Supplemental figure 1. Collection sites and numbers of strains sequenced.
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1 Supplemental figure 1. Collection sites and numbers of strains sequenced.
2 Supplemental figure 2. Neighbor joining 16S rrna gene phylogeny (636 bp). Minimum bootstrap values >50% generated using NJ and ML methods are shown. Species names are followed by 16S sequence type, country of origin, and the strain identifier. = 100% bootstrap support > 80% bootstrap support > 50% bootstrap support S. pacifica A, CNS-801 S. pacifica A, CNT-148 S. pacifica D, CNT-084 S. pacifica, CNT-037 S. pacifica F, CNT-029 S. pacifica C, CNS-863 S. pacifica C, CNT-045 S. pacifica C, CNT-094 S. pacifica C, CNT-138 S. pacifica B, CNT-150 S. pacifica B, CNS-237 S. tropica, CNB-392 S. tropica, CNB-440 S. tropica, CNB-476 S. tropica, CNB-536 S. tropica, CNH-898 S. tropica, CNS-193 S. tropica, CNS-197 S. tropica, CNS-416 S. tropica, CNT-254 S. tropica, CNT-253 S. tropica, CNT-257 S. tropica, CNT-280 S. arenicola B, CNP-152 S. arenicola B, CNH-964 S. arenicola, CNT-088 S. arenicola, CNT-137 S. arenicola, CNT-086 S. arenicola, CNS-992 S. arenicola, CNS-991 S. arenicola, CNB-458 S. arenicola, CNB-527 S. arenicola, CNH-643 S. arenicola, CNS-205 S. arenicola, CNS-673 S. arenicola, CNS-744 S. arenicola, CNS-759 S. arenicola, CNS-803 S. arenicola, CNS-820 S. arenicola, CNS-823 Polymorphospora sp. YIM (NR_044592) Actinaurispora siamensis CM2-8 (AB454379) Verrucosispora maris (NC_ ) Micromonospora aurantiaca ATCC (PRJNA42501) Micromonospora sp. L5 (PRJNA45895) Streptomyces griseus strain 45H (EF571002) 0.01
3 Supplemental figure 3. Neighbor joining atpd gene phylogeny (732 bp). Minimum bootstrap values >50% generated using NJ and ML methods are shown. = 100% bootstrap support > 80% bootstrap support > 50% bootstrap support S. tropica, CNS-193 S. tropica, CNT-257 S. tropica, CNS-416 S. tropica, CNB-392 S. tropica, CNT-280 S. tropica, CNT-253 S. tropica, CNB-440 S. tropica, CNS-197 S. tropica, CNT-254 S. tropica, CNB-536 S. tropica, CNH-898 S. tropica, CNB-476 S. pacifica B, CNS-237 S. pacifica B, CNT-150 S. pacifica A, CNS-801 S. pacifica A, CNT-148 S. pacifica D, CNT-084 S. pacifica, CNT-037 S. pacifica C, CNT-094 S. pacifica F, CNT-029 S. pacifica E, CNT-138 S. pacifica C, CNT-045 S. pacifica C, CNS-863 S. arenicola, CNB-527 S. arenicola, CNB-458 S. arenicola B, CNP-152 S. arenicola B, CNH-964 S. arenicola, CNS-992 S. arenicola, CNH-643 S. arenicola, CNS-803 S. arenicola, CNS-991 S. arenicola, CNS-673 S. arenicola, CNS-205 S. arenicola, CNS-744 S. arenicola, CNS-820 S. arenicola, CNS-823 S. arenicola, CNT-086 S. arenicola, CNS-759 S. arenicola, CNT-088 S. arenicola, CNT-137 Micromonospora sp. L5 (PRJNA45895) Micromonospora aurantiaca ATCC (PRJNA42501) Nakamurella multipartita DSM (NC_013235) Geodermatophilus obscurus DSM (NC_013757) Streptomyces flavogriseus ATCC (NC_016114) 0.02
