Table 2.
A selected list of intergenic regions significantly underrepresented for transposon insertion
| Intergenic locus | Annotation | Category | Functional description |
|---|---|---|---|
| IG_1 | Origin | E | Chromosome I origin |
| IG_vca0002 | Origin | D | Chromosome II origin: the essential region is the last 380 nucleotides that contain the DnaA and RctB boxes |
| IG_vc2410 | Rnase P | E | M1 ribozyme compoent of Rnase P, essential for tRNA and rRNA processing |
| IG_vc2574 | Alpha_RBS | E | Ribosome binding site containing pseudoknot required for expression of 4 essential ribosome components |
| IG_vc0647 | Rab_I_chrI_7 | S | ncRNA discovered through transcriptomics; function unknown |
| IG_vc0431 | C-CF | D | ncRNA discovered through transcriptomics; function unknown |
| IG_vc0143 | B2 | D | ncRNA discovered through transcriptomics; expression is significantly upregulated during mouse and rabbit infection |
| IG_vc0646 | S15 | D | Ribosome binding site containing pseudoknot required for expression of the essential ribosomal gene rpsO |
| IG_vc2473 | RabM9_I_chrI_27 | S | ncRNA discovered through transcriptomics; significantly upregulated during rabbit infection |
| IG_vca0933 | M9_I5_chrII_36 | D | ncRNA discovered through transcriptomics; significantly downregulated during rabbit infection, but upregulated in mice |
Each intergenic region was classified as E = essential region; D = domain essential (contains a subdomain that is essential); S = ‘sick’ (nonessential, but required for optimal growth in vitro).