Publications and Research

Authors

Wilson Leung, Washington University in St. Louis
Christopher D. Shaffer, Washington University in St. Louis
Laura K. Reed, University of Alabama
Sheryl T. Smith, Arcadia University
William Barshop, Washington University in St. Louis
William Dirkes, Washington University in St. Louis
Matthew Dothager, Washington University in St. Louis
Paul Lee, Washington University in St. Louis
Jeannette Wong, Washington University in St. Louis
David Xiong, Washington University in St. Louis
Han Yuan, Washington University in St. Louis
James E. J. Bedard, Adams State University
Joshua F. Machone, Adams State University
Seantay D. Patterson, Adams State University
Amber L. Price, Adams State University
Bryce A. Turner, Adams State University
Srebrenka Robic, Agnes Scott College
Erin K. Luippold, Agnes Scott College
Shannon R. McCartha, Agnes Scott College
Tezin A. Walji, Agnes Scott College
Karim A. Sharif, CUNY LaGuardia Community College
Tenzin Choeying, CUNY LaGuardia Community College
Jason S. Macias, CUNY LaGuardia Community College
Fareed Sanusi, CUNY LaGuardia Community College
Karvyn Torchon, CUNY LaGuardia Community College
Yuying Gosser, CUNY City College
Shubha Govind, CUNY City College
Nicole Clarke-Medley, CUNY City College
Leslie Guadron, CUNY City College
Dawn Lau, CUNY City College
Alvin Lu, CUNY City College
Cheryl Mazzeo, CUNY City College
Mariam Meghdari, CUNY City College
Simon Ng, CUNY City College
Brad Pamnani, CUNY City College
Olivia Plante, CUNY City College
Yuki Kwan Wa Shum, CUNY City College
Roy Song, CUNY City College
Gerard P. McNeil, CUNY York College
Adeola Adebayo, CUNY York College
Kate Bagaeva, CUNY York College
Justina Chinwong, CUNY York College
Chrystel Dol, CUNY York College
Eunice George, CUNY York College
Kirk Haltaufderhyde, CUNY York College
Joanna Haye, CUNY York College
Manpreet Kaur, CUNY York College
Max Semon, CUNY York College
Dmitri Serjanov, CUNY York College
Anika Toorie, CUNY York College
Christopher Wilson, CUNY York College

Document Type

Article

Publication Date

3-4-2015

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.

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