Description and complete genome sequences of Bradyrhizobium symbiodeficiens sp. nov., a non-symbiotic bacterium associated with legumes native to Canada

References

1. Parker MA. Legumes select symbiosis island sequence variants in Bradyrhizobium . Mol Ecol 2012; 21:1769–1778 [View Article]
   [Google Scholar]
2. Tang J, Bromfield ESP, Rodrigue N, Cloutier S, Tambong JT. Microevolution of symbiotic Bradyrhizobium populations associated with soybeans in east North America. Ecol Evol 2012; 2:2943–2961 [View Article]
   [Google Scholar]
3. Bromfield ESP, Cloutier S, Tambong JT, Tran Thi TV. Soybeans inoculated with root zone soils of canadian native legumes harbour diverse and novel Bradyrhizobium spp. that possess agricultural potential. Syst Appl Microbiol 2017; 40:440–447 [View Article]
   [Google Scholar]
4. Yu X, Cloutier S, Tambong JT, Bromfield ESP. Bradyrhizobium ottawaense sp. nov., a symbiotic nitrogen fixing bacterium from root nodules of soybeans in Canada. Int J Syst Evol Microbiol 2014; 64:3202–3207 [View Article]
   [Google Scholar]
5. Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 2012; 9:772 [View Article]
   [Google Scholar]
6. Altekar G, Dwarkadas S, Huelsenbeck JP, Ronquist F. Parallel metropolis coupled markov chain monte carlo for bayesian phylogenetic inference. Bioinformatics 2004; 20:407–415 [View Article]
   [Google Scholar]
7. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [View Article]
   [Google Scholar]
8. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article]
   [Google Scholar]
9. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article]
   [Google Scholar]
10. Rivas R, Martens M, de Lajudie P, Willems A. Multilocus sequence analysis of the genus Bradyrhizobium . Syst Appl Microbiol 2009; 32:101–110 [View Article]
    [Google Scholar]
11. Durán D, Rey L, Mayo J, Zúñiga-Dávila D, Imperial J et al. Bradyrhizobium paxllaeri sp. nov. and Bradyrhizobium icense sp. nov., nitrogen-fixing rhizobial symbionts of Lima bean (Phaseolus lunatus L.) in Peru. Int J Syst Evol Microbiol 2014; 64:2072–2078 [View Article]
    [Google Scholar]
12. Avontuur JR, Palmer M, Beukes CW, Chan WY, Coetzee MPA et al. Genome-informed Bradyrhizobium taxonomy: where to from here?. Syst Appl Microbiol 2019; 42:427–439 [View Article]
    [Google Scholar]
13. Ormeño-Orrillo E, Martínez-Romero E. A genomotaxonomy view of the Bradyrhizobium genus. Front Microbiol 2019; 10:1334–1346 [View Article]
    [Google Scholar]
14. Stothard P. The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 2000; 28:1102–1104 [View Article]
    [Google Scholar]
15. Ardui S, Ameur A, Vermeesch JR, Hestand MS. Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 2018; 46:2159–2168 [View Article]
    [Google Scholar]
16. Nguyen HDT, Cloutier S, Bromfield ESP. Complete genome sequence of Bradyrhizobium ottawaense OO99^{ T}, an efficient nitrogen-fixing symbiont of soybean. Microbiol Resour Announc 2018; 7:e01477–18 [View Article]
    [Google Scholar]
17. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article]
    [Google Scholar]
18. de Lajudie PM, Young JPW. International committee on systematics of prokaryotes subcommittee on the taxonomy of rhizobia and agrobacteria minutes of the closed meeting, Granada, 4 September 2017. Int J Syst Evol Microbiol 2018; 68:3363–3368 [View Article]
    [Google Scholar]
19. Ciufo S, Kannan S, Sharma S, Badretdin A, Clark K et al. Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI. Int J Syst Evol Microbiol 2018; 68:2386–2392 [View Article]
    [Google Scholar]
20. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article]
    [Google Scholar]
21. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article]
    [Google Scholar]
22. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. Ncbi prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article]
    [Google Scholar]
23. Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V et al. Refseq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 2018; 46:D851–D860 [View Article]
    [Google Scholar]
24. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 2017; 45:D535–D542 [View Article]
    [Google Scholar]
25. Bertelli C, Laird MR, Williams KP, Lau BY, Hoad G et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 2017; 45:W30–W35 [View Article]
    [Google Scholar]
26. VanInsberghe D, Maas KR, Cardenas E, Strachan CR, Hallam SJ et al. Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils. Isme J 2015; 9:2435–2441 [View Article]
    [Google Scholar]
27. Rivas R, Willems A, Palomo JL, García-Benavides P, Mateos PF et al. Bradyrhizobium betae sp. nov., isolated from roots of Beta vulgaris affected by tumour-like deformations. Int J Syst Evol Microbiol 2004; 54:1271–1275 [View Article]
    [Google Scholar]
28. Bromfield ESP, Cloutier S, Nguyen HDT. Description and complete genome sequence of Bradyrhizobium amphicarpaeae sp. nov., harbouring photosystem and nitrogen-fixation genes. Int J Syst Evol Microbiol 2019; 69:2841–2848 [View Article]
    [Google Scholar]
29. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993
    [Google Scholar]
30. Garrity GM, Bell JA, Lilburn T. Family VII. Bradyrhizobiaceae fam. nov. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. (editors) Bergey's Manual of Systematic Bacteriology vol. 2, second edition. New York: Springer; 2005 p 438
    [Google Scholar]
31. Tighe SW, de Lajudie P, Dipietro K, Lindström K, Nick G et al. Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Brady rhizobium, Meso rhizobium, Rhizobium and Sino rhizobium species using the sherlock microbial identification system. Int J Syst Evol Microbiol 2000; 50 Pt 2:787–801 [View Article]
    [Google Scholar]