Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution

Dagan and Martin 1010.1073/pnas.0606318104

Supporting Information

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Table 4
SI Figure 4
SI Figure 5
SI Figure 6
Table 5
SI Figure 7
SI Figure 8
SI Figure 9
SI Figure 10
SI Table 6

SI Figure 4

Fig. 4. Distribution of gene family size using different amino acid identity cutoffs (plotted using a bin size of 5).

SI Figure 5

Fig. 5. Pairwise proportions of shared genes (color-coded as in scale) for all genome pairs using a random species order rather than species ordered by taxonomic groupings. The same random order was used to produce the random tree.

SI Figure 6

Fig. 6. Reference tree for the rRNA operon, reconstructed by dnaml (see Newick format in SI Table 6).

SI Figure 7

Fig. 7. Ancestral genome sizes reconstructed for different LGT allowances using an NJ reference tree. The color of the nodes the inferred ancestral genome size.

SI Figure 8

Fig. 8. Ancestral genome sizes reconstructed for different LGT allowances using a random reference tree (Newick topology in SI Table 6). The color of the nodes corresponds to the inferred ancestral genome (notice the different scale as compared to other reference trees).

SI Figure 9

Fig. 9. Calculated mean numbers of additional origins (LGTs) if small or large protein families are excluded from analysis. The black line shows the frequency distribution of gene family sizes. The colored lines indicate the mean number of LGTs under different models inferred from the reference tree for cumulative sample as collected from left to right. Note that the number of possible LGTs is much larger for large than for small gene families. Under our full-benefit assumptions, at most n-1 LGTs can be inferred for a gene family present in n genomes. These numbers reflect only the gene distribution patterns relative to the reference tree; they have not been constrained by the comparison of inferred of ancestral genome sizes to the distribution of modern genome sizes. (a) The effect of excluding large gene families (cumulative sample for ascending genome size). Small gene families reduce the mean number of inferred LGT events not only because they cannot accept many LGTs to produce a PAP that maps exactly upon the reference tree but also because they are the most frequent genes families across genomes. (b) The effect of excluding small gene families (cumulative sample for ascending genome size). The drop at 168 genomes corresponds to the number of eubacteria in the genome sample.

SI Figure 10

Fig. 10. (a) Frequency of gene origins reconstructed for different LGT allowances. The color of the nodes corresponds to the number of gene origins. (b) Frequencey of gene losses reconstructed for different LGT allowances. The color of the nodes corresponds to the number of gene losses.

Table 6. Newick formats of the reference trees

DnaML tree (the reference tree)

