Supplementary Information for Expanding the utility of sequence comparisons using data from whole genomes Sean Gosselina,*, Matthew S. Fullmera,c,*, Yutian Fenga, and Johann Peter Gogartena,b Corresponding Author Johann Peter Gogarten, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Rd, Storrs, CT, 06268-3125, USA, Email: [email protected] Phone 1 860 486 4061 This PDF file includes: Figures S1 to S9 Tables S1 to S5 1 Figures Frankia sp. NRRL B 16219 Frankia sp. BR AAY23 1001 Frankia sp. NRRL B 16219 A. Frankia sp. Allo2 B. Frankia sp. BR AAY23 1001 Frankia sp. CcI156 Frankia sp. Allo2 Frankia sp. CcI6 Frankia sp. CcI156 Frankia sp. CgIM4 Frankia sp. CcI6 Frankia sp. Thr Frankia sp. CgIM4 Frankia sp. CcI3 Frankia sp. Thr Frankia sp. CED Franka sp. CcI3 Frankia sp. BMG5 23 Frankia sp. CED Frankia sp. BMG5 23 Frankia sp. CpI1 S FF36 Frankia sp. CpI1-P FF86 1001 Frankia sp. CpI1 S FF36 Frankia sp. ACN1ag Frankia sp. CpI1-P− FF86 1001 Frankia sp. ACN1ag Frankia sp. AvcI1 Frankia sp. AvcI1 Frankia alni ACN14A Frankia alni ACN14A Frankia sp. QA3 Frankia sp. QA3 Frankia coriariae BMG5 1 Frankia coriariae BMG5 1 Frankia sp. BMG5 30 Frankia sp. BMG5 30 Frankia symbiont of Datisca glomerata GC Content Genome Length Frankia symbiont of Datisca glomerata Frankia sp. Dg2 1e+07 Frankia sp. Dg2 Frankia sp. R43 0.700 Frankia sp. R43 Frankia sp. CcI49 8e+06 0.675 Frankia sp. CcI49 Frankia sp. 45899 Frankia sp. 45899 6e+06 Frankia sp. EUN1f ctg00163 0.650 Frankia sp. EUN1f ctg00163 Frankia sp. EI5c UG55 1001 Frankia sp. EI5c UG55 1001 Frankia elaeagni BMG5 12 Frankia elaeagni BMG5 12 Frankia sp. Cc1 17 Frankia sp. Cc1 17 Frankia sp. EAN1pec Frankia sp. EAN1pec Frankia sp. CgIS1 Frankia sp. CgIS1 Frankia discariae BCU110501 Frankia discariae BCU110501 Frankia sp. EUN1h Frankia sp. EUN1h Frankia sp. CN3 FCB 1 Frankia sp. CN3 FCB 1 Frankia sp. NRRL B 16386 Frankia sp. NRRL B 16386 Frankia sp. BMG5 36 Frankia sp. BMG5 36 Frankia sp. EuI1c Frankia sp. EuI1c Frankia sp. DC12 Frankia sp. DC12 Frankineae bacterium MT45 Frankineae bacterium MT45 Frankia sp. Iso899 Frankia sp. Iso899 Jatrophihabitans endophyticus 45627 Jatrophihabitans endophyticus 45627 Sporichthya polymorpha 43042 Sporichthya polymorpha 43042 Cryptosporangium aurantiacum DSM 46144 Cryptosporangium aurantiacum DSM 46144 Cryptosporangium arvum 44712 Cryptosporangium arvum 44712 Fig. S1. Phylogenies of the Frankiales dataset built from the tANI methodology and color coded to investigate potential biases of the method. (A) plots the length of the genome on each tip, and (B) plots the GC content of the genome on the tip. Neither A or B shows biased patterns. 2 Asticcacaulis excentricus CB48 Asticcacaulis excentricus CB48 Brevundimonas subvibrioides ATCC15264 A Brevundimonas subvibrioides ATCC15264 Phenylobacterium zucineum HLK1 Phenylobacterium zucineum HLK1 B Caulobacter sp. K31 Caulobacter sp. K31 Caulobacter segnis ATCC21756 Caulobacter segnis ATCC21756 Caulobacter vibrioides CB15 Caulobacter crescentus CB15 Caulobacter vibrioides NA1000 Caulobacter crescentus NA1000 Hyphomonas neptunium ATCC15444 Maricaulis maris MCS10 Maricaulis maris MCS10 Hyphomonas neptunium ATCC15444 Parvularcula bermudensis