Table 1.
Genome Features from Sequencing the H. defensa A2C, AS3, NY26, and ZA17 Strains and Reannotation of the 5AT Strain
| A2C |
AS3 |
ZA17 |
NY26 | 5AT |
||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chromosome | pHDA2C.1 | pHDA2C.2 | pHDA2C.3 | Total | Chromosome | pHDAS3.1 | pHDAS3.2 | Total | Chromosome | pHDZA17.1 | pHDZA17.2 | pHDZA17.3 | Total | Chromosome | Chromosome | pHD5AT | Total | |
| GC% | 40.4% | 46.2% | 46.3% | 46% | 40.6% | 46% | 46.5% | 40.5% | 43.8% | 47.9% | 44.6% | 40.3% | 40.3% | 45.3% | ||||
| Size (pb) | 1,997,367 | 84,195 | 72,453 | 50,279 | 2,204,294 | 2,054,032 | 140,172 | 67,631 | 2,261,835 | 2,104,645 | 98,627 | 38,147 | 31,227 | 2,272,646 | 2,122,402 | 2,110,331 | 59,032 | 2,169,363 |
| Circularization | no | yes | No | yes | No | yes | no | no | no | no | yes | no | no | yes | ||||
| Coding density (pseudo) | 87.4% (8.3%) | 89.8% (13.2%) | 85.1% (12.7%) | 89.5% (16.4%) | 87.5% (8.8%) | 87.7% (11.5%) | 89.4% (12.1%) | 85.0% (17.0%) | 87.8% (11.7%) | 87.4% (7.8%) | 80.2% (18.9%) | 89.7% (18.7%) | 83.9% (13.2%) | 87.1% (8.6%) | 86.7% (17.2%) | 86.9% (11.3%) | 85.4% (13.4%) | 86.8% (11.4%) |
| CDS (pseudo) | 2,116 (156) | 85 (7) | 78 (8) | 68 (7) | 2,347 (178) | 2,181 (200) | 161 (16) | 69 (12) | 2,411 (227) | 2,185 (170) | 91 (16) | 50 (7) | 44 (5) | 2,370 (198) | 2,243 (282) | 2,241 (203) | 65 (7) | 2,306 (214) |
| ncRNA (pseudo) | 98 (13) | 10 | 4 | 6 | 118 (13) | 99 (13) | 16 | 3 (1) | 118 (14) | 99 (11) | 7 (2) | 2 | 4 | 112 (13) | 162 (18) | 158 (18) | 5 | 163 (18 |
| rRNA | 9 | 0 | 0 | 0 | 9 | 9 | 0 | 0 | 9 | 9 | 0 | 0 | 0 | 9 | 9 | 9 | 0 | 9 |
| tmRNA | 1 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | 1 | 1 | 0 | 1 |
| tRNA | 43 | 0 | 0 | 0 | 43 | 43 | 0 | 0 | 43 | 42 | 0 | 0 | 0 | 42 | 42 | 42 | 0 | 42 |
| Palindromic region | 2 | 0 | 2 | 0 | 4 | 1 | 0 | 2 | 3 | 2 | 2 | 0 | 0 | 4 | 2 | 1 | 0 | 1 |
| TEs CDS | 183 | 12 | 10 | 6 | 211 | 184 | 18 | 10 | 212 | 124 | 14 | 4 | 6 | 148 | 198 | 195 | 1 | 196 |
| Prophage island | 13 | 0 | 0 | 0 | 13 | 13 | 0 | 0 | 13 | 21 | 0 | 0 | 0 | 21 | 22 | 22 | 0 | 22 |
| Plasmid island | 7 | 0 | 0 | 0 | 7 | 8 | 0 | 0 | 8 | 7 | 0 | 0 | 0 | 7 | 11 | 11 | 0 | 11 |
| MGE (CDS) | 632 | 863 | 683 | 913 | 682 | 867 | 747 | 745 | 810 | |||||||||
Note.—Pseudo in parenthesis indicates the number of CDSs, or ncRNAs that are pseudogenized.
bp, base pairs; CDS, coding sequence; ncRNA, noncoding RNA; rRNA, ribosomal RNA; tRNA, transfer RNA; tmRNA, transfer-messenger RNA; TE, transposable element; MGE, mobile genetic element.