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We report here the whole-genome sequences of 14 strains of Bradyrhizobium canariense, isolated from root nodules of Lupinus microanthus and Lupinus angustifolius, and 1 strain of Bradyrhizobium japonicum isolated from root nodules from Lupinus angustifolius in Algeria. These sequences add to the known diversity of this agronomically important genus.
Bradyrhizobium canariense (1), a sister species of Bradyrhizobium japonicum (2), was described in 2005 as a bacterium that nodulates legumes of the tribes Genisteae and Loteae, but not Glycine, while Bradyrhizobium japonicum forms root nodules in important crops, such as soybean (Glycine max), mungbean (Vigna radiata), cowpea (Vigna unguiculata), and siratro (Macroptilium atropurpureum) (3, 4). Bacteria of both species are aerobic Gram-negative motile rods which do not form spores, grow slowly, and are highly acid tolerant (1, 2, 5). Both species produce exopolysaccharides, and the culture phenotypes are diverse among the strains. They are found as free-living organisms in soils or as plant symbionts in root nodules. Initially described from root nodules from legumes of the Canary Islands (1), Bradyrhizobium canariense has since been found at many locations, such as Poland (6, 7), Italy and central Europe (7), Greece (8), and Morocco (9). While diverse strains of Bradyrhizobium japonicum are used as seed inoculants in Glycine max cultivation, the interest in using strains of Bradyrhizobium canariense as seed inoculants for cultures of Lupinus spp. and Ornithopus compressus (serradella) is rather recent (8). The 15 strains described here were isolated from root nodules of Lupinus angustifolius and Lupinus micranthus (Papilionoideae: Genisteae), collected at 2 sites in the National Park El-Kala (El-Tarf, Algeria). For whole-genome sequencing, DNA libraries were generated with a Nextera XT kit (Illumina, USA). Sequencing was performed on a MiSeq sequencer (Illumina) in three different runs generating 2 × 250-bp paired-end reads (version 2 chemistry) and 2 × 250-bp and 2 × 300-bp paired-end reads (version 3 chemistry). Quality control of the reads was assessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Genome assemblies were computed with SPAdes genome assembler 3.10 (10) and resulted in between 163 contigs (UBMA510) and 235 contigs (UBMA181) per genome, which were arranged with BioEdit (11) and analyzed with QUAST (12). For Bradyrhizobium canariense strains, the total genome lengths ranged between 8,220,547 bp (UBMA122) and 8,379,024 bp (UBMAN05), with G+C contents from 62.94% (UBMA052, UBMA183, and UBMA192) to 63.06% (UBMA122), and Bradyrhizobium japonicum UBMA197 had a larger genome, at 10,442,239 bp, with 63.3% G+C content. Genome coverage varied from 46-fold (UBMA510) to 255-fold (UBMA060). PlasmidFinder (13) and PlasmidSPAdes (14) detected no plasmids in these strains. RAST 2.0 (15, 16) identified between 6,304 (UBMAN05) and 7,974 (UBMA122) coding sequences for Bradyrhizobium canariense sequences and 10,125 coding sequences for Bradyrhizobium japonicum UBMA197. No photosystems, complete transposons or phages, or toxin genes were found in any of the strains. All strains had a nitrogenase capacity through a regulatory nifA gene and between 11 and 25 additional nif genes grouped in a genomic island. All strains were able to nodulate due to the presence of 9 to 12 nod genes typical of the Bradyrhizobium genus. The genomes also contained between 134 and 150 genes involved in the degradation of aromatic compounds. Finally, all strains were equipped with protein secretion systems of types II, IV, and VI, except for strain N05, which was almost deprived of such genes. The 15 presented genome sequences add to the knowledge of these species, which are considered potent inoculants for cultivation of certain leguminous plants (8).
This work was supported by research funds of the University of Annaba (Algeria) and by the Strategic Research fund of the University of Applied Sciences and Arts Western Switzerland (HES-SO).
Citation Chekireb D, Crovadore J, Brachmann A, Chablais R, Cochard B, Lefort F. 2017. Whole-genome sequences of 14 strains of Bradyrhizobium canariense and 1 strain of Bradyrhizobium japonicum isolated from Lupinus spp. in Algeria. Genome Announc 5:e00676-17. https://doi.org/10.1128/genomeA.00676-17.