Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae)

We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of 10 tissues into a grand transcriptome to identify genes located on the X and Y chromosomes of a stalk-eyed fly, Teleopsis dalmanni. We use next generation sequencing of RNA to identify over 500 genes that are differentially expressed in the testes due to the effects of a driving X chromosome (XSR) in T. dalmanni. Most of these genes were X-linked, evolving more rapidly than control genes, and exhibit elevated expression in the gonads. Finally, XSR has become genetically differentiated from standard X chromosomes – using the RNA sequence data, we found nearly 1000 sites in X-linked genes and only a handful in autosomal genes where there was a fixed nucleotide difference. We conclude that XSR has led to widespread sequence and expression divergence on the X chromosome in T. dalmanni. Two-condition experiment, female vs. male DNA, for one species with 4 biological replicates