Table 1 The specifics of all large putative horizontally acquired gene clusters from chromosome I of V. vulnificus CMCP6, including their δ* (against V. vulnificus chromosome I) and GC composition values compared with chromosome I of V. vulnificus CMCP6. Vv5%, Vv10% and Vv10% are non-anomalous genomic fragments used as a reference clade. Ct1 and Ct2 represent Chlamydia trachomatis genomic fragments and are used as outgroups. The three V. vulnificus CMCP6 islands identified by Zhang and Zhang [22] are included in the last column. The presence of the V. vulnificus CMCP6 putative GIs in V. vulnificus YJ016 is verified by Web-ACT analysis [15].
From: An acquisition account of genomic islands based on genome signature comparisons
Locus | Coordinates | Size (bp) | Presence in V. vulnificus YJ016 chromosome I (fraction bp similar) | GI characteristics | δ* (× 1000) | genomic fragments with a lower δ* | GC% | genomic fragments with a lower GC% | Islands identified by [22]. |
|---|---|---|---|---|---|---|---|---|---|
VvI-1 | 6115–17532 | 11417 | Partially present (3': 2325/11417) | Preceeded by a transposase (VV10005) | 59.4 | 89.6% | 41.3% | 5.57% |  |
VvI-2 | 355728–393737 | 38010 | Partially present (3': 2343/38010) | Bordered by phage integrase (VV10372) | 87.0 | 100% | 37.8% | 1.16% | VVGI-2 |
VvI-3 | 1094281–1109572 | 15292 | Entirely present | - | 42.7 | 81.3% | 49.7% | 95.3% |  |
inter | 1109572–1122005 | 12433 | Entirely present | - | 48.4 | 82.9% | 49.6% | 95.1% |  |
VvI-4 | 1122005–1138423 | 16419 | Entirely present | - | 40.4 | 80.9% | 50.7% | 99.5% |  |
VvI-5 | 1749663–1764864 | 15202 | Entirely present | - | 46.9 | 85.6% | 50.5% | 98.6% |  |
VvI-6 | 2017768–2042744 | 24976 | Partially present(3': 50/24976) | Putative integrase (VV12048) | 74.4 | 98.5% | 40.3% | 2.29% |  |
VvI-7 | 2437730–2603335 | 165606 | Highly dispersed | Superintegron integrase (VV12401), plasmid stabilisation protein encoding genes (VV12410)) | 57.8 | 100% | 41.1% | 5.26% | VVGI-1 |
VvI-8 | 2649661–2664017 | 14357 | Entirely present | - | 27.0 | 41.7% | 42.8% | 8.33% |  |
VvI-9 | 3033569–3043967 | 10399 | Largely present (3': 6834/10399) | Preceded by a transposase (VV12969) | 51.5 | 82.5% | 42.1% | 7.94% |  |
VvI-10 | 3260213–3279905 | 19692 | Largely absent (few limited blocks of identity) | Putative transposase (VV13182) | 64.6 | 95.8% | 39.8% | 1.81% | VVG1-3 |
VvI-7a | 2437730–2519809 | 82080 | Similar as VvI-7 | See VVI-7 | 62.4 | 100% | 40.8% | 2.56% | Similar as VvI-7 |
VvI-7b | 2519810–2603335 | 83526 | Similar as VvI-7 | See VVI-7 | 53.1 | 100% | 41.4% | 2.56% | Similar as VvI-7 |
VvI-5% | 1155000–1170000 | 15001 | Entirely present | - | 14.0 | 6.0% | 47.3% | 59.6% |  |
VvI-10% | 570000–585000 | 15001 | Entirely present | - | 17.2 | 10.6% | 46.4% | 54.1% |  |
VvI-25% | 270000–285000 | 15001 | Entirely present | - | 21.2 | 24.3% | 46.5% | 38.5% |  |
Ct1 | 270000–285000# | 15001 | NR& | NR | 167 | NR | 40% | NR |  |
Ct2 | 305000–320000 | 15001 | NR | NR | 169 | NR | 39% | NR |  |