4 Supplemental figure 4. Neighbor joining gyrb gene phylogeny (696 bp). Minimum bootstrap values >50% generated using NJ and ML methods are shown. = 100% bootstrap support > 80% bootstrap support > 50% bootstrap support S. pacifica A, CNS-801 S. pacifica A, CNT-148 S. pacifica, CNT-037 S. pacifica D, CNT-084 S. pacifica E, CNT-138 S. pacifica F, CNT-029 S. pacifica C, CNT-045 S. pacifica C, CNT-094 S. pacifica C, CNS-863 S. pacifica B, CNT-150 S. pacifica B, CNS-237 S. tropica, CNT-253 S. tropica, CNT-254 S. tropica, CNT-280 S. tropica, CNS-197 S. tropica, CNB-392 S. tropica, CNS-416 S. tropica, CNB-476 S. tropica, CNS-193 S. tropica, CNT-257 S. tropica, CNH-898 S. tropica, CNB-440 S. tropica, CNB-536 S. arenicola, CNB-527 S. arenicola, CNB-458 S. arenicola, CNT-088 S. arenicola, CNS-803 S. arenicola, CNS-759 S. arenicola, CNS-823 S. arenicola, CNS-673 S. arenicola, CNT-086 S. arenicola, CNH-643 S. arenicola, CNT-137 S. arenicola, CNS-205 S. arenicola, CNS-820 S. arenicola, CNS-992 S. arenicola, CNS-991 S. arenicola, CNS-744 S. arenicola B, CNP152 S. arenicola B, CNH964 Verrucosispora sediminis MS426 (HQ199220) Micromonospora halophytica IFO14112 (AB014157) Micromonospora sp. L5 (PRJNA45895) Micromonospora aurantiaca IFO16125 (AB014160) Micromonospora aurantiaca ATCC27029 (PRJNA42501) Micromonospora carbonacea (BAA89725) Micromonospora olivasterospora IFO14304 (AB014159) Micromonospora echinospora IFO16070 (AB014153) Micromonospora echinospora IFO13150 (AB014160) Dactylosporangium matsuzakiense ATCC (AB014104) 0.02
5 Supplemental figure 5. Neighbor joining reca gene phylogeny (708 bp). Minimum bootstrap values >50% generated using NJ and ML methods are shown. = 100% bootstrap support > 80% bootstrap support > 50% bootstrap support S. pacifica D, CNT-084 S. pacifica, CNT-037 S. pacifica B, CNT-150 S. pacifica B, CNS-237 S. pacifica A, CNT-148 S. pacifica A, CNS-801 S. pacifica, CNT-094 S. pacifica, CNT-138 S. pacifica, CNT-029 S. pacifica, CNT-045 S. pacifica, CNS-863 S. tropica, CNT-280 S. tropica, CNB-536 S. tropica, CNT-254 S. tropica, CNB-440 S. tropica, CNS-197 S. tropica, CNH-898 S. tropica, CNB-476 S. tropica, CNT-257 S. tropica, CNS-193 S. tropica, CNS-416 S. tropica, CNT-253 S. tropica, CNB-392 S. arenicola, CNB-527 S. arenicola, CNB-458 S. arenicola, CNT-137 S. arenicola, CNS-673 S. arenicola, CNS-820 S. arenicola, CNS-759 S. arenicola, CNT-086 S. arenicola, CNT-088 S. arenicola B, CNH-964 S. arenicola B, CNP-152 S. arenicola, CNS-991 S. arenicola, CNH-643 S. arenicola, CNS-823 S. arenicola, CNS-992 S. arenicola, CNS-744 S. arenicola, CNS-205 S. arenicola, CNS-803 Micromonospora. L5 (PRJNA45895) Micromonospora aurantiaca ATCC (PRJNA42501) Actinosynnema mirum DSM (NC_013093) Streptomyces argillaceus ATCC (DQ234054) 0.02
