I thought cherry trees were only a Japanese thing, but that's not actually the case.
この場合、次のような言い方ができますよ。
ーI thought cherry trees were only a Japanese thing, but that's not actually the case.
「桜の木は日本のものだと思ってたけど、そうでもないんだね」
that's not the case.「それは真実ではない・それは事実と異なる」
ご参考まで!