General information about Wolbachia MLST

Multilocus sequence typing (MLST) is an unambiguous procedure for characterizing strains of Wolbachia using the sequences of five conserved genes as molecular markers to genotype a strain. Approximately 450-500 bp internal fragments of each gene are used, as these can be accurately sequenced on both strands using an automated DNA sequencer. These data can be used in a number of ways. One important function is to identify strain types based on the profile of their alleles.

For each of the conserved genes, every distinct sequence present within the Wolbachia genus is assigned a unique allele number. For strain typing by MLST, the number of nucleotide differences between alleles is ignored and sequences are considered different alleles whether they differ at a single nucleotide site or at many sites [Note that the level of divergence information is not lost and can be used in other analyses]. Each distinct allele is assigned an arbitrary integer. Each strain is therefore unambiguously characterized by a series of five integers which correspond to the alleles present at the five loci. For each strain, the specific combination of five alleles defines its allelic profile. Each unique allelic profile is then simply identified as a Sequence Type (ST) followed by a number (identical allelic profiles correspond to the same ST). The same ST can be shared among different strains.

Different strains are identified with different ID numbers based on their biological and genetic information. Such information is stored in two databases: the Profiles and the Isolates databases.

The Profiles database comprise tables for each of the five MLST genes and for the allelic profile definitions. These contain a single representative of each allele and allelic profile found to date. The Profiles database does not contain any strain information; these are found in the Isolates database.

The Isolates database contains all the biological information associated with a strain, plus its allelic profile. Thus this database represents the connection between a strain and the genetic information stored in the Profiles database. In the Isolates database, all strains are identified by a specific ID number, which refers to the collection of taxonomic, biological and genetic information (allelic profile) specific for that strain. The same information fields are available for all the strains, allowing extensive comparative analyses.