TABLE 1.
Characteristics of the 46 most abundant dormant B. subtilis spore mRNAsa
| Gene | Length (nt)b | No. of reads | RPKM valuec | Sigma factor(s) |
|---|---|---|---|---|
| RPKM > 7,000 | ||||
| sspA | 210 | 2,479 | 10,848 | F and G |
| sspE | 255 | 159,687 | 577,971 | F and G |
| sspF | 186 | 26,976 | 131,260 | G |
| sspJ | 141 | 20,095 | 133,439 | G |
| sspK | 153 | 3,947 | 23,696 | G |
| sspM | 105 | 2,878 | 25,626 | G |
| sspN* | 147 | 32,488 | 201,551 | F and G |
| tlp* | 252 | 56,102 | 202,343 | F and G |
| sspO† | 147 | 16,078 | 102,766 | F and G |
| sspP† | 147 | 13,486 | 86,361 | F and G |
| yfhD | 192 | 36,871 | 177,547 | F and G |
| yhcN | 570 | 4,689 | 7,464 | F and G |
| yhcQ | 654 | 9,699 | 13,540 | G |
| yhcV | 423 | 74,504 | 161,470 | F and G |
| yhdB | 243 | 22,294 | 82,876 | G |
| yizC | 198 | 16,362 | 75,142 | G |
| ykzE‡ | 177 | 51,891 | 271,743 | G |
| ykzP‡ | 156 | 81,390 | 480,746 | G |
| ymfJ | 258 | 24,076 | 85,309 | F and G |
| yozQ | 294 | 3,085 | 9,528 | G |
| ypzF | 147 | 133,054 | 827,125 | G |
| ypzG | 153 | 110,878 | 652,271 | G |
| yqfX | 390 | 16,853 | 39,843 | G |
| yrzQ§ | 132 | 11,482 | 81,387 | F and G |
| yrzR§ | 192 | 3,663 | 17,332 | F and G |
| ytzC | 273 | 80,936 | 269,462 | F and G |
| ytzL | 159 | 26,849 | 157,337 | F and G |
| yuzA | 237 | 2,512 | 9,616 | G |
| yxeD | 354 | 2,697 | 7,175 | G |
| RPKM = 2,000–7,000 | ||||
| sspB | 204 | 809 | 2,972 | F and G |
| sspH | 180 | 593 | 2,415 | G |
| yhcM | 456 | 1,457 | 4,044 | F and G |
| yraE¶ | 198 | 54 | 3,249 | G |
| yrrD | 525 | 1,853 | 2,674 | G |
| yusG | 237 | 628 | 2,087 | UK |
| yusN | 333 | 942 | 2,082 | F and G |
| RPKM = 567–2,000 | ||||
| pdhA | 1,116 | 823 | 683 | A |
| sscA | 87 | 124 | 1,767 | K |
| sspI | 216 | 148 | 843 | F and G |
| yhcO | 969 | 1,502 | 1,429 | E and K |
| ykzD | 138 | 108 | 714 | G |
| yoyE | 126 | 137 | 1,462 | G |
| ypzI | 132 | 119 | 850 | F and G |
| yraD¶ | 300 | 284 | 843 | G |
| yrzB | 282 | 208 | 567 | UK |
| yutC | 633 | 516 | 636 | G |
Data are averages from RNA-seq analyses on RNA from 3 independent highly purified spore preparations prepared on plates, all as described in Materials and Methods. Genes in boldface type are those for which the protein product has been identified in dormant spores (33, 34). RNA polymerase σ factors that direct the transcription of individual genes were identified using information in subtiwiki and the literature (26), including information on gene expression in sporulation and correlation of a gene’s expression with that from a gene definitively established as being under the control of a specific sigma factor. For the yusG and yrzB genes, their σ factor dependence is unknown (UK). Two genes with the same symbol are almost certainly cotranscribed, as seen by their appropriate genomic arrangement and the complete coverage of both genes by RNA-seq reads, with no gaps in intergenic spaces (data not shown; see also Fig. S2F in the supplemental material).
Note that the mRNAs for coding genes are invariably longer than the coding sequences shown; this is ∼50 nt for these 46 most abundant mRNAs (data not shown).
The average standard deviations for the average RPKM values were 8% for the 29 most abundant mRNAs, 21% for the 7 next most abundant mRNAs, and 17% for the 10 next most abundant mRNAs.