Moelcular markers for photosynthetic bacteria and insights into the origin and spread of photosynthesis. Adv Bot Res 2013;66:37-66.
153. Gupta RS. Identification of conserved indels that are useful for classification and evolutionary studies. In: Goodfellow M, Sutcliffe IC, Chun J (eds). Bacterial Taxonomy, Methods in Microbiology Volume 41. London: Elsevier, 2014a, 153-82.
154. Gupta RS. Phylum aquificae. The Prokaryotes 2014b;4:417-45.
155. Gupta RS. Molecular signatures that are distinctive characteristics of the vertebrates and chordates and supporting a grouping of vertebrates with the tunicates. Mol Phylogenet Evol 2015;94:383-91.
156. Gupta RS. Editorial: applications of genome sequences for discovering characteristics that are unique to different groups of organisms and provide insights into evolutionary relationships. Front Genet 2016a;7:27.
157. Gupta RS. Molecular signatures that are distinctive characteristics of the vertebrates and chordates and supporting a grouping of vertebrates with the tunicates. Mol Phylogenet Evol 2016b;94:383-91.
158. Gupta RS, Aitken K, Falah M et al. Cloning of Giardia lamblia heat shock protein HSP70 homologs: implications regarding origin of eukaryotic cells and of endoplasmic reticulum. P Natl Acad Sci USA 1994;91:2895-9.
159. Gupta RS, Bhandari V. Phylogeny and molecular signatures for the phylum thermotogae and its subgroups. Anton Leeuw 2011;100:1-34.
160. Gupta RS, Bhandari V, Naushad HS. Molecular signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of bacteria provide insights into their evolutionary relationships. Front Microbiol 2012; 3:327.
161. Gupta RS, Chander P, George S. Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexia class. nov. [corrected] into the suborder Chloroflexineae subord. nov., consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. nov., the suborder Roseiflexineae subord. nov., containing the family Roseiflexaceae fam. nov. Anton Leeuw 2013a;103:99-119.
162. Gupta RS, Chen WJ, Adeolu M et al. Molecular signatures for the class Coriobacteriia and its different clades; Proposal for division of the class Coriobacteriia into the emended order Coriobacteriales, containing the emended family Coriobacteriaceae and Atopobiaceae fam. nov., Eggerthellales ord. nov., containing the family Eggerthellaceae fam. nov. Int J Syst Evol Micr 2013b;63:3379-97.
163. Gupta RS, Gao B. Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I). Int J Syst Evol Micr 2009;59:285-94.
164. Gupta RS, Gao B. Recent advances in understanding microbial systematics. In: Xu J (ed.). Microbial Population Genetics. Norfolk, UK: Caister Academic Press, 2010, 1-14.
165. Gupta RS, Golding GB. Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes. J Mol Evol 1993;37:573-82.
166. Gupta RS, Golding GB. The origin of the eukaryotic cell. Trends Biochem Sci 1996;21:166-71.
167. Gupta RS, Griffiths E. Critical issues in bacterial phylogeny. Theor Popul Biol 2002;61:423-34.
168. Gupta RS, Griffiths E. Chlamydiae-specific proteins and indels: novel tools for studies. Trends Microbiol 2006;14:527-35.
169. Gupta RS, Lali R. Molecular signatures for the phylum Aquificae and its different clades: proposal for division of the phylum Aquificae into the emended order Aquificales, containing the families Aquificaceae and Hydrogenothermaceae, and a new order Desulfurobacteriales ord. nov., containing the family Desulfurobacteriaceae. Anton Leeuw 2013;104:349-68.
170. Gupta RS, Lorenzini E. Phylogeny andmolecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species. BMC Evol Biol 2007;7:71.
171. Gupta RS, Mahmood S, Adeolu M. A phylogenomic and molecular signature based approach for characterization of the phylum Spirochaetes and its major clades: proposal for a taxonomic revision of the phylum. Front Microbiol 2013c;4:217.
172. Gupta RS, Mathews DW. Signature proteins for the major clades of Cyanobacteria. BMC Evol Biol 2010;10:24.
173. Gupta RS, Mok A. Phylogenomics and signature proteins for the alpha proteobacteria and its main groups. BMC Microbiol 2007;7:106.
174. Gupta RS, Naushad S, Baker S. Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov., Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov., Natrialbaceae fam. nov. Int J Syst Evol Micr 2015a;65:1050-69.
175. Gupta RS, Naushad S, Chokshi C et al. A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., emended description of the class Chlamydiia. Anton Leeuw 2015b;108:765-81.
176. Gupta RS, Naushad S, Fabros R et al. A phylogenomic reappraisal of family-level divisions within the class Halobacteria: proposal to divide the order Halobacteriales into the families Halobacteriaceae, Haloarculaceae fam. nov., Halococcaceae fam. nov., the order Haloferacales into the families, Haloferacaceae and Halorubraceae fam nov. Anton Leeuw 2016;109:565-87.
177. Gupta RS, PereiraM, Chandrasekera C et al. Molecular signatures in protein sequences that are characteristic of Cyanobacteria and plastid homologues. Int J Syst Evol Micr 2003;53:1833-42. Gupta RS, Sethi M. Phylogeny and molecular signatures for the phylum Fusobacteria and its distinct subclades. Anaerobe 2014;28:182-98.
