MLST Panel 3: Finally, a set of 11 genetic loci were targeted in a report by Nakayama et al. 2010. The panel was used to examine variation in eight isolates and in the genome sequences of the Boryong and Ikeda isolates. Among the eight isolates specifically targeted by the study, three (Gilliam, Karp and Kato) also now have complete genome sequences available.
The MLST information for these loci consists of a subsection of each of the genes. The length of the MLST portion of a gene compared to the total length of the gene is given for each locus. These loci included:
ATP synthase beta-chain (atpD)
ATP-dependent Clp protease ATPbinding subunit (clpX)
DnaJ protein (dnaJ)
DnaK protein (dnaK)
malonyl CoA-acyl carrier protein transacylase (fabD)
DNA gyrase subunit B (gyrB)
isocitrate dehydrogenase (icd)
malate dehydrogenase (mdh)
ribonucleoside-diphosphate reductase alphachain (nrdA)
succinyl-CoA synthetase alpha-chain (sucD)
3-octaprenyl-4-hydroxybenzoate carboxylyase (ubiD)
MLST typing for genomes: For each of the three groups of MLST loci, sequences of the complete genes are also available from genome sequences of 39 isolates (see Genome Page). Both the partial sequence used for the MLST analysis and the complete gene sequences can be compared.
Information on the levels of genetic variation for each MLST partial or complete locus and the phylogenetic information from the various partial and complete MLST loci will be posted in the future as we complete various analyses.