6 Supplemental figure 6. Neighbor joining trpb gene phylogeny (558 bp). Minimum bootstrap values >50% generated using NJ and ML methods are shown. = 100% bootstrap support > 80% bootstrap support > 50% bootstrap support S. pacifica, CNT-037 S. pacifica D, CNT-084 S. pacifica A, CNS-801 S. pacifica A, CNT-148 S. pacifica B, CNS-237 S. pacifica B, CNT-150 S. pacifica C, CNT-094 S. pacifica E, CNT-138 S. pacifica F, CNT-029 S. pacifica C, CNT-045 S. pacifica C, CNS-863 S. tropica, CNH-898 S. tropica, CNT-253 S. tropica, CNS-416 S. tropica, CNB-476 S. tropica, CNT-257 S. tropica, CNT-254 S. tropica, CNT-280 S. tropica, CNS-197 S. tropica, CNB-392 S. tropica, CNS-193 S. tropica, CNB-440 S. tropica, CNB-536 S. arenicola, CNB-527 S. arenicola, CNB-458 S. arenicola B, CNP-152 S. arenicola B, CNH-964 S. arenicola, CNH-643 S. arenicola, CNT-137 S. arenicola, CNS-673 S. arenicola, CNS-759 S. arenicola, CNS-992 S. arenicola, CNT-086 S. arenicola, CNS-820 S. arenicola, CNT-088 S. arenicola, CNS-991 S. arenicola, CNS-744 S. arenicola, CNS-205 S. arenicola, CNS-823 S. arenicola, CNS-803 Micromonospora sp. L5 (PRJNA45895) Micromonospora aurantiaca ATCC (PRJNA42501) Kribbella flavida DSM17836 (CP001736) Clavibacter michiganensis subsp. sepedonicus NCPPB 382 (NC_009480) Amycolatopsis mediterranei U32 (NC_104318) 0.02
7 Supplemental figure 7. Neighbor joining rpob 3 gene phylogeny. Minimum bootstrap values >50% generated using NJ and ML methods are shown. = 100% bootstrap support > 80% bootstrap support > 50% bootstrap support S. pacifica, CNT-037 S. pacifica D, CNT-084 S. pacifica A, CNT-148 S. pacifica A, CNS-801 S. pacifica B, CNT-150 S. pacifica B, CNS-237 S. pacifica C, CNT-094 S. pacifica E, CNT-138 S. pacifica F, CNT-029 S. pacifica C, CNT-045 S. pacifica C, CNS-863 S. tropica CNH-898 S. tropica CNS-193 S. tropica CNB-476 S. tropica CNB-392 S. tropica CNT-280 S. tropica CNT-257 S. tropica CNS-416 S. tropica CNT-254 S. tropica CNB-440 S. tropica CNT-253 S. tropica CNS-197 S. tropica CNB-536 S. arenicola CNB-527 S. arenicola CNB-458 S. arenicola CNT-088 S. arenicola CNS-820 S. arenicola CNT-137 S. arenicola CNS-744 S. arenicola CNT-086 S. arenicola CNS-205 S. arenicola CNS-823 S. arenicola CNS-759 S. arenicola CNS-673 S. arenicola CNS-991 S. arenicola CNS-992 S. arenicola CNS-803 S. arenicola CNH-643 S. arenicola B, CNP-152 S. arenicola B, CNH-964 Micromonospora aurantiaca ATCC Micromonospora sp. L5 0.01
