Table 5.
In silico-detected and not corroborated large insertions, deletions, and structural variations
PCR amplifications were performed using genomic DNA from both NCIMB 8052 (reference strain) and SA-1 as template. CDS, Coding sequence; COG, clusters of orthologous groups. Primer positions are indicated by the number followed by the direction F (forward) or R (reverse).
| Large indels | |||
| Location | Size (bp) | Position | Primer |
| Between hypothetical protein CDS and hypothetical protein CDS | 49 | 3 829 123–3 829 172 | 3828725F 5′-ATGCAGCCAAATAATGAC-3′ |
| Between hypothetical protein CDS and hypothetical protein CDS | 29 | 3 829 172–3 829 201 | 3829751R 5′-GAGCTCGATAATTACTAAG-3′ |
| Between hydroxylamine reductase CDS and heavy metal transport detoxification protein CDS | 37 | 1 685 323–1 685 360 | 1685136F 5′-TATATGCAGCAGAGCTAC-3′ 1685848R 5′-TCTTACCCCTGATGTTTC-3′ |
| Between EmrB/QacA family drug resistance transporter CDS and CBS domain-containing protein CDS | 35 | 1 797 550–1 797 585 | 1797141F 5′-GCTATGATGCCTATTAGC-3′ 1798121R 5′-CGCCTCTACTAATAACTCC-3′ |
| Between MATE efflux family protein CDS and TPR repeat-containing protein CDS | 30 | 2 039 733–2 039 763 | 2039609F 5′-TGGCATAAGGATATAATCG-3′ 2040035R 5′-AATGCCTTATCTAGCTTTC-3′ |
| Between GCN5-related N-acetyltransferase CDS and hypothetical protein CDS | 26 | 2 961 163–2 961 189 | 2960642F 5′-TCGGATTTATCTAGCAAAG-3′ 2961396R 5′-CTTTTATCGCACGAATATG-3′ |
| Between glycosyltransferase family protein CDS and triple helix repeat-containing collagen CDS | 26 | 3 001 786–3 001 812 | 3001353F 5′-CCAGTATGTAGCTAAGTTTC-3′ 3002219R 5′- CTTCTAAATAGGTCATTAGG-3′ |
| Between thioredoxin reductase CDS and hypothetical protein CDS | 28 | 3 117 231–3 117 259 | 3117006F 5′-CCAGGATAATTTTCCACTTC-3′ 3002219R 5′-AGACCTAGGCTATAGTTTTG-3′ |
| Between metal-dependent phosphohydrolase CDS and sulfate adenyltransferase large subunit CDS | 37 | 4 819 865–4 819 902 | 4819453F 5′-GTTAGGCTCATCTAAATAC-3′ 4820145R 5′-GAAAACTCTAGGAGATTTC-3′ |
| Structural variations | ||||
| ORF number | Associated COG/type | Size (bp) | Position | Primer |
| cbs_4437 | COG4974L/prophage inversion | 27 | 5 120 090–5 120 520 | 5119799F 5′-CACCCTTTCTACAATTAAC-3′ 5120810R 5′-TGCCATTGAGAAATATTGC-3′ |
| cbs_4182 | COG1352NT/deletion | 483 | 4 812 971–4 814 517 | 4812830F 5′-AAGTTATCTGTGGTTCTATC-3′ |
| cbs_4182 | COG1352NT/deletion | 529 | 4 814 951–4 814 980 | 4813942R 5′-ATTGAAGAAATGGGTGTATC-3′ |
| cbs_0060 | S (unknown function)/insertion | 149 | 79 389–79 831 | 79067F 5′-TGCTATATGTAGGGTAAAAG-3′ 80063R 5′-CACGTCATTCAATTTATCC-3′ |
| cbs_0878–cbs_0932 | COG1476K/internal translocation (prophage ITX1) | 39 411 | 1 071 995–1 111 510 | 1071556F 5′-GACCAGAACAAACTATTTAC-3′ 1072303R 5′-TAAGGCTACAGATGATAAAG-3′ 1111245F 5′-AGATGGCACATTGTTTTG-3′ 1111872R 5′-ACTGCTGACCTTTATAGATAG-3′ |
| cbs_1605–cbs_1680 | COG1961L/internal translocation (prophage ITX2) | 75 644 | 1 881 845–1 957 557 | 1881067F 5′-AAAATTGGACGAGGTAATAG-3′ 1958001R 5′-CAGTGAATAGTGCTATATAC-3′ 1957306F 5′-TATGAAAAGGAGCATATCAG-3′ 1883070R 5′-ATGAACTTCAGGTCTATGG-3′ |