I have whole genome sequence data for one species. Can I differentiate this species with others using PCR based methods?
I suggest you read "Survey of Simple Sequence Repeats in Completed Fungal Genomes" Molecular Biology and Evolution 22 (3) 639-649 (2005).
We use the ITS region of the rDNA. Its very easy with Sanger sequencing and ITS1f and ITS4 primers. But be sure there are also some morphology or physiology traits to support your conclusions.
you can differentiate them using SSRs, for sure, obviously their SSR profile will be different. What you cannot do is identify them using SSRs. SSRs are helpful to compare. I you want to identify is better to design specific primers.
Off course you can use them to identify and surely differentiate between species and also between different genotypes within a given species. All the depends on the number of SSRs loci you are going to amplify.
You can select SSR based on your genome sequence for one species, and compare it with the strains of another one. But, it will not give you a proof that they are in fact two different species. It is better to select a few single -copy genes present in GeneBank accessions for related taxonomic groups, and make MLST. The distance between your strains of 2 species must be comparable with difference between other species within one genus.
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