Additional file 1 of Distribution and diversity of dimetal-carboxylate halogenases in cyanobacteria

Abstract

Additional file 1: Table S1. Accession numbers of cylC homologs and aurFgenes used for primer design. Figure S1. (a) Phylogenetic tree (FastTree GTR with a rate of 100) of cylC homologs highlighted according to the groups selected for degenerate primer design. (b) Schematic representation of the different pairs of degenerate primers. Figure S2. PCR-based detection of cylC homologs in the LEGEcc. Five pairs of primers were designed based on conserved regions identified in the cylC gene. Each primer pair was used in a PCR screen of the gDNA obtained from diverse strains (n = 326) of the LEGEcc. The resulting amplicons were cloned and sequenced. Sequences for each primer pair were aligned with the corresponding regions of cylC genes found in the NCBI reference genomes (cyanobacteria only) and those from LEGEcc strains’ genomes. Shown are the resulting cladograms (RaxML, 1000 replicates) for each primer pair used in the screening. Blue squares indicate sequences obtained from the PCR screen. Figure S3. RaxML cladogram (1000 replicates) of the 16S rRNA gene of LEGEcc strains (grey squares) and from cyanobacterial strains with NCBI-deposited reference genomes, screened in this study. Taxonomy is presented at the order level (colored ranges). Strains whose genomes encode CylC homologs are denoted by black squares. Green squares indicate that at least one CylC homolog was detected by PCR-screening and verified by retrieving the sequence of the corresponding amplicon through cloning followed by Sanger sequencing. The cladogram topology is the same as shown in Fig. 3 of the main manuscript, but here bootstrap values (equal or above 0.7) are shown. Table S2. GenBank or RefSeq assembly acession number and LEGEcc genome used for CORASON analysis. Table S3. BLASTp search of CylC homologs against Aliterella sp., Chroococcidiopsis sp. and Gloeobacter sp. Figure S4. Rieske-containing biosynthetic gene clusters encoding CylC homolog(s). Figure S5. PriA-containing biosynthetic gene clusters encoding CylC homolog(s). Figure S6. Cytochrome P450/sulfotransferase-containing biosynthetic gene cluster encoding a CylC homolog. Figure S7. Type I PKS (chlorosphaerolactylate/columbamide/microginin/puwainaphycin-like) biosynthetic gene clusters encoding CylC homolog(s). Figure S8. Dialkylresorcinol biosynthetic gene clusters encoding CylC homolog(s). Figure S9. Type III PKS biosynthetic gene clusters encoding CylC homolog(s). Figure S10. Nitronate monooxygenase-containing biosynthetic gene clusters encoding a CylC homolog. Figure S11. Unclassified (likely incomplete) biosynthetic gene clusters encoding a CylC homolog. Table S4. BLAST search of Rieske-containing BGCs genes from Calothrix brevissima NIES 22 against Synechocystis sp. PCC 6803. Figure S12. Phylogenetic tree of FAD-dependent halogenases based on CORASON outputs with illustrative BGC architectures. Figure S13. Phylogenetic tree of nonheme iron-dependent halogenases based on CORASON outputs with illustrative BGC architectures. Figure S14. Phylogenetic tree of dimetal-carboxylate halogenases based on CORASON outputs with illustrative BGC architectures