178. Gupta RS, Sethi M. Phylogeny and molecular signatures for the phylum Fusobacteria and its distinct subclades. Anaerobe 2014;28:182-98
179. Gupta RS, Shami A. Molecular signatures for the Crenarchaeota and the Thaumarchaeota. Anton Leeuw 2011;99: 133-57.
180. Gupta RS, Singh B. Cloning of the HSP70 gene from Halobacterium marismortui: relatedness of archaebacterial HSP70 to its eubacterial homologs and a model for the evolution of the HSP70 gene. J Bacteriol 1992;174:4594-605.
181. Gupta RS, Sneath PHA. Application of the character compatibility approach to generalized molecular sequence data: branching order of the proteobacterial subdivisions. J Mol Evol 2007;64:90-100.
182. Haldane JBS. The Causes of Evolution. London: Longmans, Green and Co., 1932.
183. Harms U, Weiss DS, Gartner P et al. The energy conserving N5-methyltetrahydromethanopterin:coenzyme M methyltransferase complex from Methanobacterium thermoautotrophicum is composed of eight different subunits. Eur J Biochem 1995;228:640-8.
184. Hedlund BP. Phylum XXIII. Verrucomicrobia phyl. nov. In: Brenner DJ, Krieg NR, Garrity GM et al. (eds). Bergey's Manual of Systematic Bacteriology Volume 4: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. New York: Springer, 2010, 795-9.
185. Hedlund BP, Gosink JJ, Staley JT. Verrucomicrobia div. nov., a new division of the bacteria containing three new species of Prosthecobacter. Anton Leeuw 1997;72:29-38.
186. HennigW. Phylogenetic Systematics. Urbana: University of Illinois, 1966. Hennig W. 'Cladistic analysis or cladistic classification?': a reply to Ernst Mayr. Syst Zool 1975;24:244-56.
187. Henz SR, Huson DH, Auch AF et al. Whole-genome prokaryotic phylogeny. Bioinformatics 2005;21:2329-35.
188. Hibbett DS, Binder M, Bischoff JF et al. A higher-level phylogenetic classification of the Fungi. Mycol Res 2007;111:509-47.
189. Hobbolt A, Christensen OF, Mailund T et al. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet 2007;3:e7.
190. Horn M. Chlamydiae as symbionts in Eukaryotes. Annu Rev Microbiol 2008;62:113-31.
191. Horn M, Collingro A, Schmitz-Esser S et al. Illuminating the evolutionary history of chlamydiae. Science 2004;304:728-30.
192. Howard-Azzeh M, Shamseer L, Schellhorn HE et al. Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives. Photosynth Res 2014;122:171-85.
193. Huang J, Gogarten JP. Ancient gene transfer as a tool in phylogenetic reconstruction. Methods Mol Biol 2009;532:127-39.
194. Huber R, Hannig M. Thermotogales. The Prokaryotes 2006;7:899-922.
195. Hug LA, Baker BJ, Anantharaman K et al. A new view of the tree of life. Nat Microbiol 2016;1:1-6.
196. Hugenholtz P. Exploring prokaryotic diversity in the genomic era. Genome Biol 2002;3: REVIEWS0003.
197. Huxley JS. The Modern Synthesis. London: Allen and Unwin, 1942.
198. Huynen M, Snel B, Bork P et al. Lateral gene transfer, genome surveys, and the phylogeny of prokaryotes. Science 1999;286:1443.
199. Janecka JE, Miller W, Pringle TH et al. Molecular and genomic data identify the closest living relative of primates. Science 2007;318:792-4.
200. Jeffroy O, Brinkmann H, Delsuc F et al. Phylogenomics: the beginning of incongruence? Trends Genet 2006;22:225-31.
201. JGI Genome Portal. 2016, http://genome.jgi.doe.gov/ (2 June 2016, date last accessed).
202. Jolley KA, Bliss CM, Bennett JS et al. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 2012;158:1005-15.
203. Jones AL. The future of taxonomy. Adv Appl Microbiol 2012;80:23-35.
204. Kainth P, Gupta RS. Signature proteins that are distinctive of alpha proteobacteria. BMC Genomics 2005;6:94.
205. Kampfer P. Systematics of prokaryotes: the state of the art. Anton Leeuw 2012;101:3-11.
206. Kampfer P. Continuing importance of the phenotype in the genomic era. Methods Microbiol 2015;41:307-20.
207. Kasting JF. Earth's early atmosphere. Science 1993;259:920-6. Katz LA. Lateral gene transfers and the evolution of eukaryotes: theories and data. Int J Syst Evol Micr 2002;52: 1893-900.
208. Katz LA. Lateral gene transfers and the evolution of eukaryotes: theories and data. Int J Syst Evol Micr 2002;52: 1893-900
209. Keeling PJ, Palmer JD. Horizontal gene transfer in eukaryotic evolution 7. Nat Rev Genet 2008;9:605-18.
210. Kim M, Oh HS, Park SC et al. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Micr 2014;64:346-51.
211. Klenk HP, Goker M. En route to a genome-based classification of Archaea and Bacteria? 1. Syst Appl Microbiol 2010;33:175-82.
