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1 Supporting Information Ziemert et al /pnas Fig. S1. Geographic origin and numbers of Salinispora strains used in this study. Fig. S2. Operational biosynthetic unit (OBU) phylogeny supports duplication followed by divergence. Nonribosomal peptide synthetase (NRPS)4 was detected in all but one of the 75 Salinispora strains. NRPS19 was placed in a separate OBU that shared ca. 80% homologous C-domain sequence identity with NRPS4. It possesses an additional C domain in the NRPS gene Orf8 and was observed in 16 S. arenicola and S. pacifica strains. Individual phylogenies of the NRPS genes orf3 and 4 and the kynurenine monooxygenase orf6 from these two pathways all revealed a sister relationship between the NRPS4 and NRPS19 clades, which can best be explained by a duplication event. The products of these pathways have yet to be identified. 1, methyltransferase; 2, major facilitator superfamily; 3, NRPS; 4, NRPS; 5, MbtH; 6, kynurenine-3-monooxygenase; 7, NRPS; 8, NRPS; 9, lantibiotic dehydratase; 10, penicillin amidase. 1of10
2 Fig. S3. Polyketide synthase (PKS) and NRPS relative abundance and NaDPoS PKS classification (1). FAS, fatty acid synthase. 1. Ziemert N, et al. (2012) The natural product domain seeker NaPDoS: A phylogeny based bioinformatic tool to classify secondary metabolite gene diversity. PLoS ONE 7(3):e of10
3 Fig. S4. Salinispora species phylogeny. Concatenated maximum-likelihood phylogeny based on 10 loci (dnaa, gyrb, pyrh, reca, pgi, trpb, atpd, succ, rpob, topa) derived from the genome sequence data. Strain names are followed by a capitalized letter, which indicates the 16S rrna sequence type and geographic origin. No letter indicates standard (ST) sequence type as previously described (1). Bootstrap support for maximum-likelihood and neighbor-joining methods was the same and is indicated along with Bayesian posterior probabilities. Numbers on the right indicate major clades used in Fig Freel KC, Edlund A, Jensen PR (2012) Microdiversity and evidence for high dispersal rates in the marine actinomycete Salinispora pacifica. Environ Microbiol 14(2): of10
4 Fig. S5. Taxonomic assignments of top BLAST matches for OBUs observed in one strain (singletons). Cyano, cyanobacteria; proteo, proteobacteria. Fig. S6. Location-specific pathway acquisition. Likelihood analysis showing multiple ancestral nodes for PKS17 on the Salinispora species tree (black circles). This result was used to infer that the OBU had been acquired independently by four S. arenicola strains from Fiji (CNS-991, CNT-005, CNY-231, and CNY-280) and one S. pacifica strain from the Sea of Cortex (CNY-331). 4of10
