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Supplementary Information K-mer similarity, networks of microbial genomes and taxonomic rank Guillaume Bernard, Paul Greenfield, Mark A. Ragan, Cheong Xin Chan. Supplementary Figures Legends # Supplementary Figure S1: P- network of prokaryote phyla using !" with k=25, based on rRNAs. Edges represent connections between isolates of two phyla. The node size is proportional to the number of isolates in a phylum. Distance threshold = 6. Supplementary Figure S2: PCA analysis performed on the raw data of the COG categories profile for each genus. Each phylum is color-coded. Supplementary Figure S3: PCA analysis performed on the raw data of the COG categories profile for each genus. Each genus is color-coded according to the number of isolates. Supplementary Figure S4: PCA analysis performed on the normalised counts of center-scaled COG categories. Each phylum is color-coded. Supplementary Tables Legends Supplementary Table S1: List of the 2785 isolates used in this analysis. Supplementary Table S2: Network analysis of the I-network for 2705 complete genomes of bacteria and archaea. Supplementary Table S3: Network analysis of the I-network for 2616 genomes of bacteria and archaea, with rRNA genes removed. Supplementary Table S4: Network analysis of the rRNA gene sequences I-network of 2616 bacterial and archaeal isolates. Supplementary Table S5: Network analysis of the plasmid genomes I-network of 921 bacterial and plasmid genomes. Supplementary Table S6: Statistics of core k-mers for 151 genera. Supplementary Table S7: COG category profiles for 16 phyla. 1 Figure S1 Archaea Figure S2 Figure S3 Figure S4 Supplementary Table S1 Name RefSeq Uid Kingdom Phylum Class Order Familly Genus _Cellvibrio__gilvus_ATCC_13127 68143 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Cellulomonadaceae _Clostridium__sticklandii 59585 Bacteria Firmicutes Clostridia Clostridiales Peptostreptococcaceae Peptoclostridium _Nostoc_azollae__0708 49725 Bacteria Cyanobacteria Nostocales Nostocaceae Trichormus _Ruminococcus__obeum 197165 Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Blautia _Ruminococcus__torques 197166 Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Blautia Acaryochloris_marina_MBIC11017 58167 Bacteria Cyanobacteria Oscillatoriophycideae Chroococcales Acaryochloris Acetobacter_pasteurianus_386B 214433 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acetobacter Acetobacter_pasteurianus_IFO_3283_01_42C 158377 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acetobacter Acetobacter_pasteurianus_IFO_3283_01 59279 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acetobacter Acetobacter_pasteurianus_IFO_3283_03 158373 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acetobacter Acetobacter_pasteurianus_IFO_3283_07 158381 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acetobacter Acetobacter_pasteurianus_IFO_3283_12 158379 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acetobacter Acetobacter_pasteurianus_IFO_3283_22 158383 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acetobacter Acetobacter_pasteurianus_IFO_3283_26 158531 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acetobacter Acetobacter_pasteurianus_IFO_3283_32 158375 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acetobacter Acetobacterium_woodii_DSM_1030 88073 Bacteria Firmicutes Clostridia Clostridiales Eubacteriaceae Acetobacterium Acetohalobium_arabaticum_DSM_5501 51423 Bacteria Firmicutes Clostridia Halanaerobiales Halobacteroidaceae Acetohalobium Acholeplasma_brassicae 222823 Bacteria Tenericutes Mollicutes Acholeplasmatales Acholeplasmataceae Acholeplasma Acholeplasma_laidlawii_PG_8A 58901 Bacteria Tenericutes Mollicutes Acholeplasmatales Acholeplasmataceae Acholeplasma Acholeplasma_palmae_J233 222824 Bacteria Tenericutes Mollicutes Acholeplasmatales Acholeplasmataceae Acholeplasma Achromobacter_xylosoxidans_A8 59899 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Alcaligenaceae Achromobacter Achromobacter_xylosoxidans_NBRC_15126 232243 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Alcaligenaceae Achromobacter Achromobacter_xylosoxidans 205255 