Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

Authors

Wilson Leung, Washington University St. Louis
Christopher D. Shaffer, Washington University St. Louis
Laura K. Reed, University of Alabama
Sheryl T. Smith, Arcadia University
William Barshop, Adams State University
William Dirkes, University of the Fraser Valley
Matthew Dothager, Agnes Scott College
Paul Lee, Albion College
Jeannette Wong, Amherst College
David Xiong, Cabrini College
Han Yuan, California Lutheran University
James E.J. Bedard, California Polytechnic State University SLO
Joshua F. Machone, California State University Monterey Bay
Seantay D. Patterson, California State University Stanislaus
Amber L. Price, Calvin College
Bryce A. Turner, Cardinal Stritch University
Srebrenka Robic, College of William and Mary
Erin K. Luippold, Denison University
Shannon R. McCartha, Duke University
Tezin A. Walji, Georgetown University
Chelsea A. Walker, Grand Valley State University
Kenneth Saville, Hampden-Sydney College
Marita K. Abrams, Hofstra University
Andrew R. Armstrong, Johnson C Smith University
William Armstrong, City University of New York
Robert J. Bailey, Massasoit Community College
Chelsea R. Barberi, Lindenwood University
Lauren R. Beck, Longwood University
Amanda L. Blaker, Loyola Marymount University
Christopher E. Blunden, University of Detroit Mercy

Document Type

Article

Publication Date

1-1-2015

Journal / Book Title

G3

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.

DOI

10.1534/g3.114.015966

Montclair State University Digital Commons Citation

Leung, Wilson; Shaffer, Christopher D.; Reed, Laura K.; Smith, Sheryl T.; Barshop, William; Dirkes, William; Dothager, Matthew; Lee, Paul; Wong, Jeannette; Xiong, David; Yuan, Han; Bedard, James E.J.; Machone, Joshua F.; Patterson, Seantay D.; Price, Amber L.; Turner, Bryce A.; Robic, Srebrenka; Luippold, Erin K.; McCartha, Shannon R.; Walji, Tezin A.; Walker, Chelsea A.; Saville, Kenneth; Abrams, Marita K.; Armstrong, Andrew R.; Armstrong, William; Bailey, Robert J.; Barberi, Chelsea R.; Beck, Lauren R.; Blaker, Amanda L.; and Blunden, Christopher E., "Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution" (2015). Department of Biology Faculty Scholarship and Creative Works. 314.
https://digitalcommons.montclair.edu/biology-facpubs/314

Published Citation

Leung, W., Shaffer, C. D., Reed, L. K., Smith, S. T., Barshop, W., Dirkes, W., Dothager, M., Lee, P., Wong, J., Xiong, D., Yuan, H., Bedard, J. E., Machone, J. F., Patterson, S. D., Price, A. L., Turner, B. A., Robic, S., Luippold, E. K., McCartha, S. R., Walji, T. A., … Elgin, S. C. (2015). Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution. G3 (Bethesda, Md.), 5(5), 719–740. https://doi.org/10.1534/g3.114.015966