From: Phenotypic convergence in bacterial adaptive evolution to ethanol stress
Strain | Type | Gene | Position | Nucleotide change | Source | Gene Description | ||
---|---|---|---|---|---|---|---|---|
Reference | Gene | |||||||
A | 125 SNPs and 6 Indels (see Additional file 9: Table S3) | Â | Â | Â | ||||
B | Ins | hns a | 1294843 | −273 | 1195 bp | IS5 insertion, promoter | SOLiD and Sanger | global DNA-binding transcriptional dual regulator |
 | Ins | yeaR | 1881551 | 147 | 1342 bp | IS186 insertion | SOLiD and Sanger | conserved hypothetical protein |
 | SNP | iscR | 2660496 | 292 | A → T |  | SOLiD and MiSeq | DNA-binding transcriptional activator |
 | SNP | ilvG | 3685148 | 974 | A → T |  | SOLiD and MiSeq | acetolactate synthase II, large subunit |
C | Del | 12 genes | 575013 |  | −6775 bp |  | SOLiD and Sanger | insH,nmpC,essD,ybcS,rzpD,rzoD,borD,ybcV,ybcW,nohB,tfaD,ybcY |
 | Ins | nagE | 705229 | 864 | +3:CCG | 3 bp insertion | SOLiD and Sanger | fused N-acetyl glucosamine specific PTS enzyme |
 | Ins | hns | 1294843 | −273 | 1195 bp | IS5 insertion, promoter | SOLiD and Sanger | global DNA-binding transcriptional dual regulator |
 | SNP | yeaY | 1892079 | 168 | T → A | synonymous | SOLiD and MiSeq | predicted lipoprotein |
 | Ins | menC | 2380504 | 485 | 1343 bp | IS186 insertion | SOLiD and Sanger | o-succinylbenzoyl-CoA synthase |
 | SNP | relA | 2910761 | 1547 | A → G |  | SOLiD, MiSeq and Sanger | (p)ppGpp synthetase I/GTP pyrophosphokinase |
 | SNP | rpoC | 3448513 | 2819 | G → A |  | SOLiD and MiSeq | RNA polymerase, beta prime subunit |
 | SNP | rpoA | 4200347 | 961 | T → A |  | SOLiD and MiSeq | RNA polymerase, alpha subunit |
D | Ins | hns | 1294843 | −273 | 1195 bp | IS5 insertion, promoter | SOLiD and Sanger | global DNA-binding transcriptional dual regulator |
 | SNP | proQ | 1916977 | 272 | A → T |  | SOLiD and MiSeq | predicted structural transport element |
 | SNP | ispG | 2639469 | 992 | T → C |  | SOLiD and MiSeq | 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase |
 | SNP | rpsD | 4198966 | 226 | T → G |  | SOLiD and MiSeq | 30S ribosomal subunit protein S4 |
 | Ins | yjhA | 4544220 | −39 | 1199 bp | IS5 insertion, promoter | SOLiD and Sanger | N-acetylnuraminic acid outer membrane channel protein |
E | Ins | hns | 1294843 | −273 | 1195 bp | IS5 insertion, promoter | SOLiD and Sanger | global DNA-binding transcriptional dual regulator |
 | Ins | cspC | 1909109 | 45 | 1199 bp | IS5 insertion | SOLiD and Sanger | stress protein, member of the CspA (cold shock protein) family |
 | SNP | relA | 2910944 | 1364 | A → T |  | SOLiD, MiSeq and Sanger | (p)ppGpp synthetase I/GTP pyrophosphokinase |
 | Ins | yhcM | 3379114 | 739 | +1:C |  | SOLiD, MiSeq and Sanger | hypothetical protein with nucleoside triphosphate hydrolase domain |
 | SNP | atpE | 3715545 | 54 | T → G |  | SOLiD and MiSeq | F0 sector of membrane-bound ATP synthase, subunit c |
F | Del | miaB | 694563 | 728 | −88 bp |  | SOLiD, MiSeq and Sanger | isopentenyl-adenosine A37 tRNA methylthiolase |
 | Ins | cspC | 1909109 | 45 | 1199 bp | IS5 insertion | SOLiD and Sanger | stress protein, member of the CspA (cold shock protein) family |
 | SNP | wzxC | 2120992 | 1304 | A → T |  | SOLiD, MiSeq and Sanger | colanic acid exporter |
 | SNP | iscR | 2660468 | 320 | T → A |  | SOLiD, MiSeq and Sanger | DNA-binding transcriptional activator |
 | SNP | relA | 2911891 | 417 | T → G |  | SOLiD, MiSeq and Sanger | (p)ppGpp synthetase I/GTP pyrophosphokinase |