{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T13:49:42Z","timestamp":1791121782292,"version":"4.1.0"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2007,8,9]],"date-time":"2007-08-09T00:00:00Z","timestamp":1186617600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Mol Evol"],"published-print":{"date-parts":[[2007,10,9]]},"DOI":"10.1007\/s00239-007-9010-3","type":"journal-article","created":{"date-parts":[[2007,8,8]],"date-time":"2007-08-08T17:50:24Z","timestamp":1186595424000},"page":"249-258","source":"Crossref","is-referenced-by-count":32,"title":["Phylogenetic Relationships Among Mycoplasmas Based on the Whole Genomic Information"],"prefix":"10.1007","volume":"65","author":[{"given":"Kenro","family":"Oshima","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiromi","family":"Nishida","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2007,8,9]]},"reference":[{"key":"9010_CR1","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1038\/90129","volume":"28","author":"JR Brown","year":"2001","unstructured":"Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ (2001) Universal trees based on large combined protein sequence data sets. Nature Genet 28:281\u2013285","journal-title":"Nature Genet"},{"key":"9010_CR2","doi-asserted-by":"crossref","first-page":"2145","DOI":"10.1093\/nar\/29.10.2145","volume":"29","author":"I Chambaud","year":"2001","unstructured":"Chambaud I, Heilig R, Ferris S, Barbe V, Samson D, Galisson F, Moszer I, Dybvig K, Wroblewski H, Viari A, Rocha EP, Blanchard A (2001) The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis. Nucleic Acids Res 29:2145\u20132153","journal-title":"Nucleic Acids Res"},{"key":"9010_CR3","doi-asserted-by":"crossref","first-page":"2124","DOI":"10.1126\/science.284.5423.2124","volume":"284","author":"WF Doolittle","year":"1999","unstructured":"Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284:2124\u20132128","journal-title":"Science"},{"key":"9010_CR4","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1099\/00207713-47-1-38","volume":"47","author":"M Falah","year":"1997","unstructured":"Falah M, Gupta RS (1997) Phylogenetic analysis of mycoplasmas based on Hsp70 sequences: cloning of the dnaK (hsp70) gene region of Mycoplasma capricolum. Int J Syst Bacteriol 47:38\u201345","journal-title":"Int J Syst Bacteriol"},{"key":"9010_CR5","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1002\/(SICI)1521-1878(199910)21:10<871::AID-BIES10>3.0.CO;2-Q","volume":"21","author":"P Forterre","year":"1999","unstructured":"Forterre P, Philippe H (1999) Where is the root or the universal tree of life? Bioessays 21:871\u2013879","journal-title":"Bioessays"},{"key":"9010_CR6","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1099\/00207713-42-1-166","volume":"42","author":"GE Fox","year":"1992","unstructured":"Fox GE, Wisotzkey JD, Jurtshuk P (1992) How close is close? 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42:166\u2013170","journal-title":"Int J Syst Bacteriol"},{"key":"9010_CR7","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1126\/science.270.5235.397","volume":"270","author":"CM Fraser","year":"1995","unstructured":"Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, Fritchman RD, Weidman JF, Small KV, Sandusky M, Fuhrmann J, Nguyen D, Utterback TR, Saudek DM, Phillips CA, Merrick JM, Tomb JF, Dougherty BA, Bott KF, Hu PC, Lucier TS, Peterson SN, Smith HO, Hutchison CA 3rd, Venter JC (1995) The minimal gene complement of Mycoplasma genitalium. Science 270:397\u2013403","journal-title":"Science"},{"key":"9010_CR8","first-page":"1709","volume":"3","author":"F