5 Table S1. Salinispora strains and sequence accession numbers Species and strain IMG genome ID NCBI taxon ID S. arenicola CNB S. arenicola CNB S. arenicola CNH S. arenicola CNH S. arenicola CNH S. arenicola CNH S. arenicola CNH S. arenicola CNH S. arenicola CNP S. arenicola CNP S. arenicola CNQ S. arenicola CNR S. arenicola CNR S. arenicola CNS S. arenicola CNS S. arenicola CNS S. arenicola CNS S. arenicola CNS S. arenicola CNT S. arenicola CNT S. arenicola CNT S. arenicola CNT S. arenicola CNT S. arenicola CNT S. arenicola CNX S. arenicola CNX S. arenicola CNX S. arenicola CNX S. arenicola CNX S. arenicola CNY S. arenicola CNY S. arenicola CNY S. arenicola CNY S. arenicola CNY S. arenicola CNY S. pacifica CNQ S. pacifica CNR S. pacifica CNR S. pacifica CNR S. pacifica CNS S. pacifica CNS S. pacifica CNS S. pacifica CNS S. pacifica CNT S. pacifica CNT S. pacifica CNT S. pacifica CNT S. pacifica CNT S. pacifica CNT S. pacifica CNT S. pacifica CNT S. pacifica CNT S. pacifica CNT S. pacifica CNT S. pacifica CNT S. pacifica CNT S. pacifica CNT S. pacifica CNT S. pacifica CNT S. pacifica CNY S. pacifica CNY S. pacifica CNY S. pacifica DSM of10
6 Table S1. Cont. Species and strain IMG genome ID NCBI taxon ID S. pacifica DSM S. pacifica DSM S. pacifica DSM S. pacifica DSM S. pacifica DSM S. tropica CNB S. tropica CNB S. tropica CNB S. tropica CNH S. tropica CNR S. tropica CNS S. tropica CNS IMG, Integrated Microbial Genomes database; NCBI, National Center for Biotechnology Information. 6of10
7 Table S2. Pathway (OBU) distributions among Salinispora arenicola strains Name CNB-458 CNB-527 CNH-646 CNH-877 CNH-905 CNH-941 CNH-962 CNH-964 CNQ-748 CNR-107 CNR-921 CNP-105 CNP-193 CNS-051 CNS-205 CNS-673 CNS-744 PKS FAS NRPS lym NRPS PKS rif PKS1A PKS3A PKS3B NRPS PKS1B Sid PKS PKS1C PKS PKS NRPS PKS PKSNRPS sal NRPS NRPS PKS NRPS PKS PKS NRPS NRPS PKS PKS arn PKS PKS PKS PKS PKS PKS cym NRPS NRPS NRPS NRPS NRPS NRPS NRPS NRPS CNS-991 CNT-005 CNT-798 CNT-800 CNT-849 CNT-850 CNT-857 CNT-859 CNX-481 CNX-482 CNX-508 CNX-814 CNX-891 CNY-011 CNY-231 CNY-234 CNY-237 CNY-256 CNY-260 CNY-280 7of10
8 Table S3. Pathway (OBU) distributions among Salinispora tropica strains Pathway CNB-440 CNB-476 CNB-536 CNH-898 CNS-197 CNS-416 CNR-699 PKS FAS NRPS lym Sid lom slm sal Sid Sid NRPS spo STpks FAS NRPS cya PKS PKS NRPS Strain 8of10
9 Table S4. Pathway (OBU) distributions among Salinispora pacifica strains Strain CNQ-768 CNS-055 CNR-114 CNR-894 CNR-942 CNS-103 CNS-860 DSM45543 DSM45544 CNS-996 CNT-001 CNT-003 CNT-029 CNT-045 CNT-084 CNT-124 CNT-131 DSM45546 DSM45547 DSM45548 DSM45549 CNT-569 CNT-584 CNT-603 CNT-609 CNT-851 CNT-854 CNT-855 CNT-796 CNY-330 CNY-331 Pathway PKS FAS NRPS cya lym lom NRPS PKS slm PKS NRPS NRPS PKS NRPS NRPS sal SID NRPS PKS FAS NRPS PKS NRPS NRPS NRPS SID SID PKS PKS NRPS NRPS PKS NRPS spo STPKS PKS PKS PKS FAS PKS PKS PKS PKS PKS PKS of10
10 Table S4. Cont. Strain CNQ-768 CNS-055 CNR-114 CNR-894 CNR-942 CNS-103 CNS-860 DSM45543 DSM45544 CNS-996 CNT-001 CNT-003 CNT-029 CNT-045 CNT-084 CNT-124 CNT-131 DSM45546 DSM45547 DSM45548 DSM45549 CNT-569 CNT-584 CNT-603 CNT-609 CNT-851 CNT-854 CNT-855 CNT-796 CNY-330 CNY-331 Pathway PKS PKS PKS PKS PKS PKS PKS PKS NRPS NRPS NRPS NRPS PKS FAS NRPS PKS PKS FAS PKS PKS PKS PKS PKS PKS PKS PKS NRPS NRPS NRPS NRPS NRPS NRPS NRPS NRPS NRPS NRPS NRPS NRPS NRPS NRPS NRPS NRPS NRPS of 10
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