Phylogeny vs genome reshuffling: Horizontal gene transfer

Indian Journal of Microbiology

Volumn 48, Issue 2, 2008, Pages 228-242

  Lal, Sadhana ^a   Cheema, Simrita ^a   Kalia, Vipin C ^a  

^a CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

Author keywords

Evolution; Horizontal gene transfer; Phylogeny

Indexed keywords

ANIMALIA;

EID: 48349090342     PISSN: 00468991     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12088-008-0034-1     Document Type: Article

References (178)

1. Syvanen M (1994) Horizontal Gene Transfer: Evidence and possible consequences. Annu Rev Genet 28:237-261
2. Lopez-Garc P & Moreira D (1999) Metabolic symbiosis at the origin of eukaryotes. Trends Biochem Sci 24:88-93
3. Dutta C & Pan A (2002) Horizontal gene transfer and bacterial diversity; J Biosci (Suppl 1) 27:27-33
4. He CY, Striepen B, Pletcher CH, Murray JM & Roos DS (2001) Targeting and processing of nuclear-encoded apicoplast proteins in plastid segregation mutants of Toxoplasma gondii. J Biol Chem 276:28436-28442
5. Martin W & Mueller M (1998) The hydrogen hypothesis for the first eukaryote. Nature 392:37-41
6. Avery OT, MacLeod CM & McCarty M (1944) Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Inductions of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. J Exp Med 149:297-326
7. Smith MW, Feng DF & Doolittle RF (1992) Evolution by acquisition: the case for horizontal gene transfers. Trends Biochem Sci 17:489-493
8. Groisman EA & Ochman H (1996) Pathogenicity islands: bacterial evolution in quantum leaps. Cell 87:791-794
9. Brown JR & Doolittle WF (1997) Archaea and the prokaryote-to- eukaryote transition. Microbiol Mol Biol Rev 61:456-502
10. Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284:2124-2128
11. Woese CR (2000) Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 97:8392-8396
12. Koonin EV, Makarova KS & Aravind L (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 55:709-742
13. Philippe H & Douady CJ (2003) Horizontal gene transfer and phylogenetics. Curr Opin Microbiol 6:498-505
14. Martin W & Embley TM (2004) Early evolution comes full circle. Nature 431:134-137
15. Rivera MC & Lake JA (2004) The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431:152-155
16. Tsirigos A & Rigoutsos I (2005) A new computational method for the detection of horizontal gene transfer events. Nucleic Acids Res 33:922-933
17. Charlebois RL, Beiko RG & Ragan MA (2003) Branching out. Nature 421:217
18. Lerat E, Daubin V, Ochman H & Moran NA (2005) Evolutionary origins of genomic repertoires in bacteria. PLoS Biol 3:e130
19. Choi I-G & Kim S-H (2007) Global extent of horizontal gene transfer. Proc Natl Acad Sci USA 104:4489-4494
20. Ochman H, Herat E & Daubin V (2005) Examining bacterial species under the specter of gene transfer and exchange. Proc Natl Acad Sci USA 102:6595-6599
21. Dagan T & Martin W (2007) Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc Natl Acad Sci USA 104:870-875
22. Aertsen A & Michiels CW (2005) Diversify or die: generation of diversity in response to stress. Crit Rev Microbiol 31:69-78
23. Beiko RG, Harlow TJ & Ragan MA (2005) Highways of gene sharing in prokaryotes. Proc Natl Acad Sci USA 102:14332-14337
24. Lawrence JG (1999) Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr Opin Genet Dev 9:642-648
25. Lawrence JG & Roth JR (1996) Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics 143:1843-1860
26. Lawrence JG & Roth JR (1995) The cobalamin (coenzyme B 12 ) biosynthetic genes of Escherichia coli. J Bacteriol 177:6371-6380
