Genomic fingerprinting of Frankia microsymbionts from Ceanothus copopulations using repetitive sequences and polymerase chain reactions

Specificity between Ceanothus species and their microsymbionts, Frankia, we re investigated with nodules collected from three geographically separated copopulations of Ceanothus species. Nodules were analyzed using DNA sequenc ing and repetitive sequence polymerase chain reaction (rep-PCR) techniques. DNA sequencing of the intergenic spacer region between 16S and 23S rRNA ge nes suggested that Ceanothus-microsymbiotic Frankia are closely related at the intraspecific level. Diversity of the microsymbionts was further analyz ed by genomic fingerprinting using repetitive sequences and PCR. A newly de signed direct repeat (DR) sequence and a BOX sequence were used as PCR prim ers after justification that these primers can generate Frankia-specific fi ngerprints from nodule DNA. Analysis of the nodules using BOX- and DR-PCR s howed that Ceanothus-microsymbiotic Frankia exhibited less diversity within each copopulation than among copopulations. These data suggested that geog raphic separation plays a more important role for divergence of Ceanothus-m icrosymbiotic Frankia than host plant.