Maybe not as obvious for those without formal education in """database normalization""" but it's pretty trivial to convert from a tree structure to a flat table structure using foreign key relations. Recursive queries aren't even that difficult in SQLite, so self-referential data can be represented cleanly too, if not a bit more difficult to write. IME most applications "tree structures" aren't self-referential and are better formalized as distinct entities with one-to-one relationships (ie. a subtree gets a table).

There's always the lazy approach of storing JSON blobs in TEXT fields, but I personally shy away from that because you lose out on a huge part of the benefits of using a SQL DB in the first place, most importantly migrations and querying/indexing.