27. 12 synthesis among enteric bacteria: evidence for loss and reacquisition of a multigene complex. Genetics 142:11-24
28. Matsui K, Sano K & Ohtsubo E (1986) Complete nucleotide and deduced amino acid sequences of the Brevibacterium luctofermentum tryptophan operon. Nucleic Acids Res 14:10113-10114
29. Williams PA & JR Sayers (1994) The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas. Biodegradation 5:195-217
30. Wyndham RC, Cashore AE, Nakatsu CH & Peel MC (1994) Catabolic transposons. Biodegradation 5:323-342
31. Van der Meer JR (1997) Evolution of novel metabolic pathways for the degradation of chloroaromatic compounds. Antonie van Leeuwenhoek J Microbiol Serol 71:159-178
32. Sharma P, Raina V, Kumari R, Malhotra S, Dogra C, Kumari H, Kohler H-PE, Buser H-R, Holliger C & Lal R (2006) Haloalkane dehalogenase LinB is responsible for beta-and delta-hexachlorocyclohexane transformation in Sphingobium indicum B90A. Appl Environ Microbiol 72(9):5720-5727
33. Dogra C, Raina V, Pal R, Suar M, Lal S, Gartemann K-H, Holliger C, van der Meer JR & Lal R (2004) Organization of lin genes and IS6100 among different strains of hexachlorocyclohexane-degrading Sphingomonas paucimobilis: evidence for horizontal gene transfer. J Bacteriol 186(8):2225-2235
34. Rosen BP (1999) Families of arsenic transporters. Trends Microbiol 7:207-212
35. Gihring TM, Bond PL, Peters S & Banfield JF (2003) Arsenic resistance in the archaeon Ferroplasma acidarmanus: new insights into the structure and evolution of arsenic genes. Extremophiles 7:123-130
36. Shen Y, Buick R & Canfield DE (2001) Isotopic evidence for microbial sulphate reduction in the early Archaean era. Nature 410:77-81
37. Klein M, Friedrich M, Roger AJ, Hugenholtz P, Fishbain S, Abicht H, Blackall LL, Stahl DA & Wagner M (2001) Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. J Bacteriol 183:6028-6035
38. Aravind L, Tatusov RL, Wolf YI, Walker DR & Koonin EV (1998) Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet 14:442-444
39. Wolf YI, Aravind L & Koonin EV (1998) Rickettsiae and Chlamydia: evidence of horizontal gene transfer and gene exchange. Trends Genet 14:442-444
40. De la Cruz F & Davies J (2000) Horizontal gene transfer and the origin of species: lessons from bacteria. Trends Microbiol 8:128-133
41. Xiong J, Fischer WM, Inoue K, Nakahara M & Bauer CE (2000) Molecular evidence for the early evolution of photosynthesis. Science 289:1724-1730
42. Macalady J & Banfield JF (2003) Molecular geomicrobiology: genes and geochemical cycling. Earth and Planetary Science Letters 209:1-17
43. Di Gioia D, Peel M, Fava F & Wyndham RC (1998) Structures of homologous composite transposons carrying cbaABC genes from Europe and North America. Appl Environ Microbiol 64:1940-1946
44. Campbell A, Mrazek J & Karlin S (1999) Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. Proc Natl Acad Sci USA 96:9184-9189
45. Dubnau D (1999) DNA uptake in bacteria. Annu Rev Microbiol 53:217-244
46. Hall RM & Collis CM (1995) Mobile gene cassettes and integrons: capture and spread of genes by site-specific recombination. Mol Microbiol 15:593-600
47. Mazel D, Dychinco B, Webb VA & Davies J (1998) A distinctive class of integron in the Vibrio cholerae genome. Science 280:605-608
48. Dowson CG, Coffey TJ, Kell C & Whiley RA (1993) Evolution of penicillin resistance in Streptococcus pneumoniae; the role of Streptococcus mitis in the formation of a low affinity PBP2B in S. pneumomae. Mol Microbiol 9:635-643