((Aaeolicus,(Tmaritima,(Tthermophilus,(Pirellula,(((((((Dvulgaris,(Gsulfurreducens,(Dpsychrophila,Bbacteriovorus))),(Dradiodurans,((((((Rtyphi,Rprowazekii),Rfelis),Rconorii),(Wendosymbiont,(Eruminantium,Amarginale))),(((Goxydans,Ccrescentus),(Zmobilis,((Spomeroyi,(Rpalustris,Bjaponicum)),((Mloti,(Smeliloti,Atumefaciens)),((Bquintana,Bhenselae),((Bmelitensis,Babortus),Bsuis)))))),CPelagibacter)),(Ftularensis,(Cburnetii,(((Mcapsulatus,((Xfastidiosa,(Xcitri,(Xoryzae,Xcampestris))),(((Nmeningitidis,Ngonorrhoeae),Cviolaceum),(((Neuropaea,((Rsolanacearum,Reutropha),(Bpseudomallei,Bmallei))),(Bpertussis,(Bparapertussis,Bbronchiseptica))),(Daromatica,Azoarcus))))),Lpneumophila),(((Iloihiensis,Cpsychrerythraea),((((Hinfluenzae,(Msucciniciproducens,Pmultocida)),Hducreyi),((((Styphimurium,(Styphi,Senterica)),(Sflexneri,Ecoli)),(((Ypseudotuberculosis,Ypestis),Pluminescens),Ecarotovora)),((Wbrevipalpis,Bfloridanus),(Buchnera,Baphidicola)))),(Soneidensis,(((Vcholerae,(Vvulnificus,Vparahaemolyticus)),Vfischeri),Pprofundum)))),((((Psyringae,Pputida),Pfluorescens),Paeruginosa),(Parcticum,Acinetobacter))))))))),((Ctepidum,(Pgingivalis,(Bthetaiotaomicron,Bfragilis))),((Wsuccinogenes,(Hpylori,Hhepaticus)),Cjejuni))),((Linterrogans,((Tpallidum,Tdenticola),(Bgarinii,Bburgdorferi))),(Parachlamydia,((Ctrachomatis,Cmuridarum),(Cpneumoniae,(Ccaviae,Cabortus)))))),((Oyellows,((Mmobile,((Msynoviae,Mpulmonis),Mhyopneumoniae)),((Mmycoides,Mflorum),(((Mpneumoniae,Mgenitalium),Mgallisepticum),(Mpenetrans,Uurealyticum))))),Fnucleatum)),((Gkaustophilus,(((((Shaemolyticus,(Sepidermidis,Saureus)),((Lmonocytogenes,Linnocua),((Lplantarum,(Ljohnsonii,Lacidophilus)),(Efaecalis,(((Sthermophilum,(Spneumoniae,Smutans)),(Sagalactiae,Spyogenes)),Llactis))))),((Bthuringiensis,Bcereus),Banthracis)),(Bsubtilis,Blicheniformis)),((Bhalodurans,Bclausii),Oiheyensis))),((Cperfringens,(Ctetani,Cacetobutylicum)),(Ttengcongensis,Sthermophilus)))),(((Pacnes,Blongum),((((Nfarcinica,(Mleprae,(Mavium,(Mtuberculosis,Mbovis)))),((Cglutamicum,Cefficiens),(Cdiphtheriae,Cjeikeium))),(Tfusca,(Scoelicolor,Savermitilis))),(Twhipplei,Lxyli))),((((Telongatus,(Selongatus,(Synechococcus,Pmarinus))),(Synechocystis,Nostoc)),Gviolaceus),Dethenogenes))))))),(Nequitans,((Paerophilum,(Apernix,((Tacidophilum,Stokodaii),(Ssolfataricus,Sacidocaldarius)))),(Mkandleri,((Tkodakaraensis,((Pabyssi,Phorikoshii),Pfuriosus)),(Mthermoautotrophicum,((((Tvolcanium,Ptorridus),((Mmazei,Macetivorans),(Hmarismortui,Halobacterium))),Afulgidus),(Mmaripaludis,Mjannaschii))))))));

