Y Chromosomes of many species are gene poor and show low levels of nucleotide variation, yet they 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 large 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 almost twofold 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 and expression of Y-enriched TEs, and also influence expression of dozens of autosomal and X-linked genes. 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 Drosophila affinis, suggesting that some TEs are inherently more prone to become deregulated on Y Chromosomes.

中文翻译：

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转座因子积累驱动果蝇多态性 Y 染色体的大小差异

许多物种的 Y 染色体基因贫乏，核苷酸变异水平低，但它们通常显示出大量的结构多样性。Dobzhansky 对Drosophila pseudoobscura中的几种形态不同的 Y 染色体进行了分类，这些 Y 染色体的大小和形状各不相同，但其大小差异巨大的分子原因尚不清楚。在这里，我们使用细胞遗传学和长读长测序来研究D. pseudoobscura中多态性 Y 染色体的序列内容。我们发现 Y 染色体的大小几乎相差两倍，范围从 30 到 60 Mb。这种大小差异的大部分是由最近在最大的 Y 染色体上扩展的少数活性转座元件 (TE) 引起的，不同的元件负责不同大小的 Y 扩展D. pseudoobscura Y's。我们发现 Y 染色体在异染色质富集和富含 Y 的 TE 表达方面存在差异，并且还会影响数十种常染色体和 X 连锁基因的表达。在D. pseudoobscura的最大 Y 上表现出最剧烈扩增的相同 helitron 元件在Drosophila affinis的多态性大 Y 染色体上独立扩增，表明一些 TE 天生更容易在 Y 染色体上解除管制。