Mother Seeds are one of the types of seeds dropped by the Trees in obduction.
Summary
In-Game Description
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 Tree's locations in the center of the sphere suggested that the Trees grew from these Mother seeds.
Because of the similarities, it has been conjectured that re-swapping the entire environmental spheres might be possible with a larger scale version of the Ambassador Seed device.