Transposable element accumulation drives size differences among polymorphic Y chromosomes in Drosophila

Y chromosomes of many species are gene poor and show low levels of nucleotide variation, yet often display high amounts of structural diversity. Dobzhansky cataloged several morphologically distinct Y chromosomes in Drosophila pseudoobscura that differ in size and shape, but the molecular causes of their dramatic size differences are unclear. Here we use cytogenetics and long-read sequencing to study the sequence content of polymorphic Y chromosomes in D. pseudoobscura. We show that Y chromosomes differ by almost 2-fold in size, ranging from 30 to 60 Mb. Most of this size difference is caused by a handful of active transposable elements (TEs) that have recently expanded on the largest Y chromosome, with different elements being responsible for Y expansion on differently sized D. pseudoobscura Y’s. We show that Y chromosomes differ in their heterochromatin enrichment, expression of Y-enriched TEs, and also influence expression of dozens of autosomal and X-linked genes. Intriguingly, the same helitron element that showed the most drastic amplification on the largest Y in D. pseudoobscura independently amplified on a polymorphic large Y chromosome in D. affinis, suggesting that some TEs are inherently more prone to become deregulated on Y chromosomes.

Methods
This data set contains the key output files from the Bionano hybrid assembly workflow used in "Transposable element accumulation drives size differences among polymorphic Y chromosomes in Drosophila." The data is from a Drosophila pseudoobscura male that has a large Y chromosome.

All data was generated from high molecular gDNA derived from whole body tissue of a D. pseudoobscura male. The DLS labeling kit was used to tag the DNA and the labeled DNA was run through the Saphyr platform. The Bionano molecule data was used with a NGS-based male D. pseudoobscura genome to generate a hybrid assembly. : hybrid assembly sequences (fasta files), how NGS contigs were stitched together with Bionano data and the adjustments (.agp, .gap), the log file (.log), and the general summary statistics of the pipeline.