49. Lujan R, Zhang QY, Saez Nieto JA, Jones DM & Spratt BG (1991) Penicillin-resistant isolates of Neisseria lactamica produce altered forms of penicillin-binding protein 2 that arose by interspecies horizontal gene transfer. Antimicrob Agents Chemother 35:300-304
50. Bowler LD, Zhang QY, Riou JY & Spratt BG (1994) Interspecies recombination between the penA genes of Neisseria meningitidis and commensal Neisseria species during the emergence of penicillin resistance in N. meningitidis: Natural events and laboratory simulation. J Bacteriol 176:333-337
51. Spratt BG, Bowler LD, Zhang QY, Zhou J & Smith JM (1992) Role of interspecies transfer of chromosomal genes in the evolution of penicillin resistance in pathogenic and commensal Neisseria species. J Mol Evol 34:115-125
52. Hacker J, Blum-Oehler G, Mühldorfer I & Tschäpe H (1997) Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol Microbiol 23:1089-1097
53. Blum G, Ott M, Lischewski A, Ritter A, Imrich H, Tschape H & Hacker J (1994) Excision of large DNA regions termed pathogenicity islands from tRNA-specific loci in the chromosome of an Escherichia coli wild-type pathogen. Infect Immun 62:606-614
54. McDaniel TK & Kaper JB (1997) A cloned pathogenicity island from enteropathogenic Escherichia coli confers the attaching and effacing phenotype on E. coli K-12. Mol Microbiol 23:399-407
55. Moss JE, Cardozo TJ, Zychlinsky A & Groisman EA (1999) The selC-associated SHI-2 pathogenicity island of Shigella flexneri. Mol Microbiol 33:74-83
56. Vokes SA, Reeves SA, Torres AG & Payne SM (1999) The aerobactin iron transport system genes in Shigella flexneri are present within a pathogenicity island. Mol Microbiol 33:63-73
57. Blanc-Potard AB & Groisman EA (1997) The Salmonella selC locus contains a pathogenicity island mediating intramacrophage survival. EMBO J 16:5376-5385
58. Eisen JA (2000) Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr Opin Genet Dev 10:606-611
59. Ragan MA (2001) Detection of lateral gene transfer among microbial genomes. Curr Opin Genet Dev 11:620-626
60. Ochman H, Lawrence JG & Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304
61. Grantham R, Gautier C, Gouy M, Mercier R & Pavé A (1980) Codon catalog usage and the genome hypothesis. Nucleic Acids Res 8:197-c
62. Ellis J, Morrison DA & Kalinna B (1995) Comparison of the patterns of codon usage and bias between Brugia, Echinococcus, Onchocerca and Schistosoma species. Parasitol Res 81:388-393
63. Medigue C, Rouxel T, Vigier P, Henaut A & Danchin A (1991) Evidence for horizontal gene transfer in Escherichia coli speciation. J Mol Biol 222:851-856
64. Lawrence JG & Ochman H (1997) Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 44:383-397
65. Mrazek J & Karlin S (1999) Detecting alien genes in bacterial genomes. Ann NY Acad Sci 870:314-329
66. Garcia-Vallve S, Romeu A & Palau J (2000) Horizontal gene transfer in bacterial and archaeal complete genome. Genome Res 10:1719-1725
67. Groisman EA, Sturmoski MA, Solomon FR, Lin R & Ochman H (1993) Molecular, functional, and evolutionary analysis of sequences specific to Salmonella. Proc Natl Acad Sci USA 90:1033-1037
68. Groisman EA & Ochman H (1993) Cognate gene clusters govern invasion of host epithelial cells by Salmonella typhimurium and Shigella flexneri. EMBO J 12:3779-3787
69. Shanley MS, Harrison A, Parales RE, Kowalchuk G, Mitchell DJ & Ornston LN (1994) Unusual G+C content and codon usage in catZJF, a segment of the ben-cat supra-operonic cluster in the Acinetobacter caloaceticus chromosome. Gene 138:59-65