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Alcaligenaceae Achromobacter Acidaminococcus_fermentans_DSM_20731 43471 Bacteria Firmicutes Negativicutes Selenomonadales Acidaminococcaceae Acidaminococcus Acidaminococcus_intestini_RyC_MR95 74445 Bacteria Firmicutes Negativicutes Selenomonadales Acidaminococcaceae Acidaminococcus Acidianus_hospitalis_W1 66875 Archaea Crenarchaeota Thermoprotei Sulfolobales Sulfolobaceae Acidianus Acidilobus_saccharovorans_345_15 51395 Archaea Crenarchaeota Thermoprotei Acidilobales Acidilobaceae Acidilobus Acidimicrobidae_bacterium_YM16_304 193703 Bacteria Actinobacteria Acidimicrobidae Acidimicrobiales Acidimicrobineae Acidimicrobiaceae Acidimicrobium_ferrooxidans_DSM_10331 59215 Bacteria Actinobacteria Acidimicrobidae Acidimicrobiales Acidimicrobineae Acidimicrobiaceae Acidiphilium_cryptum_JF_5 58447 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acidiphilium Acidiphilium_multivorum_AIU301 63345 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acidiphilium Acidithiobacillus_caldus_SM_1 70791 Bacteria Proteobacteria Gammaproteobacteria Acidithiobacillales Acidithiobacillaceae Acidithiobacillus Acidithiobacillus_ferrivorans_SS3 67387 Bacteria Proteobacteria Gammaproteobacteria Acidithiobacillales Acidithiobacillaceae Acidithiobacillus Acidithiobacillus_ferrooxidans_ATCC_23270 57649 Bacteria Proteobacteria Gammaproteobacteria Acidithiobacillales Acidithiobacillaceae Acidithiobacillus Acidithiobacillus_ferrooxidans_ATCC_53993 58613 Bacteria Proteobacteria Gammaproteobacteria Acidithiobacillales Acidithiobacillaceae Acidithiobacillus Acidobacterium_capsulatum_ATCC_51196 59127 Bacteria Acidobacteria Acidobacteriales Acidobacteriaceae Acidobacterium Acidobacterium_MP5ACTX9 50551 Bacteria Acidobacteria Acidobacteriales Acidobacteriaceae Granulicella Acidothermus_cellulolyticus_11B 58501 Bacteria Actinobacteria Actinobacteridae Actinomycetales Frankineae Acidothermaceae Acidovorax_avenae_ATCC_19860 42497 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Acidovorax Acidovorax_citrulli_AAC00_1 58429 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Acidovorax Acidovorax_ebreus_TPSY 59233 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Acidovorax Acidovorax_JS42 58427 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Acidovorax Acidovorax_KKS102 176500 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Acidovorax Aciduliprofundum_boonei_T469 43333 Archaea Euryarchaeota Aciduliprofundum Aciduliprofundum_MAR08_339 184407 Archaea Euryarchaeota Aciduliprofundum Acinetobacter_ADP1 61597 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_baumannii_1656_2 158677 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_baumannii_AB0057 59083 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_baumannii_AB307_0294 59271 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_baumannii_ACICU 58765 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_baumannii_ATCC_17978 58731 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_baumannii_AYE 61637 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_baumannii_BJAB07104 210971 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_baumannii_BJAB0715 210972 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_baumannii_BJAB0868 210973 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_baumannii_D1279779 190222 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_baumannii_MDR_TJ 162739 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_baumannii_MDR_ZJ06 158685 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_baumannii_SDF 61601 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_baumannii_TCDC_AB0715 158679 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_baumannii_TYTH_1 176498 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_baumannii_ZW85_1 231518 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_calcoaceticus_PHEA_2 83123 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter_oleivorans_DR1 50119 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Actinobacillus_pleuropneumoniae_serovar_3_JL03 58891 Bacteria Proteobacteria Gammaproteobacteria Pasteurellales
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