Open AccessMolecular Genetic Basis of Ribotyping
Author(s) -
Valérie Bouchet,
Heather Huot,
Richard Goldstein
Publication year - 2008
Publication title -
clinical microbiology reviews
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.177
H-Index - 282
eISSN - 1070-6305
pISSN - 0893-8512
DOI - 10.1128/cmr.00026-07
Subject(s) - ribotyping , biology , genetics , housekeeping gene , ribosomal rna , computational biology , in silico , phylogenetics , genomics , restriction fragment length polymorphism , gene , molecular epidemiology , evolutionary biology , genome , polymerase chain reaction , genotype , gene expression
SUMMARY Nearly 2,000 ribotyping-based studies exist, ranging from epidemiology to phylogeny and taxonomy. None precisely reveals the molecular genetic basis, with many incorrectly attributing detected polymorphisms to rRNA gene sequences. Based on in silico genomics, we demonstrate that ribotype polymorphisms result from sequence variability in neutral housekeeping genes flanking rRNA operons, with rRNA gene sequences serving solely as conserved, flank-linked tags. We also reveal that from such an informatics perspective, it is readily feasible a priori to design an interpretable ribotyping scheme for a genomically sequenced microbial species, and we discuss limitations to the basic restriction fragment length polymorphism-based method as well as alternate PCR ribotyping-based schemes.