Table 1.
List of small RNAs found within the Rickettsia prowazekii genome.
| Rp_sRa | Approximate start | Approximate stop | Size (bp) | Strand | Type of sRNA | Homology | Strand orientation | Notes | References |
|---|---|---|---|---|---|---|---|---|---|
| 1 | 10482 | 10278 | 204 | R | Trans | TG | </</< | Predicted as SIPHT #22 | Schroeder et al., 2015 |
| 2 | 10774 | 11003 | 230 | F | Trans | Rp | </>/< | Identified by RNA-seq | This study |
| 3 | 14215 | 13984 | 232 | R | Cis | Rp | H375_160 | Identified by RNA-seq | This study |
| 4 | 15459 | 15203 | 257 | R | Cis | TG, TRG, SFG | H375_160 | Identified by RNA-seq | This study |
| 5 | 19850 | 19622 | 229 | R | Trans | TG, TRG | >/ < /> | Identified by RNA-seq | This study |
| 6 | 22107 | 22298 | 192 | F | Trans | Rp | </>/> | Identified by RNA-seq | This study |
| 7 | 24935 | 25206 | 272 | F | Cis | TG, TRG, SFG | H375_230 | Identified by RNA-seq | This study |
| 8 | 47692 | 47542 | 150 | F | Trans | Rp | >/>/> | Predicted as SIPHT #21 | Schroeder et al., 2015 |
| 9 | 48035 | 48200 | 166 | F | Trans | Rp | >/>/> | Identified by RNA-seq | This study |
| 10 | 48620 | 48834 | 215 | F | Trans | Rp | >/>/> | Identified by RNA-seq | This study |
| 11 | 71739 | 72043 | 305 | F | Cis | TG, TRG, SFG | H375_570 | Identified by RNA-seq | This study |
| 12 | 76189 | 76452 | 264 | F | Cis | AG, TG, TRG | H375_570 | Identified by RNA-seq | This study |
| 13 | 77115 | 77335 | 221 | F | Trans | Rp | </>/< | Identified by RNA-seq | This study |
| 14 | 78259 | 78513 | 255 | F | Trans | Rp | </>/> | Identified by RNA-seq | This study |
| 15 | 88423 | 88616 | 194 | F | Trans | Rp | >/>/ < | Identified by RNA-seq | This study |
| 16 | 100282 | 99698 | 585 | R | Cis | TG, TRG, SFG | H375_740 | Identified by RNA-seq | This study |
| 17 | 105748 | 105486 | 263 | R | Trans | Rp | >/ < /> | Identified by RNA-seq | This study |
| 18 | 116363 | 116200 | 164 | R | Cis | TG | H375_870 | Identified by RNA-seq | This study |
| 19 | 132593 | 132781 | 189 | F | Trans | Rp | </>/> | Identified by RNA-seq | This study |
| 20 | 163641 | 163556 | 85 | R | Trans | AG, TG | </</> | Predicted as SIPHT #2 | Schroeder et al., 2015 |
| 21 | 173793 | 173974 | 182 | F | Cis | TG, TRG, SFG | H375_1300 | Identified by RNA-seq | This study |
| 22 | 177789 | 178118 | 330 | F | Cis | TG, SFG | H375_1330 | Identified by RNA-seq | This study |
| 23 | 185267 | 185484 | 218 | F | Cis | TG, TRG, SFG | H375_1400 | Identified by RNA-seq | This study |
| 24 | 218432 | 218657 | 226 | F | Cis | TG, TRG, SFG | H375_1610 | Identified by RNA-seq | This study |
| 25 | 257587 | 257856 | 270 | F | Cis | TG, TRG, SFG | H375_1930 | Identified by RNA-seq | This study |
| 26 | 261134 | 261341 | 208 | F | Trans | Rp | >/>/ < | Identified by RNA-seq | This study |
| 27 | 262322 | 262601 | 280 | F | Trans | Rp | >/>/ < | Identified by RNA-seq | This study |
| 28 | 275336 | 275043 | 294 | R | Cis | TG, TRG | H375_2050 | Identified by RNA-seq | This study |
| 29 | 306070 | 305924 | 146 | F | Trans | Rp | >/>/> | Predicted as SIPHT #12 | Schroeder et al., 2015 |
| 30 | 308324 | 308042 | 282 | R | Trans | TG | >/ < / < | Predicted as SIPHT #11 | Schroeder et al., 2015 |
| 31 | 308652 | 308848 | 197 | F | Trans | Rp | >/>/ < | Identified by RNA-seq | This study |
| 32 | 309308 | 309564 | 257 | F | Cis | TG, TRG, SFG | H375_2380 | Identified by RNA-seq | This study |
| 33 | 315408 | 315772 | 365 | F | Cis | TG, TRG, SFG | H375_2380 | Identified by RNA-seq | This study |
| 34 | 326339 | 326637 | 299 | F | Cis | TG, TRG, SFG | H375_2470 | Identified by RNA-seq | This study |
| 35 | 334531 | 334333 | 199 | R | Cis | TG, TRG, SFG | H375_2560 | Identified by RNA-seq | This study |
| 36 | 342505 | 342292 | 214 | R | Cis | TG, TRG, SFG | H375_2630 | Identified by RNA-seq | This study |
| 37 | 344054 | 343930 | 125 | R | Trans | Rp | >/ < / < | Identified by RNA-seq | This study |
| 38 | 366166 | 366242 | 77 | F | Trans | Rp | >/>/> | Identified by RNA-seq | This study |