212. Kluyver AJ, van Niel CB. Prospects for a natural system of classification of bacteria. Zentbl Bakteriolog P 1936;94:369-403.
213. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. P Natl Acad Sci USA 2005;102:2567-72.
214. Koonin EV. Darwinian evolution in the light of genomics. Nucleic Acids Res 2009;37:1011-34.
215. Koonin EV. The turbulent network dynamics of microbial evolution and the statistical tree of life 1. JMol Evol 2015;80:244-50.
216. Koonin EV, Makarova KS, Aravind L. Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 2001;55:709-42.
217. Koonin EV, Puigbo P, Wolf YI. Comparison of phylogenetic trees and search for a central trend in the 'forest of life'. J Comput Biol 2011;18:917-24.
218. Koonin EV, Wolf YI. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world 7. Nucleic Acids Res 2008;36:6688-719.
219. Koonin EV, Wolf YI. Is evolution Darwinian or/and Lamarckian? Biol Direct 2009;4:42.
220. Koonin EV, Wolf YI. Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Front Cell Infect Microbiol 2012;2:119.
221. Koschwanez M, Meli M, Vogtlin A et al. Chlamydiaceae family, Parachlamydia spp., Waddlia spp. in porcine abortion. J Vet Diagn Invest 2012;24:833-9.
222. Koski LB, Golding GB. The closest BLAST hit is often not the nearest neighbor. J Mol Evol 2001;52:540-2.
223. Kumar S, Filipski AJ, Battistuzzi FU et al. Statistics and truth in phylogenomics 6. Mol Biol Evol 2012;29:457-72.
224. Kunisawa T. Gene arrangements and branching orders of Grampositive bacteria. J Theor Biol 2003;222:495-503.
225. Kunisawa T. Gene arrangements characteristic of the phylum Actinobacteria. Anton Leeuw 2007;92:359-65.
226. Kuo CH, Ochman H. The fate of new bacterial genes. FEMS Microbiol Rev 2009;33:38-43.
227. Kurland CG, Canback B, Berg OG. Horizontal gene transfer: a critical view. P Natl Acad Sci USA 2003;100:9658-62.
228. Lagkouvardos I, Jehl MA, Rattei T et al. Signature protein of the PVC superphylum. Appl Environ Microb 2014;80:440-5.
229. Lake JA, Herbold CW, RiveraMC et al. Rooting the tree of life using nonubiquitous genes. Mol Biol Evol 2007;24:130-6.
230. Lamoth F, Greub G. Fastidious intracellular bacteria as causal agents of community-acquired pneumonia. Expert Rev Anti-Infe 2010;8:775-90.
231. Lang JM, Darling AE, Eisen JA. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices 3. PLoS One 2013;8:e62510.
232. Lapage SP, Sneath PHA, Lessel EF et al. International Code of Nomenclature of Bacteria: Bacteriological Code, 1990 Revision. Washington, DC: ASM Press, 1992.
233. Lapierre P, Gogarten JP. Estimating the size of the bacterial pangenome. Trends Genet 2009;25:107-10.
234. Leigh JW, Lapointe FJ, Lopez P et al. Evaluating phylogenetic congruence in the post-genomic era 1. Genome Biol Evol 2011;3:571-87.
235. Lerat E, Daubin V, Ochman H et al. Evolutionary origins of genomic repertoires in bacteria. PLoS Biol 2005;3:e130.
236. L'Haridon S, Reysenbach AL, Tindall BJ et al. Desulfurobacterium atlanticum sp. nov., Desulfurobacterium pacificum sp. nov., Thermovibrio guaymasensis sp. nov., three thermophilic members of the Desulfurobacteriaceae fam. nov., a deep branching lineage within the Bacteria. Int J Syst Evol Micr 2006;56:2843-52.
237. Lima WC, Menck CF. Replacement of the arginine biosynthesis operon in Xanthomonadales by lateral gene transfer. J Mol Evol 2008;66:266-75.
238. Lima WC, Paquola AC, Varani AM et al. Laterally transferred genomic islands in Xanthomonadales related to pathogenicity and primary metabolism. FEMS Microbiol Lett 2008;281: 87-97.
239. Lorenzini E, Singer A, Singh B et al. Structure and protein-protein interaction studies on Chlamydia trachomatis protein CT670 (YscO Homolog). J Bacteriol 2010;192:2746-56.
240. LPSN Web Resource. List of prokaryotic names with standing in nomenclature. 2014, www.bacterio.net ( 23 May 2016, date last accessed).
241. LudwigW. Molecular phylogeny of microorganisms: is rRNA still useful marker? In: Oren A, Papke RT (eds). Molecular Phylogeny of Microorganisms. Norfolk, UK: Caister Academic Press, 2010, 65-83.
242. Ludwig W, Klenk H-P. Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systamatics. In: Brenner DJ, Krieg NR, Staley JT et al. (eds). Bergey's Manual of Systematic Bacteriology. Berlin: Springer, 2005, 49-65.
243. McCormack GP, Clewley JP. The application of molecular phylogenetics to the analysis of viral genome diversity and evolution 3. Rev Med Virol 2002;12:221-38.
