Table 1. Characteristics of the original metagenomic libraries and of the subsequently selected data used for our comparative metagenomic study.
| |
Ma29 Marmara deep-sea sediment (1300 m) |
Ma101 Marmara deep-sea plankton (1000 m) |
ALOHA deep-sea plankton (500 m, 770 m and 4000 m) |
ALOHA euphotic zone plankton (70 m) |
Peru sediment mix (1, 16, 32 and 50 m bsf; seafloor 150.5 m) |
Whale carcasse mix (rib, bone and mat) |
Waseca soil |
|---|---|---|---|---|---|---|---|
| Sequencing method | Pyrosequencing | Pyrosequencing | Sanger, fosmid ends | Pyrosequencing | Pyrosequencing | Sanger, shotgun | Sanger, shotgun |
| Original average size (bp) | 181 | 181 | ∼900 | 110 | 100 | 3400 | 2400 |
| Size range (bp) | 135–240 | 135–240 | — | 90–130 | 90–130 | — | — |
| Average size after trimming (bp) | 191.44 | 191.47 | 192 | 110 | 109 | 192 | 192 |
| No of fragments | 178 199 | 183 631 | 149 022 | 319 477 | 266 259 | 200 722 | 192 639 |
| Total nucleotides (bp) | 34 114 417 | 35 159 828 | 28 612 224 | 35 142 470 | 29 022 231 | 38 538 624 | 36 986 688 |
| GC content (%) | 55.63 | 44.41 | 51.75 | 35.35 | 45.95 | 47.44 | 58.03 |
| tRNA (total matches) | 187 | 407 | 278 | 286 | 150 | 211 | 187 |
| % COG matches (from no of reads) | 28.81 | 37.45 | 29.46 | 22.22 | 12.82 | 38.83 | 30.56 |
| % KEGG matches (from no of reads) | 15.62 | 24.29 | 17.79 | 25.70 | 10.03 | 21.47 | 15.54 |
| % of matches against nr (only Ma29 and Ma101) | 44.9 | 57.2 | ND | ND | ND | ND | ND |
| No of rRNA matches (LSU+SSU) | 119 | 476 | 154 | 723 | 146 | 921 | 102 |
| COG marker protein matches/Mbp | 24.65 | 50.83 | 32.52 | 79.13 | 46.82 | 36.72 | 19.65 |
| Effective genome size (Mbp) | 3.66 | 1.78 | 2.77 | 1.59 | 2.92 | 2.45 | 4.59 |
| % of ‘ghost reads' | 11.8 | 9.1 | 0.3 | 10.0 | 12.8 | 0.6 | 4.6 |
| Reference | This study | This study | DeLong et al. (2006) | Frias-Lopez et al. (2008) | Biddle et al. (2008) | Tringe et al. (2005) | Tringe et al. (2005) |
Abbreviations: COG, clusters of orthologous groups; KEGG, Kyoto Encyclopedia of Genes and Genomes; ND, not determined; rRNA, ribosomal RNA; tRNA, transfer RNA; bsf, below sea floor.