NJ tree

((((((((Afulgidus,(Mkandleri,(((Pabyssi,Phorikoshii),Pfuriosus),Tkodakaraensis))),(Mjannaschii,Mmaripaludis)),Mthermoautotrophicum),((Halobacterium,Hmarismortui),(Macetivorans,Mmazei))),(Ptorridus,Tvolcanium)),(((Apernix,Paerophilum),(Sacidocaldarius,Ssolfataricus)),Nequitans)),(Stokodaii,Tacidophilum)),(Bgarinii,(Dradiodurans,(((Aaeolicus,Tmaritima),Tthermophilus),(((Blongum,((((((Cdiphtheriae,(Cefficiens,Cglutamicum)),Cjeikeium),(((Mavium,(Mbovis,Mtuberculosis)),Mleprae),Nfarcinica)),((Savermitilis,Scoelicolor),Tfusca)),Pacnes),(Lxyli,Twhipplei))),(Dethenogenes,(Gviolaceus,((Nostoc,Synechocystis),(((Pmarinus,Synechococcus),Selongatus),Telongatus))))),((((((Cabortus,Ccaviae),Cpneumoniae),(Cmuridarum,Ctrachomatis)),Parachlamydia),Pirellula),(((((((((((((Banthracis,Bcereus),Bthuringiensis),(Blicheniformis,Bsubtilis)),Oiheyensis),(Bclausii,Bhalodurans)),((Efaecalis,Lplantarum),(Linnocua,Lmonocytogenes))),((Saureus,Sepidermidis),Shaemolyticus)),Gkaustophilus),((Lacidophilus,Ljohnsonii),(Llactis,((((Sagalactiae,Spyogenes),Sthermophilus),Spneumoniae),Smutans)))),(Sthermophilum,Ttengcongensis)),((Cacetobutylicum,Ctetani),Cperfringens)),(Fnucleatum,((((Mflorum,Mmycoides),(((Mgallisepticum,(Mgenitalium,Mpneumoniae)),Uurealyticum),Mpenetrans)),((Mhyopneumoniae,Mmobile),(Mpulmonis,Msynoviae))),Oyellows))),((((((((((((Acinetobacter,Parcticum),(Paeruginosa,((Pfluorescens,Psyringae),Pputida))),((Cburnetii,Lpneumophila),Mcapsulatus)),((((((Baphidicola,Buchnera),(Bfloridanus,Wbrevipalpis)),(((Ecarotovora,(Ypestis,Ypseudotuberculosis)),((Ecoli,Sflexneri),(Senterica,(Styphi,Styphimurium)))),Pluminescens)),(((Pprofundum,Vfischeri),(Vcholerae,(Vparahaemolyticus,Vvulnificus))),Soneidensis)),(Hducreyi,((Hinfluenzae,Pmultocida),Msucciniciproducens))),(Cpsychrerythraea,Iloihiensis))),((Xcampestris,(Xcitri,Xoryzae)),Xfastidiosa)),((((Azoarcus,Daromatica),(((Bbronchiseptica,Bparapertussis),Bpertussis),((Bmallei,Bpseudomallei),(Reutropha,Rsolanacearum)))),Neuropaea),(Cviolaceum,(Ngonorrhoeae,Nmeningitidis)))),Ftularensis),(((((Amarginale,Eruminantium),Wendosymbiont),((Rconorii,Rfelis),(Rprowazekii,Rtyphi))),CPelagibacter),(((((((Atumefaciens,Smeliloti),Mloti),((Babortus,(Bmelitensis,Bsuis)),(Bhenselae,Bquintana))),(Bjaponicum,Rpalustris)),Spomeroyi),Zmobilis),(Ccrescentus,Goxydans)))),(Bbacteriovorus,((Dpsychrophila,Gsulfurreducens),Dvulgaris))),(Cjejuni,((Hhepaticus,Hpylori),Wsuccinogenes))),(((Bfragilis,Bthetaiotaomicron),Pgingivalis),Ctepidum)),((Bburgdorferi,(Tdenticola,Tpallidum)),Linterrogans)))))))));

