The Mother Seeds are described as thus via in-game text:
(Postulated but unverified) First suggested by Alima Hamsa (2232BH), the notion of Mother Seeds extrapolates the behavior of the lesser seeds to a super-seed. She posited that the process that actually "created" the paired spheres was similar to all other swaps, but on a much grander scale.
The idea is that two seeds (from a Mother tree?) were scattered on the "galactic winds" to "find" appropriately similar environments. When matches were found, some process was triggered that swapped large portions of landscape between vastly different worlds. Alima further noted that the Trees locations in the center of the sphere suggested that the Trees grew from these Mother seeds.