Table 1.
Proteomics and dRNA-seq evidence for new ORFs and longer or shorter proteins than originally annotated
| Protein class | Proteins in search database | Free and Nod (dRNA-seq support) | Free (Free dRNA-seq support) | Nod (Nod dRNA-seq support) | Over all conditions |
|---|---|---|---|---|---|
| Annotated in RefSeq and ISGA | 4749 | 3187 (1958) | 2875 (1747) | 1893 (711) | 3608 |
| New in ISGA | 1391 | 78 (53) | 64 (46) | 46 (22) | 107 |
| Shorter in ISGA | 2857 | 109 (71) | 92 (60) | 41 (22) | 139 |
| Longer in RefSeq | 2857 | 108 | 86 | 51 | 144 |
| Longer in ISGA | 194 | 32 (19) | 31 (16) | 11 (3) | 39 |
| Shorter in RefSeq | 194 | - | - | - | 0 |
| iTSS ORFs | 5894 | 12 (12) | 10 (10) | 4 (0) | 14 |
| RefSeq only | 517 | 27 | 18 | 17 | 39 |
| Total | 18,653 | 3553 (2113) | 3176 (1879) | 2063 (758) | 4090 |
Numbers of proteins originally annotated in RefSeq and/or in our ISGA re-annotation are listed in column 2. Numbers of proteins identified in rich PSY medium or in symbiosis with soybean, i.e., the Free and Nod conditions studied here with dRNA-seq, are listed in columns 3-5, along with dRNA-seq support (without considering operons); column 6 “Over all conditions” refers to protein identifications in all 5 conditions - growth in rich and minimal medium, and symbiosis with soybean, cowpea or siratro. The respective protein IDs are also available in Additional file 7: Table S5