Random tree

((Acinetobacter,((Dpsychrophila,(Cpneumoniae,((Iloihiensis,Ctrachomatis),(Mflorum,Sthermophilus)))),(Xfastidiosa,((Telongatus,((Bthuringiensis,Bfragilis),Spomeroyi)),(Sagalactiae,((((Vfischeri,Tthermophilus),((Mhyopneumoniae,Ypseudotuberculosis),(Styphimurium,Cpsychrerythraea))),Bgarinii),(Wsuccinogenes,Banthracis))))))),(Pfuriosus,(Scoelicolor,(Pmarinus,(Tvolcanium,(((((((Ssolfataricus,(Shaemolyticus,(Bbronchiseptica,Lmonocytogenes))),(Dradiodurans,((((((Lxyli,Amarginale),Oiheyensis),Uurealyticum),(Pgingivalis,(Mthermoautotrophicum,Parachlamydia))),(((Selongatus,Gviolaceus),(Bhenselae,((Aaeolicus,(Mloti,Mtuberculosis)),((Mpneumoniae,(Cefficiens,Mmazei)),((Smeliloti,Mleprae),((Sthermophilum,Rconorii),Msynoviae)))))),Efaecalis)),(Cabortus,(Cviolaceum,(((Smutans,((Wendosymbiont,(Bthetaiotaomicron,(Xoryzae,Senterica))),(((Nmeningitidis,Pabyssi),Cmuridarum),(((Hducreyi,((Ptorridus,Sacidocaldarius),(Reutropha,Mbovis))),(Nfarcinica,(Tfusca,Ctepidum))),(Babortus,Rpalustris))))),Lpneumophila),(((Fnucleatum,Bquintana),((((Hinfluenzae,(Msucciniciproducens,Pmultocida)),Dvulgaris),((((Ccaviae,(Styphi,Mmobile)),(Bpseudomallei,Bbacteriovorus)),(((Nostoc,Hhepaticus),Pluminescens),Baphidicola)),((Pacnes,Cdiphtheriae),(Mjannaschii,Bclausii)))),(Goxydans,(((Vcholerae,(Sepidermidis,Tkodakaraensis)),Ljohnsonii),Cburnetii)))),((((Stokodaii,Pputida),Pfluorescens),Psyringae),(Parcticum,Apernix))))))))),((Ngonorrhoeae,(Savermitilis,(Xcampestris,Bmelitensis))),((Ttengcongensis,(Hpylori,Mpulmonis)),Ftularensis))),((Linterrogans,((Vvulnificus,Neuropaea),(Paerophilum,Bburgdorferi))),(Cglutamicum,((Bsuis,Rsolanacearum),(Ecarotovora,(CPelagibacter,Halobacterium)))))),((Bsubtilis,((Macetivorans,((Rfelis,Atumefaciens),Pprofundum)),((Bjaponicum,Blongum),(((Hmarismortui,Spyogenes),Mgallisepticum),(Sflexneri,Blicheniformis))))),Afulgidus)),((Mmaripaludis,(((((Bfloridanus,(Mgenitalium,Synechococcus)),((Tdenticola,Pirellula),((Lplantarum,(Paeruginosa,Cjeikeium)),(Rprowazekii,(((Gsulfurreducens,(Spneumoniae,Gkaustophilus)),(Rtyphi,Tacidophilum)),Saureus))))),((Azoarcus,Mcapsulatus),Mpenetrans)),(Mavium,Wbrevipalpis)),((Zmobilis,Tpallidum),Ecoli))),((Ypestis,(Bhalodurans,Ctetani)),(Mmycoides,Daromatica)))),(((Llactis,Xcitri),((((Soneidensis,(Nequitans,(Buchnera,(Oyellows,Bmallei)))),((Mkandleri,Phorikoshii),(Ccrescentus,Bpertussis))),(Vparahaemolyticus,(Eruminantium,Cjejuni))),(Twhipplei,Bparapertussis))),((((Linnocua,(Cacetobutylicum,(Tmaritima,Lacidophilus))),(Synechocystis,Dethenogenes)),Cperfringens),Bcereus))))))));