244. McGenity TJ, Oren A. Hypersaline environments. In: Bell EM (ed.). Life at Extremes. Environments, Organisms, and Strategies for Survival. Wallingford, UK: CABI Wallingford, United Kingdom. 2012, 402-37.
245. Maidak BL, Cole JR, Lilburn TG et al. The RDP-II (Ribosomal Database Project). Nucleic Acids Res 2001;29:173-4.
246. Margulis L. Symbiosis in Cell Evolution. New York: W.H. Freeman and Company, 1993.
247. Marri PR, Hao W, Golding GB. Gene gain and gene loss in streptococcus: is it driven by habitat? Mol Biol Evol 2006;23:2379-91.
248. Martin WF. Early evolution without a tree of life. Biol Direct 2011;6:36.
249. Mayr E. Systematics and the Origin of Species. New York: Columbia University Press, 1944.
250. Mazel D, Davies J. Antibiotic resistance in microbes. Cell Mol Life Sci 1999;56:742-54.
251. Meacham CA, Estabrook GF. Comaptibility methods in Systematics. Ann Rev Ecol Syst 1985;16:431-46.
252. Merhej V, Raoult D. Rhizome of life, catastrophes, sequence exchanges, gene creations, and giant viruses: how microbial genomics challenges Darwin. Front Cell Infect Microbiol 2012;2:113.
253. Migula W. System der Baketerien. Handbuch der Morphologie, Entwicklungsgeschichte und Systematik der Bakterien. Jena: G. Fischer, 1897.
254. Mindell DP. The tree of life: metaphor, model, and heuristic device. Syst Biol 2013;62:479-89.
255. Minegishi H, Kamekura M, Kitajima-Ihara T et al. Gene orders in the upstream of 16S rRNA genes divide genera of the family Halobacteriaceae into two groups. Int J Syst Evol Micr 2012;62:188-95.
256. Morden CW, Delwiche CF, Kuhsel M et al. Gene phylogenies and the endosymbiotic origin of plastids. Biosystems 1992;28:75-90.
257. Morgan CC, Foster PG, Webb AE et al. Heterogeneous models place the root of the placental mammal phylogeny. Mol Biol Evol 2013;30:2145-56.
258. Morrison DA. Is the tree of life the best metaphor, model, or heuristic for phylogenetics? Syst Biol 2014;63:628-38.
259. Murray RGE. Kingdom Procaryote. In: Sneath PHA, Mair NS, Sharpe ME et al. (eds). Bergey's Manual of Systematic Bacteriology. Baltimore: Williams and Willkins, 1986a, 34-6.
260. Murray RGE. The higher taxa, or, a place for everything? In: Sneath PHA, Mair NS, Sharpe ME et al. (eds). Bergey's Manual of Systematic Bacteriology. Baltimore: Williams and Wilkins, 1986b, 31-4.
261. Mushegian AR, Koonin EV. A minimal gene set for cellular life derived by comparison of complete bacterial genomes [see comments]. P Natl Acad Sci USA 1996;93:10268-73.
262. Narra HP, Cordes MH, Ochman H. Structural features and the persistence of acquired proteins. Proteomics 2008;8:4772-81.
263. Naushad HS, Gupta RS. Molecular signatures (conserved indels) in protein sequences that are specific for the order Pasteurellales and distinguish two of its main clades. Anton Leeuw 2012;101:105-24.
264. Naushad HS, Gupta RS. Phylogenomics and molecular signatures for species from the plant pathogen-containing order xanthomonadales. PLoS One 2013;8:e55216.
265. Naushad HS, Lee B, Gupta RS. Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria. Int J Syst Evol Micr 2014;64:366-83.
266. Naushad S, Adeolu M, Goel N et al. Phylogenomic and molecular demarcation of the core members of the polyphyletic pasteurellaceae genera actinobacillus, haemophilus, and pasteurella. Int J Genomics 2015;2015:198560.
267. NCBI. NCBI Completed Microbial Genomes. 2015, http://www. ncbi.nlm.nih.gov/genome/browse/ (2 June 2016, date last accessed).
268. Nelson KE, Clayton R, Gill S et al. Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature 1999;399:323-9.
269. Nelson-Sathi S, Sousa FL, Roettger M et al. Origins of major archaeal clades correspond to gene acquisitions from bacteria 1. Nature 2015;517:77-80.
270. Nesbo CL, Dlutek M, Zhaxybayeva O et al. Evidence for existence of 'mesotogas,' members of the order Thermotogales adapted to low-temperature environments. Appl Environ Microb 2006;72:5061-8.
271. Norris SJ, Cox DL, Weinstock GM. Biology of Treponema pallidum: correlation of functional activities with genome sequence data. J Mol Microb Biotech 2001;3:37-62.
272. Norris SJ, Paster BJ, Moter A et al. The genus treponema. In: Dworkin M, Falkow S, Schleifer KH et al. (eds). The Prokaryotes. New York: Springer, 2006, 211-34.
273. Nosenko T, Schreiber F, Adamska M et al. Deep metazoan phylogeny: when different genes tell different stories. Mol Phylogenet Evol 2013;67:223-33.
