Joplin woud be my suggestion but then again I'm biased because I'm involved with the team... Markdown, mobile apps, multiple sync platforms.

Trilium has some really interesting features - very much powered by a single tree but no direct markdown, its a WYSIWYG editor (which is a bonus if you like that kind of thing).

Logseq is good if you prefer the "block based" type of notes - more like Notion.