What is the advantage of incorporating virulence genes into the chromosome instead of retaining them as plasmids?
Maintenance and stability mostly - plasmids can be lost and expelled from the cell relatively quickly especially without selection pressure. Copy number is also regulated at the "chromosome level" (1 gene dose) compared to high copy number on plasmids (many plasmids in the cell resulting in high gene dose).
I agree with Christian's answer. In addition we don't have to be too finalist. Some virulence genes are included in transposable pathogenicity islands that might be introduced into the cells not only by plasmids but also by phage transduction, bacterial conjugation or natural DNA transformation for example and these virulence genes might thus be acquired on the chromosome.
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