| 39 | 371859 | 371506 | 353 | R | Trans | TG | >/ < / < | Predicted as SIPHT #10 | Schroeder et al., 2015 |
| 40 | 373780 | 373983 | 204 | F | Cis | TG, TRG, SFG | H375_2910 | Identified by RNA-seq | This study |
| 41 | 378222 | 378333 | 112 | F | Cis | TG, TRG, SFG | H375_2940 | Identified by RNA-seq | This study |
| 42 | 407851 | 407640 | 212 | R | Trans | Rp | >/ < / < | Identified by RNA-seq | This study |
| 43 | 427133 | 426907 | 227 | R | Trans | Rp | >/ < /> | Identified by RNA-seq | This study |
| 44 | 457001 | 456876 | 125 | F | Trans | TG | >/>/> | Predicted as SIPHT #9 | Schroeder et al., 2015 |
| 45 | 458370 | 458555 | 227 | R | Trans | TG | >/ < /> | Identified by RNA-seq | This study |
| 46 | 462025 | 462293 | 268 | F | Cis | TG, TRG, SFG | H375_3670 | Identified by RNA-seq | This study |
| 47 | 481518 | 481833 | 316 | F | Cis | TG, TRG, SFG | H375_3890 | Identified by RNA-seq | This study |
| 48 | 494600 | 494387 | 214 | R | Trans | Rp | </</< | Identified by RNA-seq | This study |
| 49 | 504250 | 504506 | 256 | F | Trans | Rp | >/>/> | Identified by RNA-seq | This study |
| 50 | 514132 | 513893 | 240 | R | Trans | TG | </</< | Identified by RNA-seq | This study |
| 51 | 531332 | 531187 | 146 | R | Trans | Rp | >/ < / < | Identified by RNA-seq | This study |
| 52 | 535456 | 535256 | 201 | R | Trans | Rp | >/ < / < | Identified by RNA-seq | This study |
| 53 | 558930 | 558719 | 212 | R | Trans | Rp | >/ < / < | Identified by RNA-seq | This study |
| 54 | 644329 | 644199 | 130 | R | Trans | Rp | </</< | Predicted as SIPHT #6 | Schroeder et al., 2015 |
| 55 | 659164 | 659057 | 107 | R | Trans | Rp | </</< | Predicted as SIPHT #5 | Schroeder et al., 2015 |
| 56 | 669521 | 669772 | 252 | F | Trans | Rp | >/>/ < | Identified by RNA-seq | This study |
| 57 | 697106 | 696934 | 173 | R | Trans | Rp | >/ < / < | Identified by RNA-seq | This study |
| 58 | 812662 | 812412 | 251 | R | Trans | Rp | </</< | Identified by RNA-seq | This study |
| 59 | 830223 | 830416 | 194 | F | Trans | Rp | >/>/ < | Identified by RNA-seq | This study |
| 60 | 844283 | 844606 | 324 | F | Trans | Rp | >/>/> | Identified by RNA-seq | This study |
| 61 | 859237 | 859436 | 200 | F | Trans | Rp | >/>/> | Identified by RNA-seq | This study |
| 62 | 909871 | 910281 | 411 | F | Cis | TG, TRG, SFG | H375_7470 | Identified by RNA-seq | This study |
| 63 | 925625 | 925929 | 305 | F | Trans | Rp | </>/< | Identified by RNA-seq | This study |
| 64 | 958095 | 957827 | 269 | R | Trans | Rp | </</< | Identified by RNA-seq | This study |
| 65 | 968393 | 968664 | 272 | F | Trans | Rp | >/>/> | Identified by RNA-seq | This study |
| 66 | 973818 | 973352 | 467 | R | Trans | TG | >/ < /> | Identified by RNA-seq | This study |
| 67 | 998167 | 997927 | 240 | R | Trans | Rp | >/ < / < | Predicted as SIPHT #25 | Schroeder et al., 2015 |
| 68 | 1039473 | 1039278 | 195 | R | Trans | Rp | </</< | Predicted as SIPHT #24 | Schroeder et al., 2015 |
| 69 | 1046344 | 1046671 | 328 | F | Trans | Rp | </>/< | Identified by RNA-seq | This study |
| 70 | 1105018 | 1104959 | 59 | F | Trans | Rp | >/>/> | Predicted as SIPHT #23 | Schroeder et al., 2015 |
a
RNA sequencing data demonstrates that R. prowazekii strain Breinl encodes for at least 58 novel candidate sRNAs. Each of these candidates are listed here. The sRNA number, the approximate start location based on the start of the RNA sequencing reads, the approximate stop location based again on the RNA sequencing reads, the nucleotide size, the sRNA carrying strand, the nature of sRNA, and its homology to other Rickettsia species are shown. The column labeled as “Strand Orientation” refers to the orientation of the upstream gene, the trans-acting sRNA, and downstream gene, respectively. For cis-acting sRNAs, the corresponding ORF is listed in this column (F, forward; R, reverse; Rp, R. prowazekii only; TG, typhus group (both R. prowazekii and R. typhi); TRG, transitional group; SFG, spotted fever group; >, sense strand; <, anti-sense strand). Sequences may not be found in all species of a particular group.