274. Ochman H. Bacterial evolution: jittery genomes. Curr Biol 1999;9:R485-6.
275. Ochman H, Moran NA. Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 2001;292: 1096-9.
276. Olendzenski L, Gogarten JP. Gene transfer in early evolution. In: Seckbach J (ed.). Enigmatic Microorganisms and Life. New York: Kluwer Academic Publishers, 1999, 17-27.
277. Olsen GJ, Woese CR. Ribosomal RNA: a key to phylogeny. FASEB J 1993;7:113-23.
278. Olsen GJ, Woese CR, Overbeek R. The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 1994;176:1-6.
279. Olsen I, Paster BJ, Dewhirst FE. Taxonomy of Spirochetes. Anaerobe 2000;6:39-57.
280. O'Malley MA. What did Darwin say about microbes, and how did microbiology respond? Trends Microbiol 2009;17: 341-7.
281. O'Malley MA. When integration fails: prokaryote phylogeny and the tree of life. Stud Hist Philos Biol Biomed Sci 2013;44: 551-62.
282. O'Malley MA, Koonin EV. How stands the Tree of Life a century and a half after The Origin? 2. Biol Direct 2011;6:32.
283. Oren A. Prokaryote diversity and taxonomy: current status and future challenges. Philos T Roy Soc B 2004;359:623-38.
284. Oren A. The family Halobacteriaceae. In: Rosenberg E, Delong EF, Lory S et al. (eds). The Prokaryotes -Other Major Lineages of Bacteria and the Archaea. Berlin Heidelberg: Springer-Verlag Berlin Heidelberg, 2014, 41-121.
285. Oren A. Concepts about phylogeny of microorganisms-an historical overview. In: Oren A, Papke RT (eds). Molecular Phylogeny of Microorganisms. Norfolk: Caister Academic Press, 2010a, 1-21.
286. Oren A. Microbial systematics. In: Wang LK, Ivanov V, Tay J-H, Hung YT (eds). Handbook of Environmental Engineering, Volume 10: Environmental Biotechnology. New York: Springer Science + Business Media, 2010b, 81-120.
287. Oren A. Taxonomy of the family Halobacteriaceae: a paradigm for changing concepts in prokaryote systematics. Int J Syst Evol Micr 2012;62:263-71.
288. Oren A, Garrity GM. Then and now: a systematic review of the systematics of prokaryotes in the last 80 years 13. Anton Leeuw 2014;106:43-56.
289. Orla-Jensen S. Die Hauptlinien de natürlichen Baketeriensystems nebst einer Uebersicht der Gärungsphenomene. Zentr Bakt Parasitenk II 1909;22:305-46.
290. Pal C, Hurst LD. Evidence against the selfish operon theory. Trends Genet 2004;20:232-4.
291. Papke RT, White E, Reddy P et al. Amultilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales. Int J Syst Evol Micr 2011;61:2984-95.
292. Paster BJ. 'Phylum XV. Spirochaetes Garrity and Holt (2001)'. In: Brenner DJ, Krieg NR, Garrity GM et al. (eds). Bergey's Manual of Systematic Bacteriology Volume 4: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. New York: Springer, 2010.
293. Paster BJ, Dewhirst FE. Phylogenetic foundation of spirochetes. J Mol Microb Biotech 2000;2:341-4.
294. Patel BKC, Morgan HW, Daniel RM. Fervidobacterium nodosum gen. nov., spec. nov., a novel chemoorganotrophic, caldoactive, anaerobic bacterium. Arch Microbiol 1985;141:63-69.
295. Penny D. Darwin's theory of descent with modification, versus the biblical tree of life. PLoS Biol 2011;9:e1001096.
296. Philippe H, Delsuc F, Brinkmann H et al. Phylogenomics. Annu Rev Ecol Syst 2005;36:541-62.
297. Philippe H, Douady CJ. Horizontal gene transfer and phylogenetics. Curr Opin Microbiol 2003;6:498-505.
298. Pilhofer M, Rappl K, Eckl C et al. Characterization and evolution of cell division and cell wall synthesis genes in the bacterial phyla Verrucomicrobia, Lentisphaerae, Chlamydiae, and Planctomycetes and phylogenetic comparison with rRNA genes. J Bacteriol 2008;190:3192-202.
299. Pillonel T, Bertelli C, Salamin N et al. Taxogenomics of the order Chlamydiales. Int J Syst Evol Micr 2015;65:1381-93.
300. Popa O, Hazkani-Covo E, Landan G et al. Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res 2011;21: 599-609.
301. Puigbo P, Wolf YI, Koonin EV. Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol 2009;8:59.
302. Puigbo P, Wolf YI, Koonin EV. The tree and net components of prokaryote evolution. Genome Biol Evol 2010;2:745-56.
303. Puigbo P, Wolf YI, Koonin EV. Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life 1. Methods Mol Biol 2012;856:53-79.
304. Puigbo P, Wolf YI, Koonin EV. Seeing the Tree of Life behind the phylogenetic forest. BMC Biol 2013;11:46.
305. Qin QL, Xie BB, Zhang XY et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014;196:2210-5.
306. Ragan MA. Detection of lateral gene transfer among microbial genomes. Curr Opin Genet Dev 2001a;11:620-6.
307. Ragan MA. On surrogate methods for detecting lateral gene transfer. FEMS Microbiol Lett 2001b;201:187-91.
308. Rahman NA, Parks DH, Vanwonterghem I et al. A phylogenomic Analysis of the bacterial Phylum Fibrobacteres. Front Microbiol 2016;6:1469.