70. Groisman EA, Saier Jr MH & Ochman H (1992) Horizontal transfer of a phosphatase gene as evidence for the mosaic structure of the Salmonella genome. EMBO J 11:1309-1316
71. Lan R & Reeves PR (1996) Gene transfer is a major factor in bacterial evolution. Mol Biol Evol 13:47-55
72. Bult CJ, White O, Olsen GJ, Zhou L, Fleishmann RD, Sutton GG, Blake JA, Fitzgerald LM, Clayton RA, Gocayne JD, Kertavage AR, Dougherty BA, Tomb JF, Adams MD, Reich CI, Overbeek R, Kirkness EF, Weinstock KG, Merrick JM, Glodek A, Scott JL, Geoghagen NSM, Weidman JF, Fuhrmann JL, Nguyen D, Utterback TR, Kelley JM, Peterson JD, Sadow PW, Hanna MC, Cotton MD, Roberts KM, Hurst MA, Kaine BP, Borodovsky M, Klenk HP, Fraser CM, Smith HO, Woese CR & Ventor JC (1996) Complete genome sequence of the methanogenic Archaeon, Methanococcus jannaschii. Science 273:1058-1073
73. Klenk H-P, Clayton RA, Tomb J-F, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, Quackenbush J, Lee NH, Sutton GG, Gill S, Kirkness EF, Dougherty BA, McKenney K, Adams MD, Loftus B, Peterson S, Reich CI, McNeil LK, Badger JH, Glodek A, Zhou L, Overbeek R, Gocayne JD, Weidman JF, McDonald L, Utterback T, Cotton MD, Spriggs T, Artiach P, Kaine BP, Sykes SM, Sadow PW, D'Andrea KP, Bowman C, Fujii C, Garland SA, Mason TM, Olsen GJ, Fraser CM, Smith HO, Woese CR & Venter JC (1997) The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364-370
74. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg, J, Sutton, GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC & Fraser CM (1999) Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritime. Nature 399:323-329
75. Karlin S & Burge C (1995) Dinucleotide relative abun-dance extremes: a genomic signature. Trends Genet 11:283-290
76. Sharp PM & Li W-H (1987) The codon adaptation index-a measure of directional synonymous codon usage bias and its potential applications. Nucleic Acids Res 15:1281-1295
77. Karlin S, Mrázek J & Campbell AM (1998) Codon usages in different gene classes of the Escherichia coli genome. Mol Microbiol 29:1341-1355
78. Tatusov RL, Koonin EV & Lipman DJ (1997) A genomic perspective on protein families. Science 278:631-637
79. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND & Koonin EV (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29:22-28
80. Glazko GV & Mushegian AR (2004) Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns. Genome Biol 5:R32
81. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D & Yeaster TO (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA 96:4285-4288
82. Koonin EV, Mushegian AR, Galperin MY & Walker DR (1997) Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the Archaea. Mol Microbiol 25:619-637
83. Doolittle WF & Logsdon JM Jr (1998) Archaeal genomics: do archaea have a mixed heritage? Curr Biol 8: R209-R211
84. Jain R, Rivera MC & Lake JA (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA 96:3801-3806
85. Mongodin EF, Nelson KE, Daugherty S, DeBoy RT, Wister J, Khouri H, Weidman J, Walsh DA, Papke RT, Sanchez Perez G, Sharma AK, Nesbø CL, MacLeod D, Bapteste E, Doolittle WF, Charlebois RL, Legault B & Rodriguez-Valera F (2005) The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc Natl Acad Sci USA 102:18147-18152
86. Kurland CG, Canback B & Berg OG (2003) Horizontal gene transfer: A critical view. Proc Natl Acad Sci USA 100:9658-9662
87. Huynen MA, Snel B & Bork P (1999) Lateral gene transfer, genome surveys, and the phylogeny of prokaryotes. Science 286:1443a
88. Snel B, Bork P & Huynen MA (1999) Genome phylogeny based on gene content. Nat Genet 21:108-110
