Table 1.
RPKM values calculated for transcribed genes of interest
| Gene function | Gene or ORF | Function or predicted function | RPKMa |
|||
|---|---|---|---|---|---|---|
| Control | Ffl | Amp | Str | |||
| Putative maintenance and stability genes | repA | Replication initiation | 4,376 | 3,780 | 4,772 | 4,753 |
| pAR060302_0051 | Putative ParA partition protein | 6,942 | 11,306 | 7,534 | 7,066 | |
| pAR060302_0052 | Putative ParB partition protein | 14,265 | 20,154 | 13,480 | 14,939 | |
| Putative DNA binding genes | pAR060302_0023 | Putative IHFb transcriptional regulator | 5,130 | 2,097 | 5,583 | 5,243 |
| pAR060302_0025 | Putative antitoxin component protein | 206,070 | 361,900 | 201,615 | 203,271 | |
| pAR060302_0026 | Putative toxin component protein | 86,543 | 148,982 | 85,362 | 81,898 | |
| pAR060302_0027 | Putative DNA binding protein | 3,176 | 3,074 | 3,431 | 3,769 | |
| pAR060302_0188 | Putative H-NS-like protein | 23,351 | 14,876 | 26,414 | 27,179 | |
| Resistance genes | floR | Phenicol resistance | 8,543 | 71,346c | 8,463 | 8,845 |
| tetA | Tetracycline resistance | 991 | 1,544 | 958 | 993 | |
| blaCMY-2 | Extended-spectrum β-lactamase | 34,314 | 35,415 | 32,488 | 32,308 | |
| aadA | Aminoglycoside resistance | 323,889 | 217,434 | 334,860 | 330,472 | |
| aacA | Aminoglycoside resistance | 64,841 | 61,992 | 56,338 | 61,287 | |
| Genes within the putative transfer loci | pAR060302_0075 | Hypothetical protein | 8,277 | 3,343 | 8,070 | 8,170 |
| pAR060302_0097 | Hypothetical protein | 13,364 | 6,383 | 14,597 | 13,921 | |
| pAR060302_0183 | Hypothetical protein | 3,452 | 5,266 | 3,985 | 4,104 | |
a
RPKM is calculated as the number of reads aligned per kilobase of gene per millions total reads. Antibiotics are abbreviated as follows: ampicillin, Amp; florfenicol, Ffl; and streptomycin, Str.
b
IHF, integration host factor.
c
A >3-fold change in expression that is statistically significant (q < 0.05).