Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution.

Abstract

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25-50%) than euchromatic reference regions (3-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11-27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4-3.6 vs. 8.4-8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.

Department

Description

Provenance

Citation

Published Version (Please cite this version)

10.1534/g3.114.015966

Publication Info

Leung, Wilson, Christopher D Shaffer, Laura K Reed, Sheryl T Smith, William Barshop, William Dirkes, Matthew Dothager, Paul Lee, et al. (2015). Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution. G3 (Bethesda, Md.), 5(5). pp. 719–740. 10.1534/g3.114.015966 Retrieved from https://hdl.handle.net/10161/23707.

This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.

Scholars@Duke

Spana

Eric P. Spana

Associate Professor of the Practice of Biology

Dustin Scott Woyski

Clinical Associate in the Department of Orthopaedic Surgery
Waldman

Leah Esther Waldman

Assistant Professor in the Department of Radiology

Unless otherwise indicated, scholarly articles published by Duke faculty members are made available here with a CC-BY-NC (Creative Commons Attribution Non-Commercial) license, as enabled by the Duke Open Access Policy. If you wish to use the materials in ways not already permitted under CC-BY-NC, please consult the copyright owner. Other materials are made available here through the author’s grant of a non-exclusive license to make their work openly accessible.