Where does the letter ‘R’ in EcoRI comes from?

From the name of strain.

The letter 'R' in EcoRI comes from the name of the strain of bacteria from which the enzyme was isolated.

The convention for naming these enzymes is the first letter of the name comes from the genus and the second two letters come from the species of the prokaryotic cell from which they were isolated, e.g., EcoRI comes from Escherichia coli RY 13. In EcoRI, the letter ‘R’ is derived from the name of strain. Roman numbers following the names indicate the order in which the enzymes were isolated from that strain of bacteria.