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Based on it, in your BundleConfig you can redefine Styles.DefaultTagFormat and Scripts.DefaultTagFormat.
So if you need to change version on every build of application you can do this in RegisterBundles method:
var assemblyVersion = System.Reflection.Assembly.GetExecutingAssembly().GetName().Version.ToString();
Styles.DefaultTagFormat = "<link href='{0}?v=" + assemblyVersion + "' rel='stylesheet'/>";
Scripts.DefaultTagFormat = "<script src='{0}?v=" + assemblyVersion + "'></script>";
Of course you can get version from your Config.