8 Supplemental Table 1. PCR primers and conditions. All reactions included 2 µl genomic DNA template ( ng), 4 µl 10X PCR buffer, 4 µl of MgCl 2 (25 mm), 0.5 µl of each primer (25 mm), 1.6 µl dntp mix (10 mm), 5U Taq DNA polymerase, 2.4 µl DMSO, and 23.6 µl sterile MilliQ water. The initial denaturation was at 94 C for 10 min followed by 35 cycles of 94 C for 1min, annealing temperatures listed below followed by a 1 min elongation step at 72 C and a final extension step at 72 C for 7 min. Gene Primer name Primer sequence (5'-3') Annealing temp ( C) *modified from (3) Amplicon size (bp) 1. McVeigh HP, Munro J, Embley TM Molecular evidence for the presence of novel actinomycete lineages in a temperate forest soil. Journal of Industrial Microbiology 17: Freel KC, Edlund A, Jensen PR Microdiversity and evidence for high dispersal rates in the marine actinomycete Salinispora pacifica. Environmental Microbiology 14: Guo YP, Zheng W, Rong XY, Huang Y A multilocus phylogeny of the Streptomyces griseus 16S rrna gene clade: use of multilocus sequence analysis for streptomycete systematics. International Journal of Systematic and Evolutionary Microbiology 58: Reference 16S FC27 CCGCGGCTGCTGGCACGTA (1) rrna RC1492 GTGCGGGCCCCCGTCAATT atpd atpd_af GTGGGYGACACGGTCAAGGGSCACGTGTTCAACGCG this study* atpd_ar GTTGAACTGCTCYGCYGCYTAGGTGTTCTGCGACAGGAA trpb trpb_af GCGGGAGGACCTCAACCACACYGGGGCGCACAAGGTGCG this study* trpb_ar TCTCGATCGCGGGGATGATSCCCTCGGTBCGYCAGAGCAY gyrb 7G_gyrB_F GTICGYAWVCGICCSGGHATGTAC this study 7G_gyrB_R CCGTCVACRTCRGCRTCSGCCATS gyrb_tpf CGACGAGGGCGACGATGGCAAGAT this study gyrb_tpr GGATRCCGGTGCCGAGCG reca reca_af TTGCTCTCGCTCAGATCGACAAACAGTTC (2) reca_ar GCCACGTCCGGGTTCTCCCGAAGGAACTCGCG rpob (2) rpob_pf GAGCGCATGACCACCCAGGACGTCGAGGC (3) rpob_pr CCTCGTAGTTGTGACCCTCCCACGGCATGA rpob (3) rpob (N) rpob_f2226 rpob_r3122 rpob_nf GAACGTCAGCGAGGAGATGCT AGCACTCCATCTCACCGAAG CTGGCTGGTCGGCAACGAGG this study this study rpob_nr CTCCATCCGGGACAGGCCGA rifk rif_f1247 GCGGCAGGGTGAGTGTTC (1) rif_r1247 CACCGTGCTGTCCGAAGG
9 Supplemental Table 2. Sequence lengths and accession numbers. Species (ST) Strain Number Collection Location rpob 1 (540 bp) rpob 2 (780 bp) rpob 3 (720 bp) trpb (558 bp) reca (708 bp) atpd (732 bp) gyrb (696 bp) 16S rrna (636 bp) S. tropica CNB-392 BA JQ JQ JX JN JN JN JQ JN S. tropica CNB-440 BA JQ JQ JX JN JN JN DQ AY S. tropica CNB-476 BA JQ JQ JX JN JN JN JQ JN S. tropica CNB-536 BA JQ JQ JX JN JN JN DQ AY S. tropica CNH-898 BA JQ JQ JX JN JN JN DQ AY S. tropica CNS-193 BA