Ribosomal proteins tree

((Nequitans,(((Mthermoautotrophicum,Mkandleri),(((Tvolcanium,Tacidophilum),Ptorridus),((Afulgidus,(((Hmarismortui,Halobacterium),(Mmazei,Macetivorans)),(Mmaripaludis,Mjannaschii))),(Tkodakaraensis,(Pfuriosus,(Phorikoshii,Pabyssi)))))),(Paerophilum,(((Stokodaii,Ssolfataricus),Sacidocaldarius),Apernix)))),((((((((Tthermophilus,Dradiodurans),(Ttengcongensis,((Cacetobutylicum,(Ctetani,Cperfringens)),Gsulfurreducens))),Sthermophiluslumlus),((Wendosymbiont,(Eruminantium,Amarginale)),((Pacnes,(((Twhipplei,Lxyli),(((Tfusca,(Scoelicolor,Savermitilis)),(Nfarcinica,(Mleprae,((Mtuberculosis,Mbovis),Mavium)))),((Cglutamicum,Cefficiens),(Cjeikeium,Cdiphtheriae)))),Blongum)),(((Dpsychrophila,(Oyellows,(Fnucleatum,Dethenogenes))),((((Oiheyensis,(((Gkaustophilus,Bclausii),((Banthracis,Bcereus),Bthuringiensis)),(Blicheniformis,Bsubtilis))),(Lmonocytogenes,Linnocua)),(((Lplantarum,(Ljohnsonii,Lacidophilus)),((((Sthermophi,Spyogenes),Spneumoniae),(Smutans,Sagalactiae)),Llactis)),(Pirellula,Efaecalis))),((Shaemolyticus,Sepidermidis),Saureus))),((Mmycoides,Mflorum),(((Selongatus,((Synechocystis,Nostoc),(Telongatus,(Synechococcus,Pmarinus)))),Gviolaceus),Bhalodurans)))))),(((CPelagibacter,((Zmobilis,(((Rfelis,((Rtyphi,Rprowazekii),Rconorii)),Ccrescentus),(Goxydans,((((Bsuis,(Babortus,Bmelitensis)),(Mloti,(Bquintana,Bhenselae))),(Smeliloti,Atumefaciens)),(Rpalustris,Bjaponicum))))),Spomeroyi)),(((Parachlamydia,((Ccaviae,(Ctrachomatis,Cmuridarum)),(Cpneumoniae,Cabortus))),Bbacteriovorus),((((Msynoviae,(Mpulmonis,Mmobile)),Mhyopneumoniae),((Mpneumoniae,Mgenitalium),((Uurealyticum,Mpenetrans),Mgallisepticum))),(Pgingivalis,(Bthetaiotaomicron,Bfragilis))))),(Dvulgaris,Ctepidum))),((Cjejuni,(Wsuccinogenes,(Hpylori,Hhepaticus))),((((Tpallidum,Tdenticola),(Bgarinii,Bburgdorferi)),Linterrogans),((Cburnetii,Lpneumophila),(Parcticum,(((Ftularensis,((Mcapsulatus,((Paeruginosa,((Psyringae,Pfluorescens),Pputida)),(Xfastidiosa,(Xoryzae,(Xcitri,Xcampestris))))),(Iloihiensis,((Soneidensis,(((Vparahaemolyticus,(Vfischeri,Pprofundum)),(Vcholerae,Vvulnificus)),((Hducreyi,((Msucciniciproducens,Hinfluenzae),Pmultocida)),((((Wbrevipalpis,Bfloridanus),(Baphidicola,Buchnera)),((Sflexneri,Ecoli),(Senterica,(Styphimurium,Styphi)))),(Pluminescens,((Ypseudotuberculosis,Ypestis),Ecarotovora)))))),Cpsychrerythraea)))),((Cviolaceum,(Daromatica,(((Bpseudomallei,Bmallei),((Rsolanacearum,Reutropha),(Neuropaea,Azoarcus))),((Bpertussis,Bparapertussis),Bbronchiseptica)))),(Nmeningitidis,Ngonorrhoeae))),Acinetobacter)))))),Tmaritima),Aaeolicus))