Ge","year":"2005","unstructured":"Ge F, Wang LS, Kim J (2005) The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol 3:1709\u20131718","journal-title":"PLoS Biol"},{"key":"9010_CR9","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1038\/35037619","volume":"407","author":"JI Glass","year":"2000","unstructured":"Glass JI, Lefkowitz EJ, Glass JS, Heiner CR, Chen EY, Cassell GH (2000) The complete sequence of the mucosal pathogen Ureaplasma urealyticum. Nature 407:757\u2013762","journal-title":"Nature"},{"key":"9010_CR10","doi-asserted-by":"crossref","first-page":"5244","DOI":"10.1128\/jb.176.17.5244-5254.1994","volume":"176","author":"DE Gundersen","year":"1994","unstructured":"Gundersen DE, Lee IM, Rehner SA, Davis RE, Kingsbury DT (1994) Phylogeny of mycoplasmalike organisms (phytoplasmas) \u2014 a basis for their classification. J Bacteriol 176:5244\u20135254","journal-title":"J Bacteriol"},{"key":"9010_CR11","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1099\/00207713-46-1-64","volume":"46","author":"DE Gundersen","year":"1996","unstructured":"Gundersen DE, Lee IM, Schaff DA, Harrison NA, Chang CJ, Davis RE, Kingsbury DT (1996) Genomic diversity and differentiation among phytoplasma strains in 16S rRNA groups I (aster yellows and related phytoplasmas) and III (X-disease and related phytoplasmas). Int J Syst Bacteriol 46:64\u201375","journal-title":"Int J Syst Bacteriol"},{"key":"9010_CR12","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1016\/0047-2484(89)90075-4","volume":"18","author":"M Hasegawa","year":"1989","unstructured":"Hasegawa M, Kishino H, Yano TA (1989) Estimation of branching dates among primates by molecular clocks of nuclear DNA which slowed down in hominoidea. J Hum Evol 18:461\u2013476","journal-title":"J Hum Evol"},{"key":"9010_CR13","doi-asserted-by":"crossref","first-page":"4420","DOI":"10.1093\/nar\/24.22.4420","volume":"24","author":"R Himmelreich","year":"1997","unstructured":"Himmelreich R, Hilbert H, Plagens H, Pirkl E, Li BC, Herrmann R (1997) Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res 24:4420\u20134449","journal-title":"Nucleic Acids Res"},{"key":"9010_CR14","doi-asserted-by":"crossref","first-page":"5849","DOI":"10.1073\/pnas.95.11.5849","volume":"95","author":"MA Huynen","year":"1998","unstructured":"Huynen MA, Bork P (1998) Measuring genome evolution. Proc Natl Acad Sci USA 95:5849\u20135856","journal-title":"Proc Natl Acad Sci USA"},{"key":"9010_CR15","doi-asserted-by":"crossref","first-page":"1447","DOI":"10.1101\/gr.2674004","volume":"14","author":"JD Jaffe","year":"2004","unstructured":"Jaffe JD, Stange-Thomann N, Smith C, DeCaprio D, Fisher S, Butler J, Calvo S, Elkins T, FitzGerald MG, Hafez N, Kodira CD, Major J, Wang S, Wilkinson J, Nicol R, Nusbaum C, Birren B, Berg HC, Church GM (2004) The complete genome and proteome of Mycoplasma mobile. Genome Res 14:1447\u20131461","journal-title":"Genome Res"},{"key":"9010_CR16","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1099\/00207713-48-1-269","volume":"48","author":"R Jomantiene","year":"1998","unstructured":"Jomantiene R, Davis RE, Maas J, Dally EL (1998) Classification of new phytoplasmas associated with diseases of strawberry in Florida, based on analysis of 16S rRNA and ribosomal protein gene operon sequences. Int J Syst Bacteriol 48:269\u2013277","journal-title":"Int J Syst Bacteriol"},{"key":"9010_CR17","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/0378-1119(95)00884-5","volume":"171","author":"V Kamla","year":"1996","unstructured":"Kamla V, Henrich B, Hadding U (1996) Phylogeny based on elongation factor Tu reflects the