De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture

While short-read sequencing technology has resulted in a sharp increase in the number of species with genome assemblies, these assemblies are typically highly fragmented.Repeats pose the largest challenge for reference genome assembly, and pericentromeric regions and the repeat-rich Y chromosome are typically ignored from sequencing projects.Here, we assemble the genome of Drosophila miranda using long reads for contig formation, chromatin interaction maps for scaffolding and short reads, and optical mapping and bacterial artificial chromosome (BAC) clone sequencing for consensus validation.Our assembly recovers entire chromosomes and contains large fractions of repetitive DNA, including about 41.5 Mb of pericentromeric and telomeric regions, and >100 Mb of the recently formed highly repetitive neo-Y chromosome.While Y chromosome evolution is typically characterized by global sequence loss and shrinkage, the neo-Y increased in size by almost 3-fold because of the accumulation of repetitive sequences.Our high-quality assembly allows us to reconstruct the chromosomal events that have led to the unusual sex chromosome karyotype in D. miranda, including the independent de novo formation of a pair of sex chromosomes at two distinct time points, or the reversion of a former Y chromosome to an autosome. Author summaryY chromosomes determine the gender in many species, but their molecular investigation has been hampered by a lack of high-quality sequence assemblies.Here, we create a genome assembly of unprecedented quality and contiguity for the fruit fly Drosophila miranda, a model for Y chromosome research, which allows us to reconstruct the evolutionary events that create and dismantle sex chromosomes.Our assembly recovers entire chromosomes and notoriously difficult regions to assemble, including entire centromeres, large repetitive gene families embedded in heterochromatin, and more than 100 Mb of the highly repetitive and heterochromatic Y chromosome.We identify the putative