Additional file 1 of A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes
Creators: name: Podell, Sheila
name: Blanton, Jessica M.
name: Oliver, Aaron
name: Schorn, Michelle A.
name: Vinayak Agarwal
name: Biggs, Jason S.
name: Moore, Bradley S.
name: Allen, Eric E.
Publisher: name: figshare
Year: 2020
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Additional file 1: Supplementary Figure 1. Cyanobacteria MAGs classified taxonomically. A) PhyloPhlAn multi-locus concatenated tree, with Crinalium epipsammum as an outgroup. B) 16S rRNA gene/and average amino acid identity matrix with closest database relatives. Guidelines for assigning species, genus, family, and order-level taxonomic granularity were based on [25, 26] for AAI and [38] for 16S rRNA gene percent nucleotide identity. Supplementary Figure 2. Bacteroidetes MAGs classified taxonomically. A) PhyloPhlAn multi-locus concatenated tree, with SP5OBV1 as an outgroup. B) 16S rRNA gene/and average amino acid identity matrix with closest database relatives. Supplementary Figure 3. Alphaproteobacteria MAGs classified taxonomically. A) PhyloPhlAn multi-locus concatenated tree, with SP5OBV1 as an outgroup. B) 16S rRNA gene/and average amino acid identity matrix with closest database relatives. Supplementary Figure 4. Gammaproteobacteria MAGs classified taxonomically. A) PhyloPhlAn multi-locus concatenated tree, with SP5OBV1 as an outgroup. B) 16S rRNA gene/and average amino acid identity matrix with closest database relatives. Supplementary Figure 5. Oligoflexia MAG classified taxonomically. A) PhyloPhlAn multi-locus concatenated tree, with Oceanobaculum indicum as an outgroup. B) 16S rRNA gene/and average amino acid identity matrix with closest database relatives. Supplementary Figure 6. Relative abundance of metagenomically assembled sequences in 16S rRNA gene amplicon data sets. Amplified 16S rRNA gene sequences were recruited by blastn search at 97% identity to metagenomically assembled 16S rRNA genes and pooled into taxonomic groups as shown in Figure 3. Relative abundances in this chart are normalized to compensate for differences in total number of 16S rRNA reads obtained for each sponge sample (see Supplementary table 2 for total numbers of cleaned, merged amplicon reads). MAGs GM102CHS1, GM7ARS4, SP5ARS3, GM102ARS1 could not be included in this table because they did not contain any sequences overlapping the amplified region of the 16S rRNA gene. Supplementary Figure 7. Relative abundance of raw metagenomic reads mapping to assembled MAGS. Percentages are based on Bowtie read recruitment at 100% identity. MAGs were pooled into taxonomic groups as shown in Figure 3. A) Relative abundances for all classified reads; B) read recruitment percentages, including unclassified reads. All percentages have normalized for number of reads per sample, but not adjusted for potential differences in genome size. Supplementary Figure 8. Host associations of Type III secretion protein YscR homologs. A) Highlighted YscR homologs from MAGs of this study are shown in the context of a phylogenetic tree annotated with host types as described in [41]. B) Position of YscR homolog in Yersinia Type III secretion structure, adapted from [103]. Supplementary Figure 9. VirSorter candidate scaffolds in holobiont assemblies. Virus taxonomic groups were obtained by DarkHorse assignment based on blastx matches to a custom database containing all viral sequences in the GenBank nr database as of January 2, 2019. Supplementary Figure 10. Flavin-dependent aromatic halogenases from SP12AHP1 and SP5AHP2. A) Operon structure map from IMG-MER [102] showing relative positions of tandem repeats in red. B) Phylogenetic tree of protein sequences, showing positions of putative halogenase sequences from this study relative to experimentally characterized database examples described in [71]. The tree is rooted with the bmp5 gene of Pseudoalteromonas putida [104]. PBDE pathway halogenases from Hormoscilla strains SP5, SP12, GUM102, and GUM202 clade with the bmp5 outgroup. Supplementary Figure 11. Comparison of candidate haloaromatic degradation gene neighborhoods. A) Gene neighborhood maps with halocatechol dioxygenase genes indicated in red. Maps and tables of predicted genes for B) SP12AHP1, C) SP5AHP2 and D) Altererythrobacter marensis were obtained using the automated IMG-ER annotation pipeline [102]. Supplementary Figure 12. Phylogenetic tree of halocatechol 1,2 dioxygenases. Tree shows SP12AHP1 and SP5AHP1 halocatechol 1,2-dioxygenases, highlighted in red, compared to closest GenBank nr database protein relatives. Chemically characterized chlorocatechol 1,2-dioxygenases are highlighted in blue. Supplementary Figure 13. MySQL schema for extracting sample metadata and abundance statistics from the Sponge Microbiome Database. Tables were populated using data in Supplementary tables 3,4, and 5 from [30]. Supplementary Table 1. Lamellodysidea sponge sampling metadata. Supplementary Table 2. Sponge holobiont and trichome metagenomic assembly statistics. Note: *GUM202 trichome enrichment reads were assembled in combination with Illumina GUM202 holobiont sequences, as previously described in [13]. Supplementary Table 3. MIMAG parameters for assembled genomes. Supplementary Table 4. Closest environmental matches from the GenBank nr database to 16S rRNA genes obtained from MAGs. GM102CHS1, GM7ARS4, SP5ARS3, GM102ARS1 are not included in this table because they did not include any 16S rRNA genes of 300 nt or longer. Supplementary Table 5. Assembled MAG 16S rRNA gene matches to Sponge Microbiome Database samples at 97% nucleotide identity. Database sequences were 99 bp segments amplified from the V4 region of the 16S rRNA gene [30]. Sponge Microbiome Database samples with the maximum number of matches to each MAG-associated 16S rRNA gene from this study were selected to determine the number and percent of matched sequences, and reported here along with host genus and geographical collection site. GM102CHS1, GM7ARS4, SP5ARS3, GM102ARS1 are not included in this table because they did not include any sequences overlapping the V4 region of the 16S rRNA gene. Supplementary Table 6. Tally of membrane-associated gene products in MAGs. Values for adhesive genes, signal sequences, and transporter types were tallied based on keyword searches of MAG annotations at IMG-MER [102]. Supplementary Table 7. Viral defense genes in assembled MAGs. Values were tallied based on keyword searches of MAG annotations at IMG-MER [102]. Supplementary Table 8. Biosynthetic gene clusters predicted by AntiSmash [62], supplemented with aromatic halogenases predicted by Pfam database model PF04820 [70].