How to get X509Certificate from certificate store and generate xml signature data?

As far as I know, certificates are not saved by XML Format , you should combine it by yourself.

Is this what you want ?

   static void Main(string[] args)
   {
        X509Certificate2 cer = new X509Certificate2();
        cer.Import(@"D:\l.cer");
        X509Store store = new X509Store(StoreLocation.CurrentUser);
        store.Certificates.Add(cer);

        store.Open(OpenFlags.ReadOnly);
        X509Certificate2Collection cers = store.Certificates.Find(X509FindType.FindBySubjectName, "My Cert's Subject Name", false);
        if (cers.Count>0)
        {
            cer = cers[0];
        };
        store.Close();
   }