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Genomic and Phylogenomic Insights Into the Family Streptomycetaceae Lead

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Genomic and Phylogenomic Insights Into the Family Streptomycetaceae Lead 1 Supplementary Material 2 Genomic and phylogenomic insights into the family Streptomycetaceae lead 3 to proposal of Charcoactinosporaceae fam. nov. and 8 novel genera with 4 emended descriptions of Streptomyces calvus 5 Munusamy Madhaiyan1, †, *, Venkatakrishnan Sivaraj Saravanan2, †, Wah-Seng See-Too3, † 6 1Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 7 Singapore 117604; 2Department of Microbiology, Indira Gandhi College of Arts and Science, 8 Kathirkamam 605009, Pondicherry, India; 3Division of Genetics and Molecular Biology, 9 Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 10 Malaysia 1 11 Table S3. List of the core genes in the genome used for phylogenomic analysis. NCBI Protein Accession Gene WP_074993204.1 NUDIX hydrolase WP_070028582.1 YggS family pyridoxal phosphate-dependent enzyme WP_074992763.1 ParB/RepB/Spo0J family partition protein WP_070022023.1 lipoyl(octanoyl) transferase LipB WP_070025151.1 FABP family protein WP_070027039.1 heat-inducible transcriptional repressor HrcA WP_074992865.1 folate-binding protein YgfZ WP_074992658.1 recombination protein RecR WP_074991826.1 HIT domain-containing protein WP_070024163.1 adenylosuccinate synthase WP_009190566.1 anti-sigma regulatory factor WP_071828679.1 preprotein translocase subunit SecG WP_070026304.1 50S ribosomal protein L13 WP_009190144.1 30S ribosomal protein S5 WP_014674378.1 30S ribosomal protein S8 WP_070026314.1 50S ribosomal protein L5 WP_009300593.1 30S ribosomal protein S13 WP_003998809.1 50S ribosomal protein L36 WP_070026864.1 WhiB family transcriptional regulator WP_023550764.1 50S ribosomal protein L27 WP_070027822.1 ATP synthase F0 subcomplex C subunit WP_039656223.1 30S ribosomal protein S17 WP_070024148.1 DUF5063 domain-containing protein WP_009190136.1 50S ribosomal protein L16 WP_070024021.1 MoaD/ThiS family protein WP_070028831.1 30S ribosomal protein S6 WP_003956500.1 50S ribosomal protein L34 WP_070025179.1 glycine--tRNA ligase WP_018544333.1 DUF3117 domain-containing protein WP_003974250.1 50S ribosomal protein L30 WP_070022292.1 30S ribosomal protein S16 WP_070023573.1 2-phospho-L-lactate transferase WP_074993184.1 PHP domain-containing protein 2 12 Table S4. Similarity in polyphasic data observed between S. asterosporus DSM 41452T and S. 13 calvus CECT 3271T Streptomyces asterosporus Streptomyces calvus Characteristic† DSM 41452T CECT 3271T Morphological characters: Spore color Gray Gray Spore chain morphology Spira Spira Melanoid pigment production − − Spore wall ornamentation Spiny Hairy Physiological tests: D-Glucose + + D-Xylose − + L-Arbinose + + D-Rhamnose + + L-Rhamnose + + D-Galactose + + Raffinose − + D-Mannitol + + i-Inositol n + Salicin n + Sucrose n + G+C content (mol%) 72.5 72.5 Genome size (Mbp) 7.77 7.94 14 +, positive; −, negative; n-not determined. 15 †Data from Kämpfer et al. (2014). 