design: Whole organism DNA extraction from 10-20 pooled adult Aphis fabae using Illustra Nucleon Phytopure extraction kit. Aphids were laboratory-raised clones of a single genotype. Each genotype was infected by a different strain of the bacterial symbiont Hamiltonella defensa. All samples naturally contained the same genotype of another bacterial symbiont, Buchnera aphidicola. Samples were barcoded and sequenced using PacBio HIFI sequencing and then demultiplexed.