Files in this Data Supplement:

• Supplemental file 1 - Prophage loci in Silicibacter sp. strain TM1040 (Table S1); flagellar structural proteins in Roseobacter strains (Table S2); chemotaxis-related proteins in Roseobacter strains (Table S3); phototrophy-related genes in Jannaschia sp. strain CCS1 and other anoxygenic phototrophs (Table S4).
  MS Word document, 280K.
• Supplemental file 2 - Roseobacter type IV secretion system Vir proteins (Table S5); unique Roseobacter-specific genes and the number of total Roseobacter genomes that also contain the gene (Table S6); Roseobacter genes with a statistically significantly biased distribution in other marine bacterioplankton genomes (Table S8).
  MS Word document, 467K.
• Supplemental file 3 - Core Roseobacter genes in the three complete genomes and all nine draft genomes (Table S7).
  MS Word document, 937K.
• Supplemental file 4 - Comparative gene arrangements on Roseobacter chromosomes (Fig. S1A), on Roseobacter megaplasmids (Fig. S1B), and on small Roseobacter plasmids (Fig. S1C); multidimensional scaling plot of transporter families (Fig. S2); photosynthetic gene clusters of Jannaschia sp. strain CCS1, other cultured anoxygenic phototrophs, and environmental BAC clones (Fig. S3).
  MS Word document,6.5MB.
• Supplemental file 5 - Use of ammonium and urea, but not nitrate, as a source of nitrogen by S. pomeroyi DSS-3 (Fig. S4); use of inorganic phosphorus and phosphonate as a source of phosphorus by S. pomeroyi DSS-3 (Fig. S5); denitrification by S. pomeroyi DSS-3 (Fig. S6).
  MS Word document, 259K.