16 3 Streptomyces lincolnensis NRRL 2936T (CP016438) Streptomyces caeruleatus NRRL B-24802T (KQ948975) Streptomyces griseoruber DSM 40281T (LIQS01000280) Streptomyces acidiscabies NRRL B-16524T (D63865) Streptomyces curacoi DSM 40107T (KQ948008) Streptomyces humi MUSC 119T (LBMU02000042) Streptomyces hyaluromycini NBRC 110483T (BCFL01000051) Streptomyces murinus NRRL B-2286T (AB184155) 100 Streptomyces griseofuscus NRRL B-5429T (AB184206) Streptomyces corchorusii DSM 40340T (KQ948396) Streptomyces bungoensis DSM 41781T (KQ948892) 73 Streptomyces longwoodensis DSM 41677T (KQ948572) Streptomyces griseochromogenes ATCC 14511T (CP016279) Streptomyces cellostaticus DSM 40189T (KQ948097) Streptomyces achromogenes subsp. achromogenes NRRL B-2120T (AB184109) Streptomyces durhamensis NRRL B-3309T (JNXR01000068) 93 Streptomyces puniciscabiei NRRL B-24456T (AF361785) Streptomyces avermitilis MA-4680T (BA000030) Streptomyces atriruber NRRL B-24165T (LIPN01000196) Streptomyces davaonensis JCM 4913T (HE971709) Streptomyces cinnabarinus NRRL B-12382T (JNXQ01000585) Streptomyces yokosukanensis DSM 40224T (KQ948269) 92 Streptomyces hokutonensis R1-NS-10T (BARG01000157) Streptomyces prunicolor NBRC 13075T (BARF01000082) Streptomyces aureocirculatus NRRL ISP-5386T (JOAP01000131) Streptomyces bobili NRRL B-1338T (MUBA01000087) Streptomyces phaeoluteigriseus DSM 41896T (MPOH01000466) Streptomyces populi A249T (MF100127) Streptomyces resistomycificus DSM 40133T (JOBA01000220) Streptomyces canus DSM 40017T (KQ948708) Streptomyces pseudovenezuelae DSM 40212T (KQ948163) Streptomyces alboniger NRRL B-1832T (LIQN01000245) 98 Streptomyces recifensis NRRL B-3811T (AB184165) Streptomyces seoulensis NRRL B-24310T (JNXP01000045) Streptomyces olivochromogenes DSM 40451T (KQ948511) 84 Streptomyces aureus NRRL B-2808T (AB249976) Streptomyces kanamyceticus NRRL B-2535T (AB184388) Streptomyces aurantiacus NRRL ISP-5412T (AB184259) 67 Streptomyces phaeochromogenes NRRL B-1248T (AB184738) Streptomyces bottropensis ATCC 25435T (KB911581) 90 Streptomyces stelliscabiei NRRL B-24447T (LBNW01000338) Streptomyces capitiformicae 1H-SSA4T (KX777629) Streptomyces graminilatus NRRL B-59124T (LIQQ01000213) Streptomyces dengpaensis XZHG99T (CP026652) Streptomyces rishiriensis NBRC 13407T (AB184383) Streptomyces reticuliscabiei NRRL B-24446T (MUNI01000325) 76 Streptomyces geranii A301T (MF100124) 99 Streptomyces flavovariabilis NRRL B-16367T (JNXD01000071) Streptomyces variegatus NRRL B-16380T (JYJH01000110) Streptomyces griseorubiginosus DSM 40469T (KQ948757) Streptomyces yerevanensis NRRL B-16943T (JNWJ01000157) Streptomyces kebangsaanensis SUK12T (HM449824) Streptomyces hirsutus NRRL B-2713T (LIQT01000254) 100 Streptomyces prasinus NRRL B-2712T (LIRH01000162) Streptomyces indicus CGMCC 4.5727T (EF157833) 99 Streptomyces amritsarensis MTCC 11845T (MQUR01000179) Streptomyces yangpuensis fd2-tbT (LBMK01000002) 91 Streptomyces virginiae NRRL ISP-5094T (JOAK01000082) Streptomyces xanthophaeus NRRL B-5414T (JOFT01000080) Streptomyces lavendulae subsp. lavendulae NRRL B-2774T (JOEW01000098) 86 Streptomyces vietnamensis GIM4.0001T (DQ311081) Streptomyces bikiniensis NRRL B-1049T (JNWL01000107) Streptomyces laurentii ATCC 31255T (AP017424) Streptomyces venezuelae ATCC 10712T (FR845719) Streptomyces exfoliatus NRRL B-2924T (JNZP01000081) Streptomyces wedmorensis NRRL 3426T (JNWK01000124) Streptomyces purpureus NBRC 13927T (AB184547) Streptomyces