My group has been working for many years on the identification of Y-linked genes, and on the evolution of gene content in the Y-chromosomes of a large number of Drosophila species. These genes are embedded within highly repetitive DNA that comprises the vast majority of the Drosophila Y-chromosome. Although highly repetitive sequences cannot be fully sequenced and assembled using current technologies, we developed computational methods that allowed the identification of pieces of the genes (usually individual exons with some intronic sequences). These methods allowed us, in collaboration with Andrew Clark (Cornell University), to identify the majority of known Y-linked protein coding genes in Drosophila. The above studies shed light on the evolution of the Drosophila Y-chromosome which, unexpectedly for a Y chromosome, is gaining genes, instead of losing them. A recent valuable "side-product" of the above work was the improvement of the assembly algorithm of PacBio reads (Genome Research, 2016).