309. Ramasamy D, Mishra AK, Lagier JC et al. A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species 1. Int J Syst Evol Micr 2014;64:384-91.
310. Raoult D, Koonin EV. Microbial genomics challenge Darwin. Front Cell Infect Microbiol 2012;2:127.
311. Rasko DA, Rosovitz MJ, Myers GS et al. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 2008;190:6881-93.
312. Ravinesan DA, Gupta RS. Molecular signatures for members of the genus Dehalococcoides and the class Dehalococcoidia. Int J Syst Evol Micr 2014;64:2176-81.
313. Raymond J, Zhaxybayeva O, Gogarten JP et al. Wholegenome analysis of photosynthetic prokaryotes. Science 2002;298:1616-20.
314. Reysenbach AL, Liu Y, Lindgren AR et al. Mesoaciditoga lauensis gen. nov., sp. nov., a moderate thermoacidophilic Thermotogales from a deep-sea hydrothermal vent. Int J Syst Evol Micr 2013;63:4724-9.
315. Richter M, Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. P Natl Acad Sci USA 2009;106:19126-31.
316. Rivera MC, Lake JA. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 1992;257:74-76.
317. Roberts RJ. Identifying protein function-a call for community action. PLoS Biol 2004;2:E42.
318. Rocha EP, Danchin A. Base composition bias might result from competition for metabolic resources. Trends Genet 2002;18:291-4.
319. Rokas A, Holland PW. Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 2000;15:454-9.
320. Rokas A, Williams BL, King N et al. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003;425:798-804.
321. Romiguier J, Ranwez V, Delsuc F et al. Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals. Mol Biol Evol 2013;30:2134-44.
322. Rossello-Mora R, Amann R. The species concept for prokaryotes. FEMS Microbiol Rev 2001;25:39-67.
323. Rossello-Mora R, Amann R. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 2015;38: 209-16.
324. Sachse K, Bavoil PM, Kaltenboeck B et al. Emendation of the family Chlamydiaceae: proposal of a single genus, Chlamydia, to include all currently recognized species. Syst Appl Microbiol 2015;38:99-103.
325. Sangwan P, Kovac S, Davis KE et al. Detection and cultivation of soil verrucomicrobia. Appl Environ Microb 2005;71:8402-10.
326. Santarella-Mellwig R, Franke J, Jaedicke A et al. The compartmentalized bacteria of the planctomycetesverrucomicrobia-chlamydiae superphylum have membrane coat-like proteins. PLoS Biol 2010;8:e1000281.
327. Santos SR, Ochman H. Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol 2004;6:754-9.
328. Sapp J. The bacterium's place in nature. In: Sapp J (ed.). Microbial Phylogeny and Evolution: Concepts and Controversies. New York: Oxford University Press, 2006, 3-52.
329. Sawana A, Adeolu M, Gupta RS. Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species. Front Genet 2014;5:429.
330. Schachter J, Stamm WE. Chlamydia. In: Murray PR, Baron EJ, Pfaller MA et al. (eds). Manual of Clinical Microbiology. Washinton, DC: ASM Press, 1999, 795-806.
331. Schachter J, Stephens RS, Timms P et al. Radical changes to chlamydial taxonomy are not necessary just yet. Int J Syst Evol Micr 2001;51:249251-3.
332. Schlesner H, Jenkins C, Staley JT. The phylum verrucomicrobia: a phylogenetically heterogeneous bacterial group. In: Dworkin M, Falkow S, Schleifer KH et al. (eds). The Prokaryotes. New York: Springer, 2006, 881-96.
333. Schopf JW. The evolution of the earliest cells. Sci Am 1978;239:110-20.
334. Schopf JW, Packer BM. Early Archaen (3.3 to 3.5 Ga-old) fossil microorganisms from theWarrawoona Group,Western Australia. Science 1987;237:70-73.
335. Segata N, Bornigen D, Morgan XC et al. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 2013;4:2304.
336. Sentausa E, Fournier PE. Advantages and limitations of genomics in prokaryotic taxonomy. Clin Microbiol Infect 2013;19:790-5. Siew N, Fischer D. Analysis of singleton ORFans in fully sequenced microbial genomes. Proteins 2003;53:241-51.
337. Siew N, Fischer D. Analysis of singleton ORFans in fully sequenced microbial genomes. Proteins 2003;53:241-51
338. Singh B, Gupta RS. Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth. Mol Genet Genomics 2009;281:361-73.
339. Sneath PHA. Numerical taxonomy. In: Boone DR, Castenholz RW (eds). Bergey's Manual of Systematic Bacteriology. Berlin: Springer, 2001, 39-42.
340. Sneath PHA, Sokal RR. Numerical Taxonomy -The Principles and Practice of Numerical Classification. San Francisco: W.H. Freeman, 1973.
