Recombination Suppression Drives Expansion of the Drosophila Dot Chromosome

Authors

• Timothy J Stanek
• Wilson Leung
• Christopher D Shaffer
• Ishtar Olaveja
• Annabelle Laughlin
• Jaquelyn Hester
• Darwin Garrido
• Emily K Oh
• Maria Volski
• Nistha Panda
• Mia Mo
• Ethan Cordes
• Martin Dalling
• Kacie Kershaw
• Malcolm Arnott
• Stephen Daly
• Silvia Garcia Valenzuela
• Paige Thompson
• Kayla L Hastert
• Destiny Sabb
• Kathryn Karpinski
• Meher Naaz Arora
• Nicholas Rius
• Larissa LoBello
• Sebastian Jaramillo
• Omkar Sonavane
• Alice Herrmann
• Laura K Reed
• Sarah C R Elgin
• Cindy Arrigo
• Christopher E Ellison

Language

English

Publication Date

11-28-2025

Journal

Molecular Biology and Evolution

DOI

10.1093/molbev/msaf304

PMID

41442496

PMCID

PMC12728734

PubMedCentral® Posted Date

12-24-2025

PubMedCentral® Full Text Version

Post-print

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.

Keywords

Animals, Drosophila, Recombination, Genetic, DNA Transposable Elements, Chromosomes, Insect, Evolution, Molecular, Selection, Genetic, Genome Size, Drosophila melanogaster, Drosophila, genome size, heterochromatin

Published Open-Access

yes

Recommended Citation

Stanek, Timothy J; Leung, Wilson; Shaffer, Christopher D; et al., "Recombination Suppression Drives Expansion of the Drosophila Dot Chromosome" (2025). Faculty, Staff and Student Publications. 960.
https://digitalcommons.library.tmc.edu/uthshis_docs/960