89. Korbel JO, Snel B, Huynen MA & Bork P (2002) SHOT: a web server for the construction of genome phylogenies. Trends Genet 18:158-162
90. Tekaia F, Lazcano A & Dujon B (1999) The genomic tree as revealed from whole proteome comparisons. Genome Res 9:550-557
91. Fitz-Gibbon ST & House CH (1999) Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res 27:4218-4222
92. House CH & Fitz-Gibbon ST (2002) Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J Mol Evol 54:539-547
93. Wolf YI, Rogozin IB, Grishin NV, Tatusov RL & Koonin EV (2001) Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol 1:8
94. Lin J & Gerstein M (2000) Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res 10:808-818
95. Beck JT, Zhao S & Wang CC (1994) Cloning, sequencing, and structural analysis of the DNA encoding inosine monophosphate dehydrogenase (EC1.1.1.205) from Tritrichomonas foetus. Exp Parasitol 78:101-112
96. Berg OG & Kurland CG (2002) Evolution of microbial genomes: sequence acquisition and loss. Mol Biol Evol 19:2265-2276
97. Mount DM (2001) Bioinformatics Sequence and Genome Analysis, New York Cold Spring Harbour Laboratory Press p. 247-248
98. Natale DA, Shankavaram UT, Galperin MY, Wolf YI, Aravind L & Koonin EV (2000) Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs). Genome Biol 1 research0009.1-0009.19
99. Clarke GDP, Beiko RG, Ragan MA & Charlebois RL (2002) Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J Bacteriol 184:2072-2080
100. Wolf YI, Brenner SE, Bash PA & Koonin EV (1999) Distribution of protein folds in the three superkingdoms of life. Genome Res 9:17-26
101. Eisen JA (1995) The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J Mol Evol 41:1105-1123
102. Brown JW, Daniels CJ & Reeve JN (1989) Gene structure, organization and expression in archaebacteria. Crit Rev Microbiol 16:287-338
103. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221-271
104. Woese CR, Kandler O & Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576-4579
105. Fox GE, Magrum LJ, Balch WE, Wolfe RS & Woese CR (1977) Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proc Natl Acad Sci USA. 74:4537-4541
106. Woese CR & Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088-5090
107. Danson MJ (1988) Archaebacteria: the comparative enzymology of their central metabolic pathways. Adv Microb Physiol 29:165-231
108. Danson MJ (1989) Central metabolism of the archaebacteria: An overview. Can J Microbiol 35:58-64
109. Schönheit P & Schäfer T (1995) Metabolism of hyperthermophiles. World J Microbiol Biotechnol 11:26-75
110. Schloss PD & Handelsman J (2004) Status of the Microbial Census. Microbiol Mol Biol Rev 68:686-691
111. Pace NR, Olsen OJ & Woese CR (1986) Ribosomal RNA phylogeny and the primary lines of evolutionary descent. Cell 45:325-326
112. Yap WH, Zhong Z & Wang Y (1999) Distinct Types of rRNA Operons exist in the genome of the Actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J Bacteriol 181:5201-5209
113. Yanai I, Wolf YI & Koonin EV (2002) Evolution of gene fusions: horizontal transfer versus independent events. Genome Biol 3:research0024.1- 0024.13
114. Olsen GJ, Woese CR & Overbeek R (1994) The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 176:1-6
115. Doolittle RF & Handy J (1998) Evolutionary anomalies among the aminoacyl-tRNA synthetases. Curr Opin Genet Dev 8:630-636
116. Lawrence JG & Ochman H (1998) Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA 95:9413-9417
