It can all be automated to make sure it keeps it all up to date by automagic. I would create a crontab that loops through all usernames in AD, stores username, full name and department in strings and then runs an update on the database once a day or week, offloading all this work and clicking to a simple script.
Assuming you would like to automate it and have a list of usernames with department name, you could generate a bunch of queries that update the cwd_user table reading out the old username, appending the department and run an update query (display names are in the column "display_name" on MySQL installs of Jira).
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