Table 4. R. rubrum gene candidates identified from RNAseq and comparisons with RQ producer R. ferrireducens and RQ non-producer R. sphaeroides.
| Gene candidate (NCBI) | RPKM Anaerobic:Aerobic | Log (E-value Rr:Rf /E-value Rr:Rs) | eggNOG orthologous gene cluster | Proposed Function |
|---|---|---|---|---|
| rquA (Rru_A3227) | 8.4 | -57.8 | 179MD | methyltransferase |
| Rru_A1274 | 24.3 | -67.6 | 176BB | Radical SAM family protein |
| Rru_A2871 | 15.2 | -18.3 | — | Peptidase/amidohydrolase |
| Rru_A2553 | 13.5 | -5.1 | — | Ubiquinone/menaquinone biosynthesis methyltransferase |
| Rru_A2106 | 7.7 | -68.4 | 16QF5 | Hypothetical protein |
| Rru_A3606 | 7.1 | -31.8 | 16RW4 | Hypothetical protein |
| Rru_A1729 | 6.9 | -35.2 | 16YKK | Hypothetical protein |
| Rru_A3004 | 4.5 | -73.4 | 16Q21 | Class I and Class II aminotransferases |
| Rru_A3121 | 3.2 | -170.0 | — | Asparagine synthase |
| Rru_A3231 | 3.0 | -57.0 | 1748D | Isoprenoid biosynthesis protein with amidotransferase-like domain |
RNA expression differences in anaerobic and aerobic conditions are shown as ratios of RPKM measured in each condition. Comparisons in similarity between each R. rubrum (Rr) gene and its closest relative in R. ferrireducens (Rf) and R. sphaeroides (Rs) are shown as ratios of BLASTp E-values. When R. rubrum genes are members of orthologous gene clusters shared with R. ferrireducens but not with R. sphaeroides, the eggNOG cluster number is shown. Proposed functions are the annotations on each gene in the R. rubrum ATCC 11170 genome from NCBI. The complete set of RNAseq data and eggNOG analysis may be found in the S1 Table.