HTCC25033 Hirschia baltica ATCC49814 Hirschia baltica ATCC49814 Parvularcula bermudensis HTCC25033 Rhodobacterales bacterium HTCC2255 Rhodobacter capsulatus SB1003 Rhodobacteraceae bacterium HTCC2150 Rhodobacter sphaeroides KD131 Rhodobacteraceae bacterium HTCC2083 Rhodobacter sphaeroides 241 Thalassiobium sp. R2A62 Rhodobacter sphaeroides ATCC17025 Octadecabacter antarcticus 307 Oceaniovalibus guishaninsula JLT2003 Octadecabacter arcticus 238 Oceanicola granulosus HTCC2516 Loktanella koreensis 17925 Wenxinia marina DSM24838 Loktanella sediminum 28715 Loktanella pyoseonensis DSM21424 Loktanella sp. S4079 Loktanella hongkongensis DSM174922 Loktanella tamlensis 26879 Loktanella cinnabarina LL001 Loktanella litorea 29433 Jannaschia sp. CCS1 Loktanella rosea 29591 Dinoroseobacter shibae DFL12 Roseobacter sp. CCS2 Maritimbacter alkaliphilus HTCC2654 Loktanella vestfoldensis DSM16212 Oceanicola batsensis HTCC2597 Loktanella fryxellensis 16213 Oceanicola sp. S124 Loktanella atrilutea 29326 Sagittula stellata E37 Loktanella salsilacus 16199 Citreicella sp. 357 Jannaschia sp. CCS1 Pelagibaca bermudensis HTCC2601 Rhodobacter capsulatus SB1003 Citreicella sp. SE45 Rhodobacter sphaeroides ATCC17025 Roseovarius nubinhibens ISM Rhodobacter sphaeroides KD131 Roseobacter sp. AzwK3b Rhodobacter sphaeroides 241 Roseovarius sp. TM1035 Rhodobacter sphaeroides ATCC17029 Roseovarius sp. 217 Oceaniovalibus guishaninsula JLT2003 Tateyamaria sp. ANG-M1 Oceanicola granulosus HTCC2516 Roseobacter litoralis Och149 Wenxinia marina DSM24838 Roseobacter denitrificans OCh114 Loktanella pyoseonensis DSM21424 Oceanibulbus indolifex HEL-45 Loktanella cinnabarina LL001 Roseobacter sp. GAI101 Loktanella hongkongensis DSM174922 Sulfitobacter sp. EE36 Oceanicola batsensis HTCC2597 Sulfitobacter sp. NAS141 Maritimibacter alkaliphilus HTCC2654 Rhodobacterales bacterium HTCC2083 Dinoroseobacter shibae DFL12 Rhodobacterales bacterium HTCC2255 Oceanicola sp. S124 Rhodobacterales bacterium HTCC2150 Sagittula stellata E37 Thalassiobium sp. R2A62 Citreicella sp. 357 Octadecabacter arcticus 238 Citreicella sp. SE45 Octadecabacter antarcticus 307 Pelagibaca bermudensis HTCC2601 Loktanella salsilacus 16199 Roseovarius nubinhibens ISM Loktanella atriluea 29326 Roseobacter sp. AzwK3b Loktanella fryxellensis 16213 Roseovarius sp. 217 Loktanella vestfoldensis DSM16212 Roseovarius sp. TM1035 Loktanella koreensis 17925 Tateyamaria sp. ANG-M1 Loktanella sediminum 28715 Roseobacter denitrificans Och114 Loktanella litorea 29433 Roseobacter litoralis Och149 Loktanella tamlensis 26879 Oceanibulbus indolifex HEL45 Loktanella sp. S4079 Roseobacter sp. GAI101 Roseobacter sp. CCS2 Sulfitobacter sp. EE36 Loktanella rosea 29591 Sulfitobacter sp. NAS141 Sedimentitalea nanhaiensis DSM24252 Sedimentitalea nanhaiensis DSM24252 Ruegeria marina CGMCC Ruegeria marina CGMCC Rugeria pomeroyi DSS3 Ruegeria pomeroyi DSS3 Rugeria lacuscaerulensis ITI1157 Ruegeria lacuscaerulensis ITI1157 Rugeria lacuscaerulensis ITI1157S Ruegeria lacuscaerulensis ITI1157S Ruegeria sp. ANG-S4 Ruegeria atlantica CECT4292 Ruegeria atlantica CECT4293 Ruegeria halocynthiae MOLA Ruegeria halocynthiae MOLA Ruegeria sp. ANG-S4 Ruegeria