flavidovirens DSM 40150T (AB184270) Streptomyces kanasensis ZX01T (JN572690) Streptomyces lunaelactis MM109T (KM207217) Streptomyces puniceus NRRL ISP-5083T (AB184163) Streptomyces bacillaris ATCC 15855T (AB184439) 74 99 Streptomyces mutomycini NRRL B-65393T (MAPV01000102) Streptomyces atroolivaceus NRRL ISP-5137T (JNXG01000049) 75 Streptomyces halstedii NRRL ISP-5068T (AB184142) Streptomyces cyaneofuscatus NRRL B-2570T (JOEM01000050) Streptomyces griseus subsp. griseus DSM 40236T (M76388) Streptomyces fulvissimus DSM 40593T (CP005080) Streptomyces luridiscabiei NRRL B-24455T (LIQV01000394) Streptomyces setonii NRRL ISP-5322T (MUNB01000146) Kitasatospora papulosa NRRL B-16504T (JNYQ01000038) Streptomyces niveus NCIMB 11891T (DQ442532) Streptomyces clavuligerus ATCC 27064T (CM000913) 76 Streptomyces tsukubensis NRRL18488T (AJSZ01000237) Streptomyces alni CGMCC 4.3510T (DQ460470) 99 Streptomyces lushanensis NRRL B-24994T (MAUD01000416) Streptomyces odonnellii NRRL B-24891T (LATD01000204) Streptomyces scopuliridis NRRL B-24574T (JOEI01000056) Streptomyces eurocidicus ATCC 27428T (AY999790) 80 Streptacidiphilus jiangxiensis NBRC 100920T (BBPN01000092) Streptacidiphilus anmyonensis NBRC 103185T (BBPQ01000139) 74 Streptacidiphilus melanogenes NBRC 103184T (BBPP01000099) 84 Streptacidiphilus rugosus AM-16T (JQMJ01000004) 74 Streptacidiphilus pinicola MMS16-CNU450T (MG189375) Streptacidiphilus carbonis DSM 41754T (AF074412) Streptacidiphilus T 87 Streptacidiphilus albus NBRC 100918 (BBPL01000138) Streptacidiphilus neutrinimicus DSM 41755T (AF074410) 97 Streptacidiphilus bronchialis DSM 106435T (CP031264) 70 Streptacidiphilus griseoplanus NRRL B-3064T (LIQR01000258) Streptacidiphilus oryzae TH49T (JQMQ01000005) 95 Kitasatospora cineracea DSM 44780T (RJVJ01000002) 88 Kitasatospora niigatensis DSM 44781T (RKQG01000001) Kitasatospora setae KM-6054T (AP010968) 96 Kitasatospora cheerisanensis KCTC 2395T (KK853997) Kitasatospora phosalacinea NRRL B-16230T (JNWZ01000148) 87 Kitasatospora viridis DSM 44826T (VIWT01000001) Kitasatospora T Kitasatospora aureofaciens ATCC 10762 (JPRF02000033) T Kitasatospora atroaurantiaca NRRL B-24282 (DQ026645) T Streptomyces novaecaesareae NRRL B-1267 (JNWQ01000181) T Kitasatospora azatica KCTC 9699 (JQMO01000002) 98 T Kitasatospora purpeofusca NRRL B-1817 (JODS01000077) T Streptomyces inhibens NEAU-D10 (QUAC01000041) T 95 Streptomyces kasugaensis BCRC 12349 (NDXL01000004) T Streptomyces celluloflavus NRRL B-2493 (JOEL01000102) T Streptomyces decoyicus NRRL 2666 (LGUU01000106) T Streptomyces platensis DSM 40041 (AB045882) T Streptomyces monomycini NRRL B-24309 (JNYL01000005) T 76 Streptomyces niger NRRL B-3857 (AB184352) T Streptomyces ochraceiscleroticus NRRL ISP-5594 (JOAX01000062) 92 T Streptomyces violens NRRL ISP-5597 (JOBH01000039) T Streptomyces rimosus subsp. rimosus NRRL ISP-5260 (ANSJ01000404) T Streptomyces sclerotialus NRRL ISP-5269 (JOBC01000056) T Streptomyces albofaciens JCM 4342 (AB045880) 77 T Streptomyces chrestomyceticus NBRC 13444 (BHZC01000001) T Streptomyces chattanoogensis NRRL ISP-5002 (LGKG01000206) T Streptomyces noursei ATCC 11455 (CP011533) T Streptomyces lydicus NRRL ISP-5461 (RDTD01000009) T Streptomyces angustmyceticus
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