117. Rivera MC, Jain R, Moore JE & Lake JA (1998) Genomic evidence for two functionally distinct gene classes. Proc Natl Acad Sci USA 95:6239-6244
118. Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, Koonin EV & Daly MJ (2001) Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev 65:44-79
119. Iyer LM, Koonin, EV & Aravind L (2004) Evolution of bacterial RNA polymerase: implications for large scale phylogeny, domain accretion and horizontal gene transfer. Gene 335:73-88
120. Bapteste E, Moreira D & Philippe H (2003) Rampant horizontal gene transfer and phospho-donor change in the evolution of the phosphofructokinase. Gene 318:185-191
121. Müller M, Lee JA, Gordon P, Gaasterland T & Sensen CW (2001) Presence of prokaryotic and eukaryotic species in all subgroups of the PPi-dependent group II phosphofructokinase protein family. J Bacteriol 183:6714-6716
122. Venkatesh R, Ganesh N, Guhan N, Reddy MS, Chandrasekhar T & Muniyappa K (2002) RecX protein abrogates ATP hydrolysis and strand exchange promoted by RecA: insights into negative regulation of homologous recombination. Proc Natl Acad Sci USA 99:12091-12096
123. Stohl EA, Brockman JP, Burkle KL, Morimatsu K, Kowalczykowski SC & Seifert NS (2003) Escherichia coli RecX inhibits RecA recombinase and coprotease activities in vitro and in vivo. J Biol Chem 278:2278-2285
124. Lin J, Chen Z-Z, Tian B & Hua Y-J (2007) Evolutionary pathways of an ancient gene recX. Gene 387, 15-20 doi: 10.1016/j.gene.2006.07.031
125. Schlieper D, Oliva MA, Andreu JM & Löwe J (2005) Structure of bacterial tubulin BtubA/B: evidence for horizontal gene transfer. Proc Natl Acad Sci USA 102:9170-9175
126. Fuxelius H-H, Darby A, Min C-K, Cho, N-H & Andersson Siv GE (2007) The genomic and metabolic diversity of Rickettsia. Res Microbiol 158:745-753
127. Eppinger M, Baar C, Linz B, Raddatz G, Lanz C, Keller H, Morelli G, Gressmann H, Achtman M & Schuster SC (2006) Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines. PLoS Genet 2, e120
128. Backert S & Meyer TF (2006) Type IV secretion systems and their effectors in bacterial pathogenesis. Curr Opin Microbiol 9:207-217
129. Linz B & Schuster SC (2007) Genomic diversity in Helicobacter and related organisms. Res Microbiol 158:737-744
130. Gophna U, Ron EZ & Graur D (2003) Bacterial type III secretion systems are ancient and evolved by multiple horizontal transfer events. Gene 312:151-163
131. Rahme LG, Ausubel FM, Cao H, Drenkard E, Goumnerov BC, Lau, GW, Mahajan-Miklos S, Plotnikova J, Tan M-W, Tsongalis J, Walendziewicz CL & Tompkins RG (2000) Plants and animals share functionally common bacterial virulence factors. Proc Natl Acad Sci USA 97(16):8815-8821
132. Qiu X, Gurkar AU & Lory S (2006) Interstrain transfer of the large pathogenicity island (PAPI-1) of Pseudomonas aeruginosa. Proc Natl Acad Sci USA 103:19830-19835
133. Hughes AL & Friedman R (2005) Poxvirus genome evolution by gene gain and loss. Mol Phyl Evol 35:186-195
134. Pisurek O & Okada, N (2007) Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals. Proc Natl Acad Sci USA 104:12046-12051
135. Gophna U, Charlebois RL & Doolittle WF (2004) Have archaeal genes contributed to bacterial virulence? Trends Microbiol 12: 213-219
136. Kechris KJ, Lin JC, Bickel PJ & Glazer AN (2006) Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study. Proc Natl Acad Sci USA 103:9584-9589
137. Raizada N, Sonakya V, Anand V & Kalia VC (2002) Waste management and production of future fuels. J Sci Ind Res 61:184-207
138. Kalia VC & Purohit HJ (2008) Microbial diversity and genomics in aid of bioenergy. J Ind Microbiol Biotechnol 35:403-419
