Non-coding genes and miscellaneous features were predicted using tRNAscan-SE [36], RNAMMer [37], Nilotinib Leukemia Rfam [38], TMHMM [39], and SignalP [40]. Additional gene prediction analyses and functional annotation were performed within the Integrated Microbial Genomes (IMG-ER) platform [41]. Genome properties The genome is 7,784,016 nucleotides with 63.40% GC content (Table 3) and comprised of 1 scaffold (Figure 3a, Figure 3b) of 2 contigs. From a total of 7430 genes, 7,372 were protein encoding and 58 RNA only encoding genes. Within the genome, 274 pseudogenes were also identified. The majority of genes (74.10%) were assigned a putative function whilst the remaining genes were annotated as hypothetical. The distribution of genes into COGs functional categories is presented in Table 4.

Table 3 Genome Statistics for Bradyrhizobium sp. strain WSM471. Figure 3a Graphical circular map of the chromosome of Bradyrhizobium sp. strain WSM471. From outside to the center: Genes on forward strand (color by COG categories as denoted by the IMG platform), Genes on reverse strand (color by COG categories), RNA genes (tRNAs … Figure 3b Graphical circular map of the plasmid of Bradyrhizobium sp. strain WSM471. From outside to the center: Genes on forward strand (color by COG categories as denoted by the IMG platform), Genes on reverse strand (color by COG categories), RNA genes (tRNAs … Table 4 Number of protein coding genes of Bradyrhizobium sp. strain WSM471 associated with the general COG functional categories.

Acknowledgements This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We gratefully acknowledge the funding received from the Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI) and the Centre for Rhizobium Studies (CRS) at Murdoch University. The authors would like to thank the Australia-China Joint Research Centre for Wheat Improvement (ACCWI) and SuperSeed Technologies (SST) for financially supporting Mohamed Ninawi��s PhD project.

Biological fixation of inert atmospheric dinitrogen gas is a process that can only be performed by certain prokaryotes in the domains Archaea and Bacteria. By far the greatest amounts of nitrogen (N) are fixed by specialized soil bacteria (root nodule bacteria or rhizobia) that form proto-cooperative, non-obligatory symbiotic relationships with legumes [1]. Indeed, these symbioses contribute Batimastat ~40 million tonnes of N annually to support global food production [2]. Species of the legume genus Trifolium (clovers) are amongst the most widely cultivated pasture legumes.