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Genome Announc. 2017 July; 5(29): e00676-17.
Published online 2017 July 20. doi:  10.1128/genomeA.00676-17
PMCID: PMC5522942

Whole-Genome Sequences of 14 Strains of Bradyrhizobium canariense and 1 Strain of Bradyrhizobium japonicum Isolated from Lupinus spp. in Algeria

ABSTRACT

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.

GENOME ANNOUNCEMENT

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).

Accession number(s).

All genome sequences have been deposited at GenBank under the accession numbers reported in Table 1.

TABLE 1
Nucleotide sequence accession numbers

ACKNOWLEDGMENTS

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).

Footnotes

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.

REFERENCES

1. Vinuesa P, León-Barrios M, Silva C, Willems A, Jarabo-Lorenzo A, Pérez-Galdona R, Werner D, Martínez-Romero E 2005. Bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (Papilionoideae: Genisteae) from the Canary Islands, along with Bradyrhizobium japonicum bv. genistearum, Bradyrhizobium genospecies alpha and Bradyrhizobium genospecies beta. Int J Syst Evol Microbiol 55:569–575. doi:.10.1099/ijs.0.63292-0 [PubMed] [Cross Ref]
2. Jordan DC. 1982. Notes: transfer of Rhizobium japonicum Buchanan 1980 to Bradyrhizobium gen. nov., a genus of slow-growing, root nodule bacteria from leguminous plants. Int J Syst Bacteriol 32:136–139. doi:.10.1099/00207713-32-1-136 [Cross Ref]
3. Göttfert M, Grob P, Hennecke H 1990. Proposed regulatory pathway encoded by the nodV and nodW genes, determinants of host specificity in Bradyrhizobium japonicum. Proc Natl Acad Sci U S A 87:2680–2684. doi:.10.1073/pnas.87.7.2680 [PubMed] [Cross Ref]
4. Zhang YF, Wang ET, Tian CF, Wang FQ, Han LL, Chen WF, Chen WX 2008. Bradyrhizobium elkanii, Bradyrhizobium yuanmingense and Bradyrhizobium japonicum are the main rhizobia associated with Vigna unguiculata and Vigna radiata in the subtropical region of China. FEMS Microbiol Lett 285:146–154. doi:.10.1111/j.1574-6968.2008.01169.x [PubMed] [Cross Ref]
5. León-Barrios M, Gutiérrez-Navarro AM, Pérez-Galdona R, Corzo J 1991. Characterization of Canary Island isolates of Bradyrhizobium sp. (Chamaecytisus proliferus). Soil Biol Biochem 23:487–489. doi:.10.1016/0038-0717(91)90015-C [Cross Ref]
6. Narożna D, Pudełko K, Króliczak J, Golińska B, Sugawara M, Mądrzak CJ, Sadowsky MJ 2015. Survival and competitiveness of Bradyrhizobium japonicum strains 20 years after introduction into field locations in Poland. Appl Environ Microbiol 81:5552–5559. doi:.10.1128/AEM.01399-15 [PMC free article] [PubMed] [Cross Ref]
7. Stępkowski T, Żak M, Moulin L, Króliczak J, Golińska B, Narożna D, Safronova VI, Mądrzak CJ 2011. Bradyrhizobium canariense and Bradyrhizobium japonicum are the two dominant rhizobium species in root nodules of lupin and serradella plants growing in Europe. Syst Appl Microbiol 34:368–375. doi:.10.1016/j.syapm.2011.03.002 [PubMed] [Cross Ref]
8. Tiwari R, Howieson J, Yates R, Tian R, Held B, Tapia R, Han C, Seshadri R, Reddy TBK, Huntemann M, Pati A, Woyke T, Markowitz V, Ivanova N, Kyrpides N, Reeve W 2015. Genome sequence of Bradyrhizobium sp. WSM1253; a microsymbiont of Ornithopus compressus from the Greek Island of Sifnos. Stand Genomic Sci 10:113. doi:.10.1186/s40793-015-0115-9 [PMC free article] [PubMed] [Cross Ref]
9. Vinuesa P, Silva C, Werner D, Martínez-Romero E 2005. Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation. Mol Phylogenet Evol 34:29–54. doi:.10.1016/j.ympev.2004.08.020 [PubMed] [Cross Ref]
10. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi:.10.1089/cmb.2012.0021 [PMC free article] [PubMed] [Cross Ref]
11. Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98.
12. Gurevich A, Saveliev V, Vyahhi N, Tesler G 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. doi:.10.1093/bioinformatics/btt086 [PMC free article] [PubMed] [Cross Ref]
13. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H 2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895–3903. doi:.10.1128/AAC.02412-14 [PMC free article] [PubMed] [Cross Ref]
14. Antipov D, Hartwick N, Shen M, Raiko M, Lapidus A, Pevzner PA 2016. plasmidSPAdes: assembling plasmids from whole genome sequencing data. Bioinformatics 32:3380–3387. pii: btw493 doi:.10.1093/bioinformatics/btw493 [PubMed] [Cross Ref]
15. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. doi:.10.1186/1471-2164-9-75 [PMC free article] [PubMed] [Cross Ref]
16. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R 2014. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:D206–D214. doi:.10.1093/nar/gkt1226 [PMC free article] [PubMed] [Cross Ref]

Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)