Answer:
As for all multi-celled organisms, the final systems of tissues and organs start with a single cell that has a genetic plan for development, which starts specializing in master cell types within just a few divisions.
These cell types then further segregate into more specialized types, which start to interact with each other to cause clustering, buildup of tissue mass, innervation (in animals) and vascularization. As cells start to make their own specialized chemicals, they can influence other tissues around them to respond.
So a seed started with one cell surrounded by many food stores to help it grow far enough to start gathering nutrients and making food on its own. That one cell divides into a few early master cell types-- in many seeds like a bean, you can actually see that it has already developed what looks like a tiny white plant with leaves and a root.
So the systems and organs aren't made separately-- they develop in place and interact with each other, and all can be traced back to the lineage of that one original cell.