2) A second Panel of loci that has been studied by Duong et al. 2013a. The loci in this set include:
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 (as determined from genome sequences) is given for each locus.
Adenosine kinase (adk)
GTP-binding protein (lepB)
lipoyl synthase (lipA)
lipoyltransferase (lipB)
preprotein translocase (secY)
Superoxide dismutase (sodB)
2-oxoglutarate dehydrogenase (sucA) [note: when examing the complete genome sequences of the Boryong and Ikeda isolates, the primer sites provided in the paper for sucA seem not to target the sucA gene, but rather target the adjacent sucB gene that is a part of the first MLST set above].
Information concerning the variability of the genes and the number of alleles at each MLST locus are provided in the original paper by Duong et al., 2013.
MLST typing for genomes: For each of the three panels 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.