phenotypic features of mycoplasmas better than that based on 16S rRNA. Gene 171:83\u201387","journal-title":"Gene"},{"key":"9010_CR18","doi-asserted-by":"crossref","first-page":"1714","DOI":"10.1128\/JCM.37.6.1714-1720.1999","volume":"37","author":"BJ Kim","year":"1999","unstructured":"Kim BJ, Lee SH, Lyu MA, Kim SJ, Bai GH, Chae GT, Kim EC, Cha CY, Kook YH (1999) Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB). J Clin Microbiol 37:1714\u20131720","journal-title":"J Clin Microbiol"},{"key":"9010_CR19","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/S0378-1097(03)00618-9","volume":"226","author":"KS Kim","year":"2003","unstructured":"Kim KS, Ko KS, Chang MW, Hahn TW, Hong SK, Kook YH (2003) Use of rpoB sequences for phylogenetic study of Mycoplasma species. FEMS Microbiol Lett 226:299\u2013305","journal-title":"FEMS Microbiol Lett"},{"key":"9010_CR20","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1093\/bib\/5.2.150","volume":"5","author":"S Kumar","year":"2004","unstructured":"Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150\u2013163","journal-title":"Brief Bioinform"},{"key":"9010_CR21","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/36786","volume":"390","author":"F Kunst","year":"1997","unstructured":"Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Carter NM, Choi SK, Codani JJ, Connerton IF, Cummings NJ, Daniel RA, Denizot F, Devine KM, Dusterhoft A, Ehrlich SD, Emmerson PT, Entian KD, Errington J, Fabret C, Ferrari E, Foulger D, Fritz C, Fujita M, Fujita Y, Fuma S, Galizzi A, Galleron N, Ghim SY, Glaser P, Goffeau A, Golightly EJ, Grandi G, Guiseppi G, Guy BJ, Haga K, Haiech J, Harwood CR, Henaut A, Hilbert H, Holsappel S, Hosono S, Hullo MF, Itaya M, Jones L, Joris B, Karamata D, Kasahara Y, KlaerrBlanchard M, Klein C, Kobayashi Y, Koetter P, Koningstein G, Krogh S, Kumano M, Kurita K, Lapidus A, Lardinois S, Lauber J, Lazarevic V, Lee SM, Levine A, Liu H, Masuda S, Mauel C, Medigue C, Medina N, Mellado RP, Mizuno M, Moestl D, Nakai S, Noback M, Noone D, OReilly M, Ogawa K, Ogiwara A, Oudega B, Park SH, Parro V, Pohl TM, Portetelle D, Porwollik S, Prescott AM, Presecan E, Pujic P, Purnelle B, Rapoport G, Rey M, Reynolds S, Rieger M, Rivolta C, Rocha E, Roche B, Rose M, Sadaie Y, Sato T, Scanlan E, Schleich S, Schroeter R, Scoffone F, Sekiguchi J, Sekowska A, Seror SJ, Serror P, Shin BS, Soldo B, Sorokin A, Tacconi E, Takagi T, Takahashi H, Takemaru K, Takeuchi M, Tamakoshi A, Tanaka T, Terpstra P, Tognoni A, Tosato V, Uchiyama S, Vandenbol M, Vannier F, Vassarotti A, Viari A, Wambutt R, Wedler E, Wedler H, Weitzenegger T, Winters P, Wipat A, Yamamoto H, Yamane K, Yasumoto K, Yata K, Yoshida K, Yoshikawa HF, Zumstein E, Yoshikawa H, Danchin A (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390:249\u2013256","journal-title":"Nature"},{"key":"9010_CR22","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1146\/annurev.micro.54.1.221","volume":"54","author":"IM Lee","year":"2000","unstructured":"Lee IM, Davis RE, Gundersen-Rindal DE (2000) Phytoplasma: Phytopathogenic mollicutes. Annu Rev Microbiol 54:221\u2013255","journal-title":"Annu Rev Microbiol"},{"key":"9010_CR23","doi-asserted-by":"crossref","first-page":"2606","DOI":"10.1128\/jb.174.8.2606-2611.1992","volume":"174","author":"PO Lim","year":"1992","unstructured":"Lim PO, Sears BB (1992) Evolutionary relationships of a plant-pathogenic mycoplasmalike organism and Acholeplasma laidlawii deduced from 2 ribosomal protein gene sequences. J Bacteriol 174:2606\u20132611","journal-title":"J Bacteriol"},{"key":"9010_CR24","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1038\/385151a0","volume":"385","author":"W