Hi, 

you can use ITS markers to distinguish strains or any other hyper variable markers from organelle genome.

You can obtain from the genome some housekeeping gene sequences and perform a multilocus sequence analysis with the concatenated sequences of the housekeeping genes.

It depends on the organism. As of M.tuberculosis, one can use spoligotyping, MIRU-VNTR, IS elements (typically IS6110).

Bacteria do not have ITS--are these bacterial strains or eukarya? If you don't have a budget for sequencing, you could amplify a conserved gene/genes and look at restriction enzyme digest patterns. 

If the two strains are fully sequenced, you can do a full genome sequence alignment (using MUMmer for example) and identify the regions that are variable.   

Hello,

just run an ANI (Average Nucleotide Identity) comparison, e.g. using JSpecies (http://imedea.uib-csic.es/jspecies/about.html) or a dedicated website. If the genome-wide identity is above 96%, then it's the same species. If it is below 94%, then the isolates belong to two different species. In between you have a grey zone.

Best wishes,

Ralf

Thank you all for your answers.  I have complete genome sequences of bacterial strains belonging to same species and want to prove they are non-clonal. The production of particular enzyme screened for is only by one strain.  @Ralf Koebnik. I have done ANIm and ANIb and value is 98.8% and 98.7%. I don't want to prove that they belong to different species. I want to prove that they are different strains based on their genome sequences.

@ Hilary G Morrison: I have whole genome sequence of both the bacterial strains. 

Dear Shashi, with 98.8% identity they are for sure not clonal.

Best, Ralf

@Ralf Koebnik  Thanks

If you have 98% in ANI value, don't worry they are not clonal strains. Otherwise if you have raw reads from sequencing data you can perform mapping, SNP/InDels calling approach using a strain as reference.

Best.

@Slimane Khayi: Can you please tell me any software for mapping SNP/InDels in microbial genome sequence?

@Slimane Khayi: Thank you for your answer.

You can use trial version of CLC genomics to do quickly this task or BWA, VCF/SAMTools.