I don't think there is any up-to-date book on how to manage "scene graph, mesh, animation classes, etc".
-There's a chapter in GPU Pro 3 (Chapter V.4 Designing a Data-Driven Renderer) that might be helpful (it's short).
-Game Engine Architecture chapter on Animation is really good (including some actual code) and should be enough as a start of an engine animation system.
-If you want to learn rendering techniques start by the (free) GPU Gems books.
Regarding "scene graph management, etc", you'll be better served by reading other engine source code, the hundreds of topics about this in the forums and conference presentations (check GDC Vault, Frostbite, and other engine/companies websites).
There's a recent presentation about Destiny’s Multi-threaded Renderer Architecture. It probably isn't easy for a beginner to understand everything but read it carefully (and multiple times).
Horde3D source code is small and easy to follow (not the best architecture for current gen but it's a good start).