Allele specific expression and bacterial community composition in the Drosophila gut

Total RNA was extracted from female 6-day-old Drosophila melanogaster midgut (20 per replicate) and hindgut (60 per replicate) samples for 4 isofemale strains (2 from a derived Swedish population and 2 from an ancestral African population) as well as F1 hybrids between the Swedish and African strains. 3 biological replicates were performed per strain or F1 hybrid (48 samples in total). An additional hindgut replicate from the ZI418 strain was performed (49th sample) but not included in the analysis in order to maintain a balanced study design. High throughput RNA sequencing (RNA-seq) and amplicon sequencing were then performed using the same RNA extractions. RNA-seq was performed using Poly-A selection and 150-bp paired reads. Amplicon sequencing targeted the V4 region of the 16s rRNA bacterial gene.