JQ JQ JX JN JN JN JQ JN S. tropica CNS-197 BA JQ JQ JX JN JN JN JQ JN S. tropica CNS-416 BA JQ JQ JX JN JN JN JQ JN S. tropica CNT-253 BA JQ JQ JX JN JN JN JQ JN S. tropica CNT-254 BA JQ JQ JX JN JN JN JQ JN S. tropica CNS-257 BA JQ JQ JX JN JN JN JQ JN S. tropica CNS-280 BA JQ JQ JX JN JN JN JQ JN S. arenicola CNB-458 BA JQ JQ JX JN JN JN JQ JN S. arenicola CNB-527 BA JQ JQ JX JN JN JN JQ JN S. arenicola CNH-643 BA JQ JQ JX JN JN JN DQ AY S. arenicola CNS-205 PL JQ JQ JX JN JN JN JQ CP S. arenicola CNS-673 FJ JQ JQ JX JN JN JN JQ JN S. arenicola CNS-744 FJ JQ JQ JX JN JN JN JQ JN S. arenicola CNS-759 FJ JQ JQ JX JN JN JN JQ JN S. arenicola CNS-803 FJ JQ JQ JX JN JN JN JQ JN S. arenicola CNS-820 FJ JQ JQ JX JN JN JN JQ JN S. arenicola CNS-823 FJ JQ JQ JX JN JN JN JQ JN S. arenicola CNS-991 FJ JQ JQ JX JN JN JN JQ JN S. arenicola CNS-992 FJ JQ JQ JX JN JN JN JQ JN S. arenicola CNT-086 FJ JQ JQ JX JN JN JN JQ JN S. arenicola CNT-088 FJ JQ JQ JX JN JN JN JQ JN S. arenicola CNT-137 FJ JQ JQ JX JN JN JN JQ JN S. arenicola (B) CNH-941 SC JQ JQ JX JN JN JN JX JX S. arenicola (A) CNH-996 SC JQ JQ JX JN JN JN JQ JN S. arenicola (B) CNH-964 SC JQ JQ JX JN JN JN DQ AY S. arenicola (B) CNP152 SC JQ JQ JX JN JN JN DQ JN S. pacifica (A) CNS-055 PL JQ JQ JX JN JN JN DQ DQ S. pacifica CNS-143 PL JQ JQ JX JN JN JN DQ JN S. pacifica (B) CNS-237 PL JQ JQ JX JN JN JN JN HQ S. pacifica CNS-801 FJ JQ JQ JX JN JN JN JQ JN S. pacifica (C) CNS-861 FJ JQ JQ JX JN JN JN JQ JN S. pacifica (C) CNS-863 FJ JQ JQ JX JN JN JN JQ HQ S. pacifica (F) CNT-029 FJ JQ JQ JX JN JN JN JQ HQ S. pacifica CNT-037 FJ JQ JQ JX JN JN JN JQ JN S. pacifica (C) CNT-045 FJ JQ JQ JX JN JN JN JQ HQ S. pacifica (D) CNT-084 FJ JQ JQ JX JN JN JN JQ HQ S. pacifica CNT-087 FJ JQ JQ JX JN JN JN JQ JN S. pacifica (C) CNT-094 FJ JQ JQ JX JN JN JN JQ HQ S. pacifica CNT-131 FJ JQ JQ JX JN JN JN JQ HQ S. pacifica (D) CNT-133 FJ JQ JQ JX JN JN JN JQ HQ S. pacifica (E) CNT-138 FJ JQ JQ JX JN JN JN JQ HQ S. pacifica (A) CNT-148 FJ JQ JQ JX JN JN JN JQ HQ S. pacifica (B) CNT-150 FJ JQ JQ JX JN JN JN JQ HQ642900
10 Supplemental Table 3. Coordinates for all loci as observed in the S. arenicola and S. tropica genome sequences. 16S atpd trpb gyrb reca rpob S. arenicola CNS-205 (CP000850) S. tropica CNB-440 (NC_009380) Start coordinate End coordinate Locus tag Start coordinate End coordinate (1) (2) (3) (1) (2) (3) (1) Sare_R0005 (2) Sare_R0030 (3) Sare_R0045 (1) (2) (3) (1) (2) (3) Locus tag (1) Strop_R0005 (2) Strop_R0031 (3) Strop_R Sare_4012 Sare_3396 Sare_0007 Sare_1389 Sare_ Strop_3630 Strop_0678 Strop_0004 Strop_1425 Strop_3933
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