139. Kalia VC, Jain SR, Kumar A & Joshi AP (1994) Fermentation of biowaste to hydrogen by Bacillus licheniformis. World J Microbiol Biotechnol 10:224-227
140. Kalia VC & Joshi AP (1995) Conversion of waste biomass (pea-shell) into hydrogen and methane through anaerobic digestion. Bioresour Technol 53:165-168
141. Kalia VC, Anand V, Kumar A & Joshi AP (1997) Efficient biomethanation of plant materials by immobilized bacteria. In: Proceedings of R'97 Congress (Recovery, Recycling, Re-integration) Geneva, Switzerland Vol I: 200-205
142. Sonakya V, Raizada N & Kalia VC (2001) Microbial and enzymatic improvement of anaerobic digestion of waste biomass. Biotechnol Lett 23:1463-1466
143. Porwal S, Kumar T, Lal S, Rani A, Kumar S, Cheema S, Purohit HJ, Sharma R, Patel SKS & Kalia VC (2007) Hydrogen and polyhydroxybutyrate producing abilities of microbes from diverse habitats by dark fermentative process. Bioresour Technol 99:5444-5451
144. Kalia VC, Chauhan A, Bhattacharyya G & Rashmi XX (2003) Genomic databases yield novel bioplastic producers. Nat Biotechnol 21:845-846
145. Kalia VC, Lal S, Ghai R, Mandal M & Chauhan A (2003) Mining genomic databases to identify novel hydrogen producers. Trends Biotechnol 21:152-156
146. Kalia VC, Rani A, Lal S, Cheema S & Raut CP (2007) Combing databases reveals potential antibiotic producers. Expert Opin Drug Discov 2:211-224
147. Kalia VC, Lal S & Cheema S (2007) Insight in to the phylogeny of polyhydroxyalkanoate biosynthesis: Horizontal gene transfer. Gene 389: 19-26
148. Richardson AO & Jeffrey DP (2007) Horizontal gene transfer in plants. J Expt Bot 58:1-9
149. Hall C, Brachat S & Dietrich FS (2005) Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. Eukaryot Cell 4:1102-1115
150. Kondo N, Nikoh N, Ijichi N, Shimada M & Fukatsu T (2002) Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect. Proc Natl Acad Sci USA 99:14280-14285
151. Hotopp JC, Clark ME, Oliveira DC, Foster JM, Fischer P, Torres MC, Giebel JD, Kumar N, Ishmael N, Wang S, Ingram J, Nene RV, Shepard J, Tomkins J, Richards S, Spiro DJ, Ghedin E, Slatko BE, Tettelin H & Werren JH (2007) Widespread lateral gene transfer from Intracellular bacteria to multicellular eukaryotes. Science doi:10.1126/science.1142490
152. Davis CC & Wurdack KJ (2004) Host-to-parasite gene transfer in flowering plants: Phylogenetic evidence from Malpighiales. Science 305:676-678
153. Nickrent DL, Blarer A, Qiu Y-L, Vidal-Russell R & Anderson FE (2004) Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer. BMC Evol Biol 4(40). doi:10.1186/1471-2148-4-40
154. Woloszynska M, Bocer T, Mackiewicz P & Janska H (2004) A fragment of chloroplast DNA was transferred horizontally, probably from non-eudicots, to mitochondrial genome of Phaseolus. Plant Mol Biol 56:811-820
155. Doolittle FW (2000) Uprooting the tree of life. Scientific American: 72-77
156. Kunin V, Goldovsky L, Darzentas N & Ouzounis CA (2005) The net of life: Reconstructing the microbial phylogenetic netwrok. Genome Res 15: 954-959
157. Prakash O, Verma M, Sharma P, Kumar M, Gupta SK, Khanna M & Lal R (2007) Polyphasic approach of bacterial classification' An overview of recent advances. Ind J Microbiol 47:98-108
158. Oh SJ, Joung JG, Chang JH & Zhang BT (2006) Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks. BMC Bioinformatics 7:284
159. Wenzl P, Wong L, Kwang-won K & Jefferson RA (2005) A functional screen identifies lateral transfer of betaglucuronidase (gus) from bacteria to fungi. Mol Biol Evol 22:308-316
