Mitochondrial - Y Chromosome Epistasis in Drosophila melanogaster

We generate 36 otherwise isogenic Drosophila melanogaster strains differing only in the geographical origin of their mitochondrial genome and Y chromosome to experimentally examine the effects of the uniparentaly inherited parts of the genome, as well as their interaction, in males. We assay gene expression through RNA-sequencing and detect an important role for both mitochondrial and Y-linked genes, as well as extensive mitochondrial-Y chromosome epistasis. We used a 6x6 crossing design, crossing females from six mitochondrial replacement lines with males from six Y chromosome replacement lines, resulting in male offspring with 36 mito-Y combinations. Mitochondrial and Y Replacement lines share the same 4361 nuclear background, which means our 36 mitochondrial-Y replacement lines are isogenic outside of their mitochondrial haplogroup and Y haplotype. Mitochondrial genomes came from Beijing, China (2 lines; B38 and B39), Ithaca, NY, USA (1 line; I02), and the Netherlands (3 lines; N01, N02, and N23), and the Y chromosomes from Beijing, China (2 lines; B04 and B11), the Netherlands (2 lines; N03 and N07), and Zimbabwe (2 lines ; ZWH123 and YZW139). These populations represent deeply divergent mitochondrial and Y chromosome clades chosen from the Global Diversity Lines. We performed RNA sequencing on 10 3-5 day old males from each of the 36 mitochondrial-Y combinations. We used two biological replicates for each combination, with individuals for each replicate being collected from separate crosses between females from the mitochondrial-replacement and males from the Y-replacement parental lines performed on the same day.