Computer-assisted selection of restriction enzymes for rrs genes PCR-RFLP discrimination of rhizobial species

Marc Neyra, Bouchaib Khbaya, Philippe de Lajudie, Bernard Dreyfus, Philippe Normand
1998 Genetics Selection Evolution  
Restriction fragment length polymorphism analysis of amplified deoxyribonucleic acid (DNA) (polymerase chain reaction/restriction fragment length polymorphism (PCR-RFLP!) is an appropriate tool for microbial diversity characterisation, because of its universality, simplicity, rapidity and low cost. To determine which and how many restriction enzymes are optimal for the analysis, we simulated the digestion of 24 small subunit ribosomal DNA (rDNA) (rrs) available sequences of rhizobia and
more » ... hizobia and relatives by 25 tetrameric enzymes, and systematically compared the patterns generated, singly or in combination, by the enzymes. Discriminating combinations can be determined, enabling all the selected species to be distinguished. The calculation of the frequency at which each enzyme is found in discriminating combinations allows enzyme sorting. The most appropriate enzymes in combination are not necessarily those that induce higher numbers of distinct patterns singly, but those that show complementary discriminative properties when analysed together. The combination of six of the seven most discriminant enzymes results on average in the discrimination of 99.5 % of the sequences. Therefore, we propose that a minimum of six enzymes should be used to ensure a good discrimination of known and unknown species of Rhizobiaceae. © Inra/Elsevier,
doi:10.1051/gse:19980718 fatcat:q2or2juqkbhmjlyomac43ppqs4