Data from: Heterochromatin-enriched assemblies reveal the sequence and organization of the Drosophila melanogaster Y chromosome

Heterochromatic regions of the genome are repeat-rich and poor in protein
coding genes, and are therefore underrepresented in even the best genome
assemblies. One of the most difficult regions of the genome to assemble
are sex-limited chromosomes. The Drosophila melanogaster Y chromosome is
entirely heterochromatic, yet has wide-ranging effects on male fertility,
fitness, and genome-wide gene expression. The genetic basis of this
phenotypic variation is difficult to study, in part because we do not know
the detailed organization of the Y chromosome. To study Y chromosome
organization in D. melanogaster, we develop an assembly strategy involving
the in silico enrichment of heterochromatic long single-molecule reads and
use these reads to create targeted de novo assemblies of heterochromatic
sequences. We assigned contigs to the Y chromosome using Illumina reads to
identify male-specific sequences. Our pipeline extends the D. melanogaster
reference genome by 11.9 Mb, closes 43.8% of the gaps, and improves
overall contiguity. The addition of 10.6 MB of Y-linked sequence permitted
us to study the organization of repeats and genes along the Y chromosome.
We detected a high rate of duplication to the pericentric regions of the Y
chromosome from other regions in the genome. Most of these duplicated
genes exist in multiple copies. We detail the evolutionary history of one
sex-linked gene family—crystal-Stellate. While the Y chromosome does not
undergo crossing over, we observed high gene conversion rates within and
between members of the crystal-Stellate gene family, Su(Ste), and PCKR,
compared to genome-wide estimates. Our results suggest that gene
conversion and gene duplication play an important role in the evolution of
Y-linked genes.