341. Snel B, Bork P, Huynen MA. Genome phylogeny based on gene content. Nat Genet 1999;21:108-10.
342. Snel B, Huynen MA, Dutilh BE. Genome trees and the nature of genome evolution. Annu Rev Microbiol 2005;59:191-209.
343. Snir S. Ordered orthology as a tool in prokaryotic evolutionary inference. Mobile Genetic Elements 2016;6:e1120576.
344. Soucy SM, Fullmer MS, Papke RT et al. Inteins as indicators of gene flow in the halobacteria. Front Microbiol 2014;5:299.
345. Soucy SM, Huang J, Gogarten JP. Horizontal gene transfer: building the web of life 1. Nat Rev Genet 2015;16:472-82.
346. Springer MS, Stanhope MJ,Madsen O et al. Molecules consolidate the placental mammal tree. Trends Ecol Evol 2004;19:430-8.
347. Stackebrandt E. Unifying phylogeny and phenotypic diversity. In: Balows A, Trüper HG, Dworkin M et al. (eds). The Prokaryotes. New York: Springer, 1992, 19-47.
348. Stackebrandt E. Defining taxonomic ranks. In: Dworkin M, Falkow S, Rosenberg E et al. (eds). The Prokaryotes. New York: Springer, 2006, 29-57.
349. Stackebrandt E, Eber J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006;33:152-5.
350. Stackebrandt E, Frederiksen W, Garrity GM et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Micr 2002;52:1043-7.
351. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNADNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 1994;44:846-9.
352. Staley JT. The bacterial species dilemma and the genomicphylogenetic species concept. Philos T Roy Soc B 2006;361:1899-909.
353. Staley JT, Krieg NR. Classification of prokaryotic organisms: an overview. In: Krieg NR, Holt JG (eds). Bergey's Manual of Systematic Bacteriology. Baltimore:Williams andWilkins, 1984, xix-xi.
354. Stanier RY. The main outlines of bacterial classification. J Bacteriol 1941;42:437-66.
355. Stanier RY, Douroroff M, Adelberg EA. The MicrobialWorld. Englewood Cliffs, NJ: Prentice-Hall Inc., 1963.
356. Stanier RY, van Niel CB. The concept of a bacterium. Archiv Mikrobiol 1962;42:17-35.
357. Strous M, Pelletier E, Mangenot S et al. Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 2006;440:790-4.
358. Subramanian G, Koonin EV, Aravind L. Comparative genome analysis of the pathogenic spirochetes Borrelia burgdorferi and Treponema pallidum. Infect Immun 2000;68:1633-48.
359. Sutcliffe IC. Challenging the anthropocentric emphasis on phenotypic testing in prokaryotic species descriptions: rip it up and start again 1. Front Genet 2015;6:218.
360. Sutcliffe IC, Trujillo ME, Goodfellow M. A call to arms for systematists: revitalising the purpose and practises underpinning the description of novel microbial taxa. Anton Leeuw 2012;101:13-20.
361. Sutcliffe IC, Trujillo ME, Whitman WB et al. A call to action for the International Committee on Systematics of Prokaryotes. Trends Microbiol 2013;21:51-52.
362. Swithers KS, Gogarten JP, Fournier GP. Trees in the web of life. J Biol 2009;8:54.
363. Syvanen M. Evolutionary implications of horizontal gene transfer 1. Annu Rev Genet 2012;46:341-58.
364. Taylor-Brown A, Vaughan L, Greub G et al. Twenty years of research into Chlamydia-like organisms: a revolution in our understanding of the biology and pathogenicity of members of the phylum Chlamydiae. Pathog Dis 2015;73:1-15.
365. Teeling EC, Hedges SB. Making the impossible possible: rooting the tree of placental mammals. Mol Biol Evol 2013;30:1999-2000.
366. Telenti A, PhilippWJ, Sreevatsan S et al. The emb operon, a gene cluster of Mycobacterium tuberculosis involved in resistance to ethambutol. Nat Med 1997;3:567-70.
367. Tettelin H, Masignani V, Cieslewicz MJ et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial 'pan-genome'. P Natl Acad Sci USA 2005;102:13950-5.
368. Thomarat F, Vivares CP, Gouy M. Phylogenetic analysis of the complete genome sequence of Encephalitozoon cuniculi supports the fungal origin of microsporidia and reveals a high frequency of fast-evolving genes. JMol Evol 2004;59:780-91.
369. Tindall BJ, Rossello-Mora R, Busse HJ et al. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Micr 2010;60:249-66.
370. Touchon M, Hoede C, Tenaillon O et al. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 2009;5:e1000344.
371. Treangen TJ, Rocha EP. Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet 2011;7:e1001284.
372. Valas RE, Bourne PE. Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life. Biol Direct 2009;4:30.
373. Valot B, Guyeux C, Rolland JY et al. What it takes to be a pseudomonas aeruginosa? The core genome of the opportunistic pathogen updated. PLoS One 2015;10:e0126468.
374. van Niel CB. The classification and natural relationships of bacteria. Cold Spring Harb Symp 1946;11:285-301.
375. van Rheede T, Bastiaans T, Boone DN et al. The platypus is in its place: nuclear genes and indels confirm the sister group relation of monotremes and Therians. Mol Biol Evol 2006;23:587-97.
