Table 3.
Percent of reads matching a DNA ligase and a transposase domain in 19 sequenced metagenomes.
| Metagenome | Type of metagenome | Percent of reads matching a lysogeny domain (rank) | Percent of reads matching a DNA ligase | MG-RAST ID number | Reference |
|---|---|---|---|---|---|
| Marine vent virome (subset) | Viral | 0.073 (6) | 1.245 | Subset of 4448187.3 | Anderson et al. (2011) |
| Marine vent virome (full) | Viral | 0.067 (7) | 0.594 | 4448187.3 | Anderson et al. (2011) |
| Farm soil | Microbial | 0.192 (4) | 0.131 | 4441091.3 | Tringe et al. (2005) |
| Acid mine drainage | Microbial | 0.468 (1) | 0.109 | 4441137.3, 444138.3 | Tyson et al. (2004) |
| Yellowstone hot springs | Viral | 0.104 (5) | 0.085 | 4443745.3, 4443746.3, 4443747.3, 4443762.3, 4443749.3, 4443750.3 | Bhaya et al. (2007) |
| Whale fall | Microbial | 0.332 (2) | 0.070 | 4441619.3, 4441656.4, 4441620.3 | Tringe et al. (2005) |
| Lost city hydrothermal field | Microbial | 0.291 (3) | 0.069 | 4461585.3 | Brazelton and Baross (2009) |
| Alvinella symbionts | Microbial | 0.044 (9) | 0.068 | 4441102.3 | Grzymski et al. (2008) |
| Peru margin sediments, 32 mbsf | Microbial | 0.020 (11) | 0.047 | 4459940.3 | Biddle et al. (2008) |
| Peru margin sediments, 1 mbsf | Microbial | 0.017 (13) | 0.044 | 4440961.3 | Biddle et al. (2008) |
| Arctic Ocean | Viral | 0.020 (12) | 0.018 | 4441622.3 | Angly et al. (2006) |
| Peru margin sediments, 16 mbsf | Microbial | 0.005 (18) | 0.018 | 4440973.3 | Biddle et al. (2008) |
| Peru margin sediments, 50 mbsf | Microbial | 0.016 (14) | 0.016 | 4459941.3 | Biddle et al. (2008) |
| Fishgut | Microbial | 0.023 (10) | 0.010 | 4441695.3 | Dinsdale et al. (2008) |
| Gulf of Mexico | Viral | 0.008 (15) | 0.006 | 4441625.4 | Angly et al. (2006) |
| Bay of British Columbia | Viral | 0.006 (17) | 0.004 | 4441623.3 | Angly et al. (2006) |
| Microbialites | Viral | 0.063 (8) | 0.003 | 4440320.3, 4440321.3, 4440323.3 | Desnues et al. (2008) |
| Sargasso Sea | Viral | 0.004 (19) | 0.002 | 4441624.3 | Angly et al. (2006) |
| Microbialites | Microbial | 0.008 (16) | 0 | 4440061.3 | Breitbart et al. (2009) |
Metagenomes are ordered according to the percent of reads matching a DNA ligase, with the highest percentage at the top. Column 3 lists the percentage of reads to a lysogeny-related domain, followed by the rank according to the percentage of reads with a hit among other metagenomes. The marine vent virome subset consists of all reads within contigs with a coverage of eight or greater plus all reads within contigs labeled “unknown” (Anderson et al., 2011). Marine vent virome reads were dereplicated prior to analysis. Mbsf, meters below seafloor. Metagenomes were downloaded from the MG-RAST database (www.metagenomics.anl.gov) and compared to a list of lysogeny-related sequences derived from Pfam seed sequences using blastx with a minimum e-value of 10−5.