Traditional phylogenetic tree reconstruction is based on point mutations of a single gene. This approach is hardly suitable for genomes whose genes are almost identical and barely captures evolutionary scenarios. To better understand the evolution of organisms, we must not only consider the organisms' gene content but also their gene order. Here, 225 complete bacterial genomic sequences were downloaded from the National Center for Biotechnology Information (NCBI)[1]. Each individual proteome was blasted against the collection and provided a number of homologous genes shared with others. Then, the synteny (order of genes) of each two genomes can be considered as two signed permutations. One permutation can be rearranged into another in minimum finite steps, called reversal distance. Applying distance-based phylogenetic tree reconstruction tool on these distances yields a phylogenetic tree that may provide new insights into the evolution.

PGRAPH employs deep theoretical results of Hannenhalli and Pevzner[2] to calculate a reversal distance between any two genomes in our database. However, the theory does not specify when and where the synteny blocks should be reversed (flipped) in order to achieve the minimum distance. Here, PGRAPH is able to illustrate one such scenario. Please be aware that there are many possible flipping scenarios, we have yet known which one really happened in the evolution of an organism.

When comparing two genomes and considering their orthologous genes, their gene orders can be modeled as a signed permutation. The order of these genes of one genome can be rearranged into another by consecutively choosing a synteny block and reversing that block and its orientation one at a time, e.g.

Phylogenetic Tree Analysis

Please choose three or more genomes to see a phylogenetic tree. PGRAPH uses the simple neighbor-joining tool of the PHYLIP package[3] to reconstruct the tree from reversal distance data. At the resulting page, you will also be able to download the corresponding distance matrix and Newick format tree for further analysis with other more powerful phylogenetic software.

