Additional file 1 of Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster

Additional file 1: Supplementary text S1. Table S1. Basic information of 154 MAGs of the RCA cluster. Table S2. Basic sequencing and genomic information of 87 analysed RCA MAGs/genomes (82 MAGs and 5 genomes from isolates) and locations where the metagenomic samples and isolates were collected. Table S3. Metadata for metagenomic data used to estimate the proportion of the RCA cluster and 10 of the 13 RCA species. Table S4. Metadata for metatranscriptomic data used to estimate the proportion of the RCA cluster and 10 of the 13 RCA species. Table S5. Genome data of Southern Ocean SAG [21]. Table S6. Annotation of genes encoded on PGC-containing extrachromosomal replicons of two Nereidia strains. Table S6. The incomplete prophage in the Rhodobacteraceae bacterium IMCC1909. Table S7. The GC content of genomes and PR genes in the RCA cluster. Table S8. Annotation of genes encoded on PGC-containing extrachromosomal replicons of two Nereidia strains. Figure S1. The variation of the genome size, GC content and CDS number in Planktomarina and Pseudoplanktomarina species. Values at the top indicate significant p-values. The significant difference was tested using the Wilcoxon test using the R package "rstatix" v0.7.2. Figure S2. Phylogenetic tree of southern Ocean SAG [21] and the RCA cluster. Figure S3. Phylogenetic tree of the RCA cluster with two Nereida strains as most closely related non-RCA species. Figure S4. Organization and structure of the PR operon present in genomes of RCA species. Blh: 15,15′-β-carotene dioxygenase; crt: carotenoid biosynthesis genes. Figure S5. Phylogenetic tree of the pufM gene and structure and arrangements of PGC operons detected in the RCA cluster. A: Phylogenetic tree based on 43 pufM genes. B: structure and arrangements of PGC operons detected in genomes of Planktomarina C6, C7 and C8. The tree was constructed using IQ-TREE under the LG+R10 substitution model with 1000 ultrafast bootstraps. Only bootstrap values ≥75 were shown with filled blue circles. Figure S6. Geographic distribution and relative abundance of ten of the thirteen RCA species (C1, C3-C6, B1-B4, A1) in different layers based on metagenomic and metatranscriptomic data: epipelagic (EPI, 0-200 m), mesopelagic (MES, 200-1000 m) and bathypelagic (BAT >1000 m). The dots in different colors indicated the relative abundance of the species as percent of the RCA cluster. Figure S6A - Metagenomics species A1, B1, B2. Figure S6B – Metagenomics species B3, B4/5. Figure S6C – Metagenomics species C1, C3, C4/C5, C6. Figure S6D – Metatranscriptomics species A1, B1, B2, B3, B4. Figure S6E – Metatranscriptomics species C1, C3, C4/5, C6.