Can any one tell the CGR can only be used for whole genome or it can be used for 16S rRNA gene sequence (from cultivable microbes).
I think you can use for both of it. The CGR is useful to comparate sequences, and so its available for whole genome and single genes. But with a single gene sequence (like 16S rRNA gene), your representation will be more "empty" than with whole genome. I think it exist some other better representation to compare gene sequence than CGR.
CGR is merely a way to present comparative data, so you could use it if you wished. But I'm not sure why it would be beneficial if you are just comparing 16S sequences, since the point of it is to be able to represent differences and similarities over sequences too long to visualize normally.
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