Acinetobacter_sp_ADP1 Aeropyrum_pernix Agrobacterium_tumefaciens_C58_Cereon Agrobacterium_tumefaciens_C58_UWash Anaplasma_marginale_St_Maries Aquifex_aeolicus Archaeoglobus_fulgidus Azoarcus_sp_EbN1 Bacillus_anthracis_A2012 Bacillus_anthracis_Ames Bacillus_anthracis_Ames_0581 Bacillus_anthracis_str_Sterne Bacillus_cereus_ATCC14579 Bacillus_cereus_ATCC_10987 Bacillus_cereus_ZK Bacillus_clausii_KSM-K16 Bacillus_halodurans Bacillus_licheniformis_ATCC_14580 Bacillus_licheniformis_DSM_13 Bacillus_subtilis Bacillus_thuringiensis_konkukian Bacteroides_fragilis_NCTC_9434 Bacteroides_fragilis_YCH46 Bacteroides_thetaiotaomicron_VPI-5482 Bartonella_henselae_Houston-1 Bartonella_quintana_Toulouse Bdellovibrio_bacteriovorus Bifidobacterium_longum Blochmannia_floridanus Bordetella_bronchiseptica Bordetella_parapertussis Bordetella_pertussis Borrelia_burgdorferi Borrelia_garinii_PBi Bradyrhizobium_japonicum Brucella_melitensis Brucella_suis_1330 Buchnera_aphidicola Buchnera_aphidicola_Sg Buchnera_sp Burkholderia_mallei_ATCC_23344 Burkholderia_pseudomallei_K96243 Campylobacter_jejuni Campylobacter_jejuni_RM1221 Caulobacter_crescentus Chlamydia_muridarum Chlamydia_trachomatis Chlamydophila_caviae Chlamydophila_pneumoniae_AR39 Chlamydophila_pneumoniae_CWL029 Chlamydophila_pneumoniae_J138 Chlamydophila_pneumoniae_TW_183 Chlorobium_tepidum_TLS Chromobacterium_violaceum Clostridium_acetobutylicum Clostridium_perfringens Clostridium_tetani_E88 Corynebacterium_diphtheriae Corynebacterium_efficiens_YS-314 Corynebacterium_glutamicum Coxiella_burnetii Dehalococcoides_ethenogenes_195 Deinococcus_radiodurans Desulfotalea_psychrophila_LSv54 Desulfovibrio_vulgaris_Hildenborough Ehrlichia_ruminantium_Gardel Ehrlichia_ruminantium_Welgevonden Ehrlichia_ruminantium_str._Welgevonden Enterococcus_faecalis_V583 Erwinia_carotovora_atroseptica_SCRI1043 Escherichia_coli_CFT073 Escherichia_coli_K12 Escherichia_coli_O157H7 Escherichia_coli_O157H7_EDL933 Francisella_tularensis_tularensis Fusobacterium_nucleatum Geobacillus_kaustophilus_HTA426 Geobacter_sulfurreducens Gloeobacter_violaceus Gluconobacter_oxydans_621H Haemophilus_ducreyi_35000HP Haemophilus_influenzae Haloarcula_marismortui_ATCC_43049 Halobacterium_sp Helicobacter_hepaticus Helicobacter_pylori_26695 Helicobacter_pylori_J99 Idiomarina_loihiensis_L2TR Lactobacillus_acidophilus_NCFM Lactobacillus_johnsonii_NCC_533 Lactobacillus_plantarum Lactococcus_lactis Legionella_pneumophila_Lens Legionella_pneumophila_Paris Legionella_pneumophila_Philadelphia_1 Leifsonia_xyli_xyli_CTCB0 Leptospira_interrogans_serovar_Copenhageni Leptospira_interrogans_serovar_Lai Listeria_innocua Listeria_monocytogenes Listeria_monocytogenes_4b_F2365 Mannheimia_succiniciproducens_MBEL55E Mesoplasma_florum_L1 Mesorhizobium_loti Methanobacterium_thermoautotrophicum Methanococcus_jannaschii Methanococcus_maripaludis_S2 Methanopyrus_kandleri Methanosarcina_acetivorans Methanosarcina_mazei Methylococcus_capsulatus_Bath Mycobacterium_avium_paratuberculosis Mycobacterium_bovis Mycobacterium_leprae Mycobacterium_tuberculosis_CDC1551 Mycobacterium_tuberculosis_H37Rv Mycoplasma_gallisepticum Mycoplasma_genitalium Mycoplasma_hyopneumoniae_232 Mycoplasma_mobile_163K Mycoplasma_mycoides Mycoplasma_penetrans Mycoplasma_pneumoniae Mycoplasma_pulmonis Nanoarchaeum_equitans Neisseria_gonorrhoeae_FA_1090 Neisseria_meningitidis_MC58 Neisseria_meningitidis_Z2491 Nitrosomonas_europaea Nocardia_farcinica_IFM10152 Nostoc_sp Oceanobacillus_iheyensis Onion_yellows_phytoplasma Parachlamydia_sp_UWE25 Pasteurella_multocida Photobacterium_profundum_SS9 Photorhabdus_luminescens Picrophilus_torridus_DSM_9790 Pirellula_sp Porphyromonas_gingivalis_W83 Prochlorococcus_marinus_CCMP1375 Prochlorococcus_marinus_MED4 Prochlorococcus_marinus_MIT9313 Propionibacterium_acnes_KPA171202 Pseudomonas_aeruginosa Pseudomonas_putida_KT2440 Pseudomonas_syringae Pyrobaculum_aerophilum Pyrococcus_abyssi Pyrococcus_furiosus Pyrococcus_horikoshii Ralstonia_solanacearum Rhodopseudomonas_palustris_CGA009 Rickettsia_conorii Rickettsia_prowazekii Rickettsia_typhi_wilmington Salmonella_enterica_Paratypi_ATCC_9150 Salmonella_typhi Salmonella_typhi_Ty2 Salmonella_typhimurium_LT2 Shewanella_oneidensis Shigella_flexneri_2a Shigella_flexneri_2a_2457T Silicibacter_pomeroyi_DSS-3 Sinorhizobium_meliloti Staphylococcus_aureus_COL Staphylococcus_aureus_MW2 Staphylococcus_aureus_Mu50 Staphylococcus_aureus_N315 Staphylococcus_aureus_aureus_MRSA252 Staphylococcus_aureus_aureus_MSSA476 Staphylococcus_epidermidis_ATCC_12228 Staphylococcus_epidermidis_RP62A Streptococcus_agalactiae_2603 Streptococcus_agalactiae_NEM316 Streptococcus_mutans Streptococcus_pneumoniae_R6 Streptococcus_pneumoniae_TIGR4 Streptococcus_pyogenes_M1_GAS Streptococcus_pyogenes_MGAS10394 Streptococcus_pyogenes_MGAS315 Streptococcus_pyogenes_MGAS8232 Streptococcus_pyogenes_SSI-1 Streptococcus_thermophilus_CNRZ1066 Streptococcus_thermophilus_LMG_18311 Streptomyces_avermitilis Streptomyces_coelicolor Sulfolobus_solfataricus Sulfolobus_tokodaii Symbiobacterium_thermophilum_IAM14863 Synechococcus_elongatus_PCC_6301 Synechococcus_sp_WH8102 Synechocystis_PCC6803 Thermoanaerobacter_tengcongensis Thermococcus_kodakaraensis_KOD1 Thermoplasma_acidophilum Thermoplasma_volcanium Thermosynechococcus_elongatus Thermotoga_maritima Thermus_thermophilus_HB27 Thermus_thermophilus_HB8 Treponema_denticola_ATCC_35405 Treponema_pallidum Tropheryma_whipplei_TW08_27 Tropheryma_whipplei_Twist Ureaplasma_urealyticum Vibrio_cholerae Vibrio_fischeri_ES114 Vibrio_parahaemolyticus Vibrio_vulnificus_CMCP6 Vibrio_vulnificus_YJ016 Wigglesworthia_brevipalpis Wolbachia_endosymbiont_of_Brugia_malayi_TRS Wolbachia_endosymbiont_of_Drosophila_melanogaster Wolinella_succinogenes Xanthomonas_campestris Xanthomonas_citri Xanthomonas_oryzae_KACC10331 Xylella_fastidiosa Xylella_fastidiosa_Temecula1 Yersinia_pestis_CO92 Yersinia_pestis_KIM Yersinia_pestis_biovar_Mediaevails Yersinia_pseudotuberculosis_IP32953 Zymomonas_mobilis_ZM4

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