# *Bradyrhizobium diazoefficiens* USDA 110

| iPtgxDB Release     ||
| ------: | :--------: |
| Version | 1          |
| Date    | 09.09.2013 |

## Downloaded from
[/database/annotations/b-diazoefficiens-usda-110](/database/annotations/b-diazoefficiens-usda-110)

*Bradyrhizobium diazoefficiens* USDA 110 (Genbank #[NC_004463](https://www.ncbi.nlm.nih.gov/nuccore/NC_004463.1)) is a widely used model organism to study rhizobial symbiosis [1].

An iPtgxDB was created by hierarchically integrating protein coding sequences from the following annotation resources:

| Hierarchy | Resource | Link |
| :---: | :--- | :--- |
| 1 | NCBI RefSeq | NC_004463.1; from 22/07/2013 |
| 2 | Ensembl | Ensembl's Genomes project (GCA_000011365.1, Feb/2011) |
| 3 | Genoscope [2] | NC_004463, accessed 09/09/2013 |
| 4 | CMR [3] | J. Craig Venter Institute's Comprehensive Microbial Resource (CMR) |
| 5 | Prodigal [4] | *Ab initio* gene predictions from Prodigal (v2.5) |
| 6 | ChemGenome [5] | *Ab initio* gene predictions from ChemGenome (v2.0, http://www.scfbio-iitd.res.in/chemgenome/chemgenomenew.jsp; with parameters: method, Swissprot space; length threshold, 70 nt; initiation codons, ATG, CTG, TTG, GTG) |
| 7 | *in silico* ORFs | The *in silico* ORFs annotations were generated as described by Omasits and Varadarajan et al., 2017 |

Only ORFs above a selectable length threshold (here 18 aa) were considered. The iPtgxDB was created using the hierarchy RefSeq > Ensembl > Genoscope > CMR > Prodigal > *in silico*. Files were parsed to extract the identifier, coordinates and sequences of bona fide protein-coding sequences (CDS) and pseudogene entries.

### References
1. Kaneko T, Nakamura Y, Sato S, Minamisawa K, Uchiumi T, Sasamoto S, Watanabe A, Idesawa K, Iriguchi M, Kawashima K, Kohara M, Matsumoto M, Shimpo S, Tsuruoka H, Wada T, Yamada M, Tabata S. 2002. Complete genomic sequence of nitrogen-fixing symbiotic bacterium *Bradyrhizobium japonicum* USDA110. DNA Res. 9(6): 189-197.
2. Vallenet, D., Belda, E., Calteau, A., Cruveiller, S., Engelen, S., Lajus, A., Le Fevre, F., Longin, C., Mornico, D., Roche, D. et al. 2013. MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res 41: D636-647.
3. Peterson, J. D., Umayam, L. A., Dickinson, T., Hickey, E. K., White, O. 2001. The Comprehensive Microbial Resource. Nucleic Acids Res., 29, 1:123-5.
4. Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W., and Hauser, L.J. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
5. Singhal, P., Jayaram, B., Dixit, S.B., and Beveridge, D.L. 2008. Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations. Biophys J 94: 4173-4183.
6. Omasits, U., Varadarajan, A. R., Schmid, M., Goetze, S., Melidis, D., Bourqui, M., Nikolayeva, O., Quebatte, M., Patrignani, A., Dehio, C., Frey, J. E., Robinson, M. D., Wollscheid, B., and Ahrens., C. H. An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. bioRxiv, Cold Spring Harbor Labs Journals, 2017.