Messier","year":"1997","unstructured":"Messier W, Stewart CB (1997) Episodic adaptive evolution of primate lysozymes. Nature 385:151\u2013154","journal-title":"Nature"},{"key":"9010_CR25","doi-asserted-by":"crossref","first-page":"7123","DOI":"10.1128\/JB.186.21.7123-7133.2004","volume":"186","author":"FC Minion","year":"2004","unstructured":"Minion FC, Lefkowitz EJ, Madsen ML, Cleary BJ, Swartzell SM, Mahairas GG (2004) The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis. J Bacteriol 186:7123\u20137133","journal-title":"J Bacteriol"},{"key":"9010_CR26","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1046\/j.1365-2958.1997.6382009.x","volume":"26","author":"C Mollet","year":"1997","unstructured":"Mollet C, Drancourt M, Raoult D (1997) rpoB sequence analysis as a novel basis for bacterial identification. Mol Microbiol 26:1005\u20131011","journal-title":"Mol Microbiol"},{"key":"9010_CR27","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1038\/ng1381","volume":"36","author":"Y Nakamura","year":"2004","unstructured":"Nakamura Y, Itoh T, Matsuda H, Gojobori T (2004) Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nature Genet 36:760\u2013766","journal-title":"Nature Genet"},{"key":"9010_CR28","doi-asserted-by":"crossref","DOI":"10.7312\/nei-92038","volume-title":"Molecular evolutionary genetics","author":"M Nei","year":"1987","unstructured":"Nei M (1987) Molecular evolutionary genetics, Columbia University Press, New York"},{"key":"9010_CR29","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1038\/ng1277","volume":"36","author":"K Oshima","year":"2004","unstructured":"Oshima K, Kakizawa S, Nishigawa H, Jung HY, Wei W, Suzuki S, Arashida R, Nakata D, Miyata S, Ugaki M, Namba S (2004) Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma. Nature Genet 36:27\u201329","journal-title":"Nature Genet"},{"key":"9010_CR30","doi-asserted-by":"crossref","first-page":"2307","DOI":"10.1099\/mic.0.26427-0","volume":"149","author":"L Papazisi","year":"2003","unstructured":"Papazisi L, Gorton TS, Kutish G, Markham PF, Browning GF, Nguyen DK, Swartzell S, Madan A, Mahairas G, Geary SJ (2003) The complete genome sequence of the avian pathogen Mycoplasma gallisepticum strain R-low. Microbiology 149:2307\u20132316","journal-title":"Microbiology"},{"key":"9010_CR31","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1128\/MMBR.62.4.1094-1156.1998","volume":"62","author":"S Razin","year":"1998","unstructured":"Razin S, Yogev D, Naot Y (1998) Molecular biology and pathogenicity of mycoplasmas. Microbiol Mol Biol Rev 62:1094\u20131156","journal-title":"Microbiol Mol Biol Rev"},{"key":"9010_CR32","doi-asserted-by":"crossref","first-page":"5293","DOI":"10.1093\/nar\/gkf667","volume":"30","author":"Y Sasaki","year":"2002","unstructured":"Sasaki Y, Ishikawa J, Yamashita A, Oshima K, Kenri T, Furuya K, Yoshino C, Horino A, Shiba T, Sasaki T, Hattori M (2002) The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans. Nucleic Acids Res 30:5293\u20135300","journal-title":"Nucleic Acids Res"},{"key":"9010_CR33","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","volume":"21","author":"JD Thompson","year":"1994","unstructured":"Thompson JD, Higgins DG, Gibson TJ (1994) Clustal W - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 21:4673\u20134680","journal-title":"Nucleic Acids Res"},{"key":"9010_CR34","doi-asserted-by":"crossref","first-page":"5568","DOI":"10.1128\/JB.187.16.5568-5577.2005","volume":"187","author":"AT Vasconcelos","year":"2005","unstructured":"Vasconcelos AT, Ferreira HB, Bizarro CV, Bonatto