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

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

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