Intragenomic variation in the internal transcribed spacer regions between 16S–23S rRNA genes among the three copies of Sinorhizobium fredii strains

References

• van Berkum , P and Fuhrmann , JJ . 2000 . Evolutionary relationships among the soybean bradyrhizobia reconstructed from 16S rRNA gene and internally transcribed spacer region sequence divergence . Int. J. Syst. Evol. Microbiol. , 50 : 2165 – 2172 .
   PubMed Web of Science ®Google Scholar
• Chen , WX , Yan , GH and Li , JL . 1988 . Numeric taxonomic study of fast-growing soybean rhizobia and a proposal that Rhizobium frediibe assigned to Sinorhizobiumgen. nov . Int. J. Syst. Bacteriol. , 38 : 392 – 397 .
   Google Scholar
• Hiraishi , A , Kamagata , Y and Nakamura , K . 1995 . Polymerase chain reaction amplification and restriction fragment length polymorphism analysis of 16S rRNA genes from Methanogens . J. Ferment. Bioeng. , 79 : 523 – 529 .
   Google Scholar
• Jarvis , BDW , Downer , HL and Young , JPW . 1992 . Phylogeny of fast-growing soybean-nodulating rhizobia supports synonymy of Sinorhizobiumand Rhizobiumand assignment to Rhizobium fredii . Int. J. Syst. Bacteriol. , 42 : 93 – 96 .
   PubMedGoogle Scholar
• Kündig , C , Beck , C , Hennecke , H and Gottfert , M . 1995 . A single rRNA gene region in Bradyrhizobium japonicum . J. Bacteriol. , 177 : 5151 – 5154 .
   PubMed Web of Science ®Google Scholar
• Kuykendall , LD , Saxena , B , Cevine , TE and Udell , SE . 1992 . Genetic diversity in BradyrhizobiumJordan 1982 and a proposal for Bradyrhizobium elkaniisp. nov . Can. J. Microbiol. , 38 : 201 – 505 .
   Google Scholar
• Marchuk , D , Drumn , M , Saulino , A and Collins , FS . 1991 . Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products . Nucleic Acids Res. , 19 : 1154
   PubMed Web of Science ®Google Scholar
• Minami , M , Yamakawa , T , Yamamoto , A , Akao , S and Saeki , Y . 2009 . Estimation of nodulation tendency among Rj-genotype soybeans using the bradyrhizobial community isolated from an Andosol . Soil Sci. Plant Nutr. , 55 : 65 – 72 .
   Web of Science ®Google Scholar
• Peng , GX , Tan , ZY , Wang , ET , Reinhold-Hurek , B , Chen , WF and Chen , WX . 2002 . Identification of isolates from soybean nodules in Xinjiang region as Sinorhizobium xinjiangenseand genetic differentiation of S. xinjiangensefrom Sinorhizobium fredii . Int. J. Syst. Evol. Microbiol. , 52 : 457 – 462 .
   PubMed Web of Science ®Google Scholar
• Saeki , Y , Aimi , N Hashimoto , M . 2004 . Grouping of BradyrhizobiumUSDA strains by sequence analysis of 16S rDNA and 16S-23S rDNA internal transcribed spacer region . Soil Sci. Plant Nutr. , 50 : 517 – 525 .
   Web of Science ®Google Scholar
• Saeki , Y , Aimi , N , Tsukamoto , S , Yamakawa , T , Nagatomo , Y and Akao , S . 2006 . Diversity and geographical distribution of indigenous soybean-nodulating bradyrhizobia in Japan . Soil Sci. Plant Nutr. , 52 : 418 – 426 .
   Web of Science ®Google Scholar
• Saeki , Y , Akagi , I , Takaki , H and Nagatomo , Y . 2000 . Diversity of indigenous Bradyrhizobiumstrains isolated from three different Rj-soybean cultivars in terms of randomly amplified polymorphic DNA and intrinsic antibiotic resistance . Soil Sci. Plant Nutr. , 46 : 917 – 926 .
   Web of Science ®Google Scholar
• Saeki , Y , Kaneko , A Suzuki , K . 2005 . Phylogenetic analysis of soybean-nodulating rhizobia isolated from alkaline soils in Vietnam . Soil Sci. Plant Nutr. , 51 : 1043 – 1052 .
   Web of Science ®Google Scholar
• Saeki , Y , Minami , M , Yamamoto , A and Akao , S . 2008 . Estimation of the bacterial community diversity of soybean-nodulating bradyrhizobia isolated from Rj-genotype soybeans . Soil Sci. Plant Nutr. , 54 : 718 – 724 .
   Web of Science ®Google Scholar
• Saitou , N and Nei , M . 1987 . The neighbor-joining method: a new method for reconstructing phylogenetic trees . Mol. Biol. Ecol. , 4 : 406 – 425 .
   Google Scholar
• Sameshima , R , Isawa , T Sadowsky , MJ . 2003 . Phylogeny and distribution of extra-slow-growing Bradyrhizobium japonicumharboring high copy numbers of RSα, RSβ and IS1631 . FEMS Microbiol. Ecol. , 44 : 191 – 202 .
   PubMed Web of Science ®Google Scholar
• Scholla , MH and Elkan , GH . 1984 . Rhizobium frediisp. nov., a fast-growing species that effectively nodulates soybeans . Int. J. Syst. Bacteriol. , 34 : 484 – 486 .
   Google Scholar
• Staden , R . 1982 . An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences . Nucleic Acid Res. , 10 : 2951 – 2961 .
   PubMedGoogle Scholar
• Stewart , FJ and Cavanaugh , CM . 2007 . Intragenomic variation and evolution of the internal transcribed spacer of the rRNA operon in bacteria . J. Mol. Evol. , 65 : 44 – 67 .
   PubMedGoogle Scholar
• Suzuki , K , Oguro , H , Yamakawa , T , Yamamoto , A , Akao , S and Saeki , Y . 2008 . Diversity and distribution of indigenous soybean-nodulating rhizobia in the Okinawa islands, Japan . Soil Sci. Plant Nutr. , 54 : 237 – 246 .
   Web of Science ®Google Scholar
• Thompson , JD , Higgins , DG and Gibson , TJ . 1994 . CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice . Nucleic Acid Res. , 22 : 4673 – 4680 .
   PubMed Web of Science ®Google Scholar
• Xu , LM , Ge , C , Cui , Z , Li , J and Fan , H . 1995 . Bradyrhizobium liaoningensesp. nov., isolated from the root nodules of soybeans . Int. J. Syst. Bacteriol. , 45 : 706 – 711 .
   PubMedGoogle Scholar
• Young , JM . 2003 . The genus name EnsiferCasida 1982 takes priority over SinorhizobiumChen et al.1988, and Sinorhizobium morelenseWang et al.2002 is a later synonym of Ensifer adhaerensCasida 1982. Is the combination ‘Sinorhizobium adhaerens’ (Casida 1982) Willems et al.2003 legitimate? Request for an opinion . Int. J. Syst. Evol. Microbiol. , 53 : 2107 – 2110 .
   PubMed Web of Science ®Google Scholar