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Table 1 Proteomics and dRNA-seq evidence for new ORFs and longer or shorter proteins than originally annotated

From: Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis – a rich resource to identify new transcripts, proteins and to study gene regulation

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
  1. 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