16S rDNA genotyping using PCR/RFLP (restriction fragment length polymorphism) analysis among the family Vibrionaceae.
The 16S rDNA genotypes among the family Vibrionaceae were determined using PCR/RFLP analysis. Five tetrameric restriction enzymes (HhaI, DdeI, RsaI, Sau3AI and MspI) were used for RFLP analysis and adequate numbers of informative bands were obtained from each enzyme. Twenty-seven genotypes were obtained from 49 type and reference strains including 35 species. Nineteen species could be assigned to specific 16S rDNA genotypes, supporting the application of this analysis for identification. Trees constructed using five endonucleases resolved groups almost identical to those inferred from 16S rRNA gene sequencing. However, the branch lengths and detailed relationships among strains within a group differed from those inferred from sequence comparisons. The results of this study should be useful for genotyping, identification and approximate classification of natural isolates belonging to the family Vibrionaceae.
Urakawa
H
H
Ocean Research Institute, University of Tokyo, Japan.
Kita-Tsukamoto
K
K
Ohwada
K
K
D001483:Base Sequence; D004269:DNA, Bacterial / Q000032:analysis; D004275:DNA, Ribosomal / Q000032:analysis*; D005838:Genotype; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D014737:Vibrionaceae / Q000145:classification* / Q000235:genetics
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S