ML + cv=2

((Tmaritima,(Fnucleatum,(((((Telongatus,(Selongatus,(Synechococcus,Pmarinus))),(Synechocystis,Nostoc)),Gviolaceus),Dethenogenes),((((Scoelicolor,Savermitilis),((Tfusca,((Nfarcinica,(Mleprae,(Mavium,(Mtuberculosis,Mbovis)))),((Cglutamicum,Cefficiens),(Cdiphtheriae,Cjeikeium)))),((Twhipplei,Lxyli),(Pacnes,Blongum)))),((((Dvulgaris,(Gsulfurreducens,(Dpsychrophila,Bbacteriovorus))),(((((Mcapsulatus,(Xfastidiosa,(Xcitri,(Xoryzae,Xcampestris)))),Ftularensis),((((Iloihiensis,Cpsychrerythraea),(Soneidensis,((((Vcholerae,(Vvulnificus,Vparahaemolyticus)),Vfischeri),Pprofundum),(((Msucciniciproducens,(Pmultocida,Hinfluenzae)),Hducreyi),((((Styphimurium,(Styphi,Senterica)),(Sflexneri,Ecoli)),(((Ypseudotuberculosis,Ypestis),Pluminescens),Ecarotovora)),((Buchnera,Baphidicola),(Wbrevipalpis,Bfloridanus))))))),((((Psyringae,Pputida),Pfluorescens),Paeruginosa),(Parcticum,Acinetobacter))),(Cburnetii,Lpneumophila))),(Dradiodurans,((Daromatica,Azoarcus),(((Nmeningitidis,Ngonorrhoeae),Cviolaceum),(Neuropaea,((Bpertussis,(Bbronchiseptica,Bparapertussis)),((Rsolanacearum,Reutropha),(Bpseudomallei,Bmallei)))))))),(((CPelagibacter,Goxydans),(((Zmobilis,Spomeroyi),((Rpalustris,Bjaponicum),(Mloti,(((Babortus,(Bsuis,Bmelitensis)),(Bquintana,Bhenselae)),(Smeliloti,Atumefaciens))))),Ccrescentus)),((((Rtyphi,Rprowazekii),Rfelis),Rconorii),(Wendosymbiont,(Eruminantium,Amarginale)))))),(((Wsuccinogenes,(Hpylori,Hhepaticus)),Cjejuni),(Ctepidum,(Pgingivalis,(Bthetaiotaomicron,Bfragilis))))),((Linterrogans,((Tpallidum,Tdenticola),(((Tacidophilum,Stokodaii),Bgarinii),Bburgdorferi))),(Pirellula,(Parachlamydia,((Ctrachomatis,Cmuridarum),(Cpneumoniae,(Ccaviae,Cabortus)))))))),(((Tthermophilus,Oyellows),(((Mmobile,Mhyopneumoniae),(Msynoviae,Mpulmonis)),(((Uurealyticum,Mpenetrans),((Mpneumoniae,Mgenitalium),Mgallisepticum)),(Mmycoides,Mflorum)))),(((Ttengcongensis,Sthermoph),(Gkaustophilus,((Bhalodurans,Bclausii),(Oiheyensis,((Bsubtilis,Blicheniformis),(((Shaemolyticus,(Sepidermidis,Saureus)),((Lmonocytogenes,Linnocua),((Efaecalis,((Spyogenes,(Sagalactiae,(Sthermophiluslumlus,(Spneumoniae,Smutans)))),Llactis)),(Lplantarum,(Ljohnsonii,Lacidophilus))))),(Banthracis,(Bthuringiensis,Bcereus)))))))),(Cperfringens,(Ctetani,Cacetobutylicum)))))))),(((Nequitans,(Apernix,(Paerophilum,(Ssolfataricus,Sacidocaldarius)))),(Mkandleri,((Tkodakaraensis,((Pabyssi,Phorikoshii),Pfuriosus)),((Mthermoautotrophicum,(Mmaripaludis,Mjannaschii)),(((Tvolcanium,Ptorridus),((Mmazei,Macetivorans),(Hmarismortui,Halobacterium))),Afulgidus))))),Aaeolicus));