160. Baumann P & Jackson SP (1996) An archaebacterial homologue of the essential eubacterial cell division protein FtsZ. Proc Natl Acad Sci USA 93:6726-6730
161. Wang X & Lutkenhaus J (1996) FtsZ ring: the eubacterial division apparatus conserved in archaebacteria. Mol Microbiol 21:13-319
162. Ricard G, McEwan NR, Dutilh BE, Jouany JP, Macheboeuf D, Mitsumori M, McIntosh FM, Michalowski T, Nagamine T, Nelson N, Newbold CJ, Nsabimana E, Takenaka A, Thomas NA, Ushida K, Hackstein JH & Huynen MA (2006) Horizontal gene transfer from bacteria to rumen ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. BMC Genomics 7:22
163. Gomes JP, Bruno WJ, Borrego MJ & Dean D (2004) Recombination in the genome of Chlamydia trachomatis involving the polymorphic membrane protein C gene relative to ompA and evidence for horizontal gene transfer. J Bacteriol 186:4295-4306
164. Omelchenko MV, Makarova KS, Wolf YI, Rogozin IB & Koonin EV (2003) Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. Genome Biol 4:R55
165. Viale AM & Arakaki AK (1994) The chaperone connection to the origins of eukaryotic organelles. FEBS Lett 341:146-151
166. Gupta RS (1995) Evolution of the chaperonin families (Hsp60, Hsp10 and Tcp-1) of proteins and the origin of eukaryotic cells. Mol Microbiol 15:1-11
167. Jackson CR & Dugas SL (2003) Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin arsenate reductase. BMC Evol Biol 3:18
168. Sheveleva EV & Hallick RB (2004) Recent horizontal intron transfer to a chloroplast genome. Nucleic Acids Res 32:803-810
169. Klenk H-P, Palm P & Zillig W (1993) DNA-dependent RNA polymerases as phylogenetic marker molecules. Syst Appl Microbiol 16:138-147
170. Pühler G, Leffers H, Gropp F, Palm P, Klenk H-P, Lottspeich F, Garrett RA & Zillig W (1989) Archaebacterial DNAdependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome. Proc Natl Acad Sci USA 86:4569-4573
171. Ponting CP, Aravind L, Schultz J, Bork, P & Koonin EV (1999) Eukaryotic signalling domain homologues in archaea and bacteria, Ancient ancestry and horizontal gene transfer. J Mol Biol 1289:729-745
172. Kennelly PJ (2002) Protein kinases and protein phosphatases in prokaryotes: a genomic perspective. FEMS Microbiol Lett 206:1-8
173. Zhang W & Shi L (2004) Evolution of the PPM-family protein phosphatases in Streptomyces: duplication of catalytic domain and lateral recruitment of additional sensory domains. Microbiology 150:4189-4197
174. Won H & Renner SS (2003) Horizontal gene transfer from flowering plants to Gnetum. Proc Natl Acad Sci USA 100:10824-10829
175. Pruss B, Meyer HE & Holldorf AW (1993) Characterization of the glyceraldehyde 3-phosphate dehydrogenase from the extremely halophilic archaebacterium Haloarcula vallismortis. Arch Microbiol 160:5-11
176. Nolling J & Vos WM (1992) Characterization of the archaeal, plasmidencoded type II restriction-modification system MthTI from Methanobacterium thermoformicicum THF: homology to the bacterial NgoPII system from Neisseria gonorrhoeae. J Bacteriol 174:5719-5726
177. Brinkman FS, Blanchard JL, Cherkasov A, Av-Gay Y, Brunham RC, Fernandez RC, Finlay BB, Otto SP, Ouellette BF, Keeling PJ, Rose AM, Hancock RE, Jones SJ & Greberg H (2002) Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast. Genome Res 12:1159-116796.
178. Lawson FS, Charlebois RL & Dillon JA (1996) Phylogenetic analysis of carbamoylphosphate synthetase genes: evolution involving multiple gene duplications, gene fusions, and insertions and deletions of surrounding sequences. Mol Biol Evol 13:970-977