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

Area of Science:

• Genetics
• Evolutionary Biology
• Molecular Biology

Background:

• Y chromosomes are typically gene-poor with low nucleotide variation but high structural diversity.
• Previous studies noted size and shape differences in Drosophila pseudoobscura Y chromosomes, but molecular causes remained unclear.

Purpose of the Study:

• To investigate the molecular basis of size variation in polymorphic Y chromosomes of Drosophila pseudoobscura.
• To identify the sequence content and drivers of Y chromosome size differences.

Main Methods:

• Utilized cytogenetics and long-read sequencing to analyze Y chromosome sequence content.
• Examined heterochromatin enrichment and expression of Y-enriched transposable elements (TEs).

Main Results:

• Drosophila pseudoobscura Y chromosomes vary nearly twofold in size (30-60 Mb).
• Large size differences are primarily driven by recent expansions of a few active transposable elements (TEs).
• Different TEs are responsible for Y expansion in distinct Y chromosome size variants, and TE amplification influences autosomal and X-linked gene expression.

Conclusions:

• Recent transposable element (TE) activity is the main driver of Y chromosome size variation in Drosophila pseudoobscura.
• A specific helitron element independently amplified on large Y chromosomes in both D. pseudoobscura and Drosophila affinis, indicating a predisposition for TE deregulation on Y chromosomes.