ML + cv=3

(((((((((Tthermophilus,Dradiodurans),(Ttengcongensis,((Cacetobutylicum,(Ctetani,Cperfringens)),Gsulfurreducens))),Sthermophilum),((Wendosymbiont,(Eruminantium,Amarginale)),((Pacnes,(((Twhipplei,Lxyli),(((Tfusca,(Scoelicolor,Savermitilis)),(Nfarcinica,(Mleprae,((Mtuberculosis,Mbovis),Mavium)))),((Cglutamicum,Cefficiens),(Cjeikeium,Cdiphtheriae)))),Blongum)),(((Dpsychrophila,(Oyellows,(Fnucleatum,Dethenogenes))),((((Oiheyensis,(((Gkaustophilus,Bclausii),((Banthracis,Bcereus),Bthuringiensis)),(Blicheniformis,Bsubtilis))),(Lmonocytogenes,Linnocua)),(((Lplantarum,(Ljohnsonii,Lacidophilus)),((((Sthermophilus,Spyogenes),Spneumoniae),(Smutans,Sagalactiae)),Llactis)),(Pirellula,Efaecalis))),((Shaemolyticus,Sepidermidis),Saureus))),((Mmycoides,Mflorum),(((Selongatus,((Synechocystis,Nostoc),(Telongatus,(Synechococcus,Pmarinus)))),Gviolaceus),Bhalodurans)))))),(((CPelagibacter,((Zmobilis,(((Rfelis,((Rtyphi,Rprowazekii),Rconorii)),Ccrescentus),(Goxydans,((((Bsuis,(Babortus,Bmelitensis)),(Mloti,(Bquintana,Bhenselae))),(Smeliloti,Atumefaciens)),(Rpalustris,Bjaponicum))))),Spomeroyi)),(((Parachlamydia,((Ccaviae,(Ctrachomatis,Cmuridarum)),(Cpneumoniae,Cabortus))),Bbacteriovorus),((((Msynoviae,(Mpulmonis,Mmobile)),Mhyopneumoniae),((Mpneumoniae,Mgenitalium),((Uurealyticum,Mpenetrans),Mgallisepticum))),(Pgingivalis,(Bthetaiotaomicron,Bfragilis))))),(Dvulgaris,Ctepidum))),((Cjejuni,(Wsuccinogenes,(Hpylori,Hhepaticus))),((((Tpallidum,Tdenticola),(Bgarinii,Bburgdorferi)),Linterrogans),((Cburnetii,Lpneumophila),(Parcticum,(((Ftularensis,((Mcapsulatus,((Paeruginosa,((Psyringae,Pfluorescens),Pputida)),(Xfastidiosa,(Xoryzae,(Xcitri,Xcampestris))))),(Iloihiensis,((Soneidensis,(((Vparahaemolyticus,(Vfischeri,Pprofundum)),(Vcholerae,Vvulnificus)),((Hducreyi,((Msucciniciproducens,Hinfluenzae),Pmultocida)),((((Wbrevipalpis,Bfloridanus),(Baphidicola,Buchnera)),((Sflexneri,Ecoli),(Senterica,(Styphimurium,Styphi)))),(Pluminescens,((Ypseudotuberculosis,Ypestis),Ecarotovora)))))),Cpsychrerythraea)))),((Cviolaceum,(Daromatica,(((Bpseudomallei,Bmallei),((Rsolanacearum,Reutropha),(Neuropaea,Azoarcus))),((Bpertussis,Bparapertussis),Bbronchiseptica)))),(Nmeningitidis,Ngonorrhoeae))),Acinetobacter)))))),Tmaritima),Aaeolicus),(Nequitans,(((Mthermoautotrophicum,Mkandleri),(((Tvolcanium,Tacidophilum),Ptorridus),((Afulgidus,(((Hmarismortui,Halobacterium),(Mmazei,Macetivorans)),(Mmaripaludis,Mjannaschii))),(Tkodakaraensis,(Pfuriosus,(Phorikoshii,Pabyssi)))))),(Paerophilum,(((Stokodaii,Ssolfataricus),Sacidocaldarius),Apernix)))));