sp. KLH11 Ruegeria sp. KLH11 Ruegeria sp. ANG-R Ruegeria sp. ANG-R Ruegeria conchae TW15 Ruegeria conchae TW15 Ruegeria sp. TW15 Ruegeria sp. TW15 Roseobacter sp. SK20926 Ruegeria sp. TM1040 Pseudophaeobacter arcticus DSM23566 Ruegeria mobilis F1926 Roseobacter sp.MED193 Ruegeria sp. Trich CH4B Rugeria sp. TM1040 Ruegeria sp. R11 Ruegeria sp. TrichCH4B PhaeobactergallaeciensisDSM26640 Ruegeria mobilis F1926 Phaeobacter inhibens DSM17395 Ruegeria sp. R11 Phaeobacter inhibens 2-10 Phaeobacter gallaeciensis DSM26640 Phaeobacter inhibens DSM16374 Bootstrap Phaeobacter inhibens DSM17395 Roseobacter sp. SK20926 Phaeobacter inhibens DSM16374 Pseudophaeobacter arcticus DSM23566 Support Phaeobacterinhibens 2-10 Roseobacter sp. MED193 Leisingera aquimarina DSM24565 Leisingera sp. ANG-M1 Leisingera methylohalidivorans DSM14336 Leisingera sp. ANG-Vp ≥ 90 Leisingera sp. ANG-M1 Leisingera aquimarina DSM24565 Leisingera sp. ANG-Vp Leisingera methylohalidivorans DSM14336 Leisingera caerulea DSM24564 Leisingera caeruleus DSM24564 ≥ 80 Leisingera daeponensis DSM23529 Leisingera daeponensis DSM23529 Leisingera sp. Y4I Leisingera sp. Y4I Leisingera sp. JC1 Leisingera sp. ANG-M7 ≥ 70 Leisingera sp. ANG-M7 Leisingera sp. JC1 Leisingera sp. ANG-S3 Leisingera sp. ANG-S5 Leisingera sp. ANG1 Leisingera sp. ANG-DT < 70 0.3 Leisingera sp. ANG-S 0.8 Leisingera sp. ANG-M6 Leisingera sp. ANG-DT Leisingera sp. ANG-S3 Leisingera sp. ANG-M6 Leisingera sp. ANG-S Leisingera sp. ANG-S5 Leisingera sp. ANG1 Fig. S2. Comparison of phylogenies reconstructed from the Rhodobacterales dataset. (A) The multi-gene phylogeny from Collins et al., (2015), and (B) the tANI distance based phylogeny. Both sides use bootstrapped node support on a scale from 100-0 indicated by the key. 3 Rhodobacterales_bacteriuM_HTCC2150.gbk.fna Rhodobacterales_bacteriuM_HTCC2255.gbk.fna 1.0 Hirschia_baltica_ATCC49814.gbk.fna Parvularcula_berMudensis_HTCC2503.gbk.fna Octadecabacter_antarcticus_307.gbk.fna Octadecabacter_arcticus_238.gbk.fna Roseobacter_litoralis_Och149.gbk.fna Roseobacter_denitrificans_OCh114.gbk.fna Ruegeria_conchae_TW15.fna Ruegeria_sp_TW15.gbk.fna Oceanibulbus_indolifex_HEL45.gbk.fna Roseobacter_sp_GAI101.gbk.fna Ruegeria_sp_ANG-R.gbk.fna Sulfitobacter_sp_NAS-14-1.gbk.fna ThalassiobiuM_sp_R2A62.gbk.fna HyphoMonas_neptuniuM_ATCC15444.gbk.fna Ruegeria_sp_ANG-S4.gbk.fna Sulfitobacter_sp_EE36.gbk.fna Rhodobacterales_bacteriuM_HTCC2083.gbk.fna Maricaulis_maris_MCS10.gbk.fna Ruegeria_atlantica.fna TateyaMaria_sp_ANG-M1.gbk.fna Ruegeria_sp_KLH11.gbk.fna SediMentitalea_nanhaiensis_DSM24252.gbk.fna Ruegeria_halocynthiae_MOLA.fna Rugeria_poMeroyi_DSS3.gbk.fna Ruegeria_marina_CGMCC.fna Caulobacter_crescentus_NA1000.gbk.fna Caulobacter_crescentus_CB15.gbk.fna Silicibacter_lacuscaerulensis_ITI1157.fna Caulobacter_segnis_ATCC21756.gbk.fna Caulobacter_sp_K31.gbk.fna Ruegeria_lacuscaerulensis_ITI-1157.gbk.fna Leisingera_daeponensis_DSM23529.gbk.fna PhenylobacteriuM_zucineuM_HLK1.gbk.fna Leisingera_sp_ANG1.gbk.fna Leisingera_sp_Y4I.gbk.fna Leisingera_sp_JC1.contigs.fa BrevundiMonas_subvibrioides_ATCC15264.gbk.fna Leisingera_sp_ANG-M7.gbk.fna Leisingera_caerulea_DSM24564.gbk.fna Leisingera_sp_ANG-M6.gbk.fna