376. Varghese NJ, Mukherjee S, Ivanova N et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res 2015;43:6761-71.
377. Ventura M, Turroni F, Zomer A et al. The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity. PLoS Genet 2009;5:e1000785.
378. Vernikos G, Medini D, Riley DR et al. Ten years of pan-genome analyses. Curr Opin Microbiol 2015;23:148-54.
379. Wagner M, Horn M. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr Opin Biotechnol 2006;17:241-9.
380. Wang G, Schwartz I. Genus II. Borrelia Swellengrebel 1907, 582AL. In: Brenner DJ, Krieg NR, Garrity GM et al. (eds). Bergey's Manual of Systematic Bacteriology Volume 4: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. New York: Springer, 2011, 484-98.
381. Wang M, Ahrne S, Jeppsson B et al. Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes. FEMS Microbiol Ecol 2005;54:219-31.
382. Ward N, Staley JT, Fuerst JA et al. The Order Plancktomycetales, including the genera Planctomycetes, Pirellula, Gemmata, Isosphaera and the Candidatus genera Brocadia, Kuenenia and Scalindua. In: Dworkin M, Falkow S, Schleifer KH et al. (eds). The Prokaryotes. New York: Springer, 2006, 757-93.
383. Ward NL. Phylum XXV. Planctomycetes Garrity and Holt 2001. 137 emend. Ward (this volume). In: Brenner DJ, Krieg NR, Garrity GM et al. (eds). Bergey's Manual of Systematic Bacteriology Volume 4: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. New York: Springer, 2010, 897-8.
384. Watson JD. Darwin: The Indelible Stamp. Philadelphia: Running Press, 2005.
385. Wayne LG, Brenner DJ, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987;37:463-4.
386. Whitman WB. Genome sequences as the type material for taxonomic descriptions of prokaryotes 1. Syst Appl Microbiol 2015;38:217-22.
387. Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. P Natl Acad Sci USA 1998;95:6578-83.
388. Williams BA, Kay RF, Kirk EC. New perspectives on anthropoid origins. P Natl Acad Sci USA 2010;107:4797-804.
389. Williams D, Fournier GP, Lapierre P et al. A rooted net of life. Biol Direct 2011;6:45.
390. Woese CR. Bacterial evolution. Microbiol Rev 1987;51:221-71.
391. Woese CR. The use of ribosomal RNA in reconstructing evolutionary relationships among bacteria. In: Selander RK, Clark AG, Whittmay TS (eds). Evolution at Molecular Level. Sunderland, MA: Sinauer Associates Inc., 1991, 1-24.
392. Woese CR. Prokaryote systematics: the evolution of a science. In: Balows A, Trüper HG, Dworkin M et al. (eds). The Prokaryotes. New York: Springer, 1992, 3-18.
393. Woese CR. Whither microbiology? Phylogenetic trees. Curr Biol 1996;6:1060-3.
394. Woese CR. Default taxonomy: Ernst Mayr's view of themicrobial world. P Natl Acad Sci USA 1998;95:11043-6.
395. Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. P Natl Acad Sci USA 1977;74:5088-90.
396. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. P Natl Acad Sci USA 1990;87:4576-9.
397. Woese CR, Stackebrandt E, Macke RJ et al. A phylogenetic definition of the major eubacterial taxa. Syst Appl Microbiol 1985;6:143-51.
398. Wong SY, Paschos A, Gupta RS et al. Insertion/deletion-based approach for the detection of Escherichia coli O157:H7 in freshwater environments. Environ Sci Technol 2014;48:11462-70.
399. Wright ADG. Phylogenetic relationships within the order Halobacteriales inferred from 16S rRNA gene sequences. Int J Syst Evol Micr 2006;56:1223-7.
400. Wu D, Hugenholtz P, Mavromatis K et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009;462:1056-60.
401. Xiong J, Inoue K, Bauer CE. Tracking molecular evolution of photosynthesis by characterizaton of a major photosynthesis gene cluster from Heliobacillus mobilis. P Natl Acad Sci USA 1998;95:14851-6.
402. Yarza P, Richter M, Peplies J et al. The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008;31:241-50.
403. Yarza P, Yilmaz P, Pruesse E et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences 1. Nat Rev Microbiol 2014;12:635-45.
404. Yilmaz P, Parfrey LW, Yarza P et al. The SILVA and 'All-species Living Tree Project (LTP)' taxonomic frameworks. Nucleic Acids Res 2014;42:D643-8.
405. Zeilstra-Ryalls J, Fayet O, Georgopoulos C. The universally conserved GroE (Hsp60) chaperonins. Annu Rev Microbiol 1991;45:301-25.
406. Zeng Y, Feng F, Medova H et al. Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes. P Natl Acad Sci USA 2014;111:7795-800.
407. Zhaxybayeva O, Doolittle WF. Lateral gene transfer. Curr Biol 2011;21:R242-6.
408. Zhaxybayeva O, Swithers KS, Lapierre P et al. On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. P Natl Acad Sci USA 2009;106: 5865-70.
409. Zhi XY, Zhao W, Li WJ et al. Prokaryotic systematics in the genomics era. Anton Leeuw 2012;101:21-34.
410. Zuckerkandl E, Pauling L. Molecules as documents of evolutionary history. J Theor Biol 1965;8:357-66.