Recombination Suppression Drives Expansion of the Drosophila Dot Chromosome.
Publication/Presentation Date
11-28-2025
Abstract
Genome size varies widely, even among closely related species, yet much less is known about chromosome size variation. Here we use the fourth chromosome of Drosophila, also known as the "Muller F element" or "dot chromosome", as a model to investigate chromosome-specific size expansion. The F element of most Drosophila species is small (∼1.3 Mb) and almost entirely heterochromatic, yet harbors approximately 80 protein-coding genes. Here, we study D. kikkawai, D. takahashii, D. ananassae, and D. bipectinata, whose F elements are 2- to 15-fold larger in size compared to D. melanogaster. Through manual gene curation and comparative genomic analysis, we find that their F elements have expanded primarily via accumulation of transposable elements (TEs) in introns and intergenic regions. Natural selection appears less efficient on these expanded F elements: they have smaller effective population sizes and their genes exhibit reduced usage of optimal codons, compared to D. melanogaster. We propose that F element size variation is driven by differences in F element recombination rates. The ultra-long (∼20 Mb) F elements of D. ananassae and D. bipectinata display high rates of rearrangement and sequence evolution and exhibit independent TE-driven expansions. Our results suggest that F elements of most Drosophila species likely recombine enough to prevent size expansion, while F element recombination in D. ananassae and D. bipectinata is either absent or rare enough to allow TEs and other deleterious mutations to accumulate via Muller's ratchet; thus, these chromosomes evolve more like a Y chromosome than a typical Drosophila F element.
Volume
42
Issue
12
ISSN
1537-1719
Published In/Presented At
Stanek, T. J., Leung, W., Shaffer, C. D., Genomics Education Partnership , Olaveja, I., Laughlin, A., Hester, J., Garrido, D., Oh, E. K., Volski, M., Panda, N., Mo, M., Cordes, E., Dalling, M., Kershaw, K., Arnott, M., Daly, S., Valenzuela, S. G., Thompson, P., Hastert, K. L., … Ellison, C. E. (2025). Recombination Suppression Drives Expansion of the Drosophila Dot Chromosome. Molecular biology and evolution, 42(12), msaf304. https://doi.org/10.1093/molbev/msaf304
Disciplines
Medicine and Health Sciences
PubMedID
41442496
Department(s)
Fellows and Residents
Document Type
Article