SL, Carvalho MO, Pinto PM, Almeida DF, Almeida LG, Almeida R, Alves-Filho L, Assuncao EN, Azevedo VA, Bogo MR, Brigido MM, Brocchi M, Burity HA, Camargo AA, Camargo SS, Carepo MS, Carraro DM, de Mattos Cascardo JC, Castro LA, Cavalcanti G, Chemale G, Collevatti RG, Cunha CW, Dallagiovanna B, Dambros BP, Dellagostin OA, Falcao C, Fantinatti-Garboggini F, Felipe MS, Fiorentin L, Franco GR, Freitas NS, Frias D, Grangeiro TB, Grisard EC, Guimaraes CT, Hungria M, Jardim SN, Krieger MA, Laurino JP, Lima LF, Lopes MI, Loreto EL, Madeira HM, Manfio GP, Maranhao AQ, Martinkovics CT, Medeiros SR, Moreira MA, Neiva M, Ramalho-Neto CE, Nicolas MF, Oliveira SC, Paixao RF, Pedrosa FO, Pena SD, Pereira M, Pereira-Ferrari L, Piffer I, Pinto LS, Potrich DP, Salim AC, Santos FR, Schmitt R, Schneider MP, Schrank A, Schrank IS, Schuck AF, Seuanez HN, Silva DW, Silva R, Silva SC, Soares CM, Souza KR, Souza RC, Staats CC, Steffens MB, Teixeira SM, Urmenyi TP, Vainstein MH, Zuccherato LW, Simpson AJ, Zaha A (2005) Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae. J Bacteriol 187:5568\u20135577","journal-title":"J Bacteriol"},{"key":"9010_CR35","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1101\/gr.1673304","volume":"14","author":"J Westberg","year":"2004","unstructured":"Westberg J, Persson A, Holmberg A, Goesmann A, Lundeberg J, Johansson KE, Pettersson B, Uhlen M (2004) The genome sequence of Mycoplasma mycoides subsp mycoides SC type strain PG1(T), the causative agent of contagious bovine pleuropneumonia (CBPP). Genome Res 14:221\u2013227","journal-title":"Genome Res"},{"key":"9010_CR36","doi-asserted-by":"crossref","first-page":"4576","DOI":"10.1073\/pnas.87.12.4576","volume":"87","author":"CR Woese","year":"1990","unstructured":"Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms \u2014 proposal for the domains archaea, bacteria, and eucarya. Proc Natl Acad Sci USA 87:4576\u20134579","journal-title":"Proc Natl Acad Sci USA"},{"key":"9010_CR37","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1099\/ijs.0.02868-0","volume":"54","author":"M Wolf","year":"2004","unstructured":"Wolf M, Muller T, Dandekar T, Pollack JD (2004) Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data. Int J Syst Evol Microbiol 54:871\u2013875","journal-title":"Int J Syst Evol Microbiol"},{"key":"9010_CR38","doi-asserted-by":"crossref","first-page":"2131","DOI":"10.1099\/ijs.0.63655-0","volume":"55","author":"Y Zhao","year":"2005","unstructured":"Zhao Y, Davis RE, Lee IM (2005) Phylogenetic positions of \u2018Candidatus Phytoplasma asteris\u2019 and Spiroplasma kunkelii as inferred from multiple sets of concatenated core housekeeping proteins. Int J Syst Evol Microbiol 55:2131\u20132141","journal-title":"Int J Syst Evol Microbiol"}],"container-title":["Journal of Molecular Evolution"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00239-007-9010-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s00239-007-9010-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00239-007-9010-3","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,4,25]],"date-time":"2020-04-25T18:23:10Z","timestamp":1587838990000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s00239-007-9010-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,8,9]]},"references-count":38,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2007,10,9]]}},"alternative-id":["9010"],"URL":"https:\/\/doi.org\/10.1007\/s00239-007-9010-3","relation":{},"ISSN":["0022-2844","1432-1432"],"issn-type":[{"value":"0022-2844","type":"print"},{"value":"1432-1432","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,8,9]]}}}