Authors

Wilson Leung, Washington University in St. LouisFollow
Christopher D. Shaffer, Washington University in St. Louis
Elizabeth J. Chen, Washington University in St. Louis
Thomas J. Quisenberry, Washington University in St. Louis
Kevin Ko, Washington University in St. Louis
John M. Braverman, Saint Joseph's University
Thomas C. Giarla, Siena College
Nathan T. Mortimer, Illinois State University
Laura K. Reed, University of Alabama - Tuscaloosa
Sheryl T. Smith, Arcadia University
Srebrenka Robic, Agnes Scott College
Shannon R. McCartha, Agnes Scott College
Danielle R. Perry, Agnes Scott College
Lindsay M. Prescod, Agnes Scott College
Zenyth A. Sheppard, Agnes Scott College
Ken J. Saville, Albion College
Allison McClish, Albion College
Emily A. Morlock, Albion College
Victoria R. Sochor, Albion College
Brittney Stanton, Albion College
Isaac C. Veysey-White, Albion College
Dennis Revie, California Lutheran University
Luis A. Jimenez, California Lutheran University
Jennifer J. Palomino, California Lutheran University
Melissa D. Patao, California Lutheran University
Shane M. Patao, California Lutheran University
Edward T. Himelblau, California Polytechnic State University, San Luis Obispo
Jaclyn D. Campbell, California Polytechnic State University, San Luis Obispo
Alexandra L. Hertz, California Polytechnic State University, San Luis Obispo
Maddison F. McEvilly, California Polytechnic State University, San Luis Obispo
Allison R. Wagner, California Polytechnic State University, San Luis Obispo
James Youngblom, California State University, Stanislaus
Baljit Bedi, California State University, Stanislaus
Jeffery Bettincourt, California State University, Stanislaus
Erin Duso, California State University, Stanislaus
Maiye Her, California State University, Stanislaus
William Hilton, California State University, Stanislaus
Samantha House, California State University, Stanislaus
Masud Karimi, California State University, Stanislaus
Kevin Kumimoto, California State University, Stanislaus
Rebekah Lee, California State University, Stanislaus
Darryl Lopez, California State University, Stanislaus
George Odisho, California State University, Stanislaus
Ricky Prasad, California State University, Stanislaus
Holly Lyn Robbins, California State University, Stanislaus
Tanveer Sandhu, California State University, Stanislaus
Tracy Selfridge, California State University, Stanislaus
Kara Tsukashima, California State University, Stanislaus
Hani Yosif, California State University, Stanislaus
Nighat P. Kokan, Cardinal Stritch University
Latia Britt, Cardinal Stritch University
Alycia Zoellner, Cardinal Stritch University
Eric P. Spana, Duke University
Ben T. Chlebina, Duke University
Insun Chong, Duke University
Harrison Friedman, Duke University
Danny A. Mammo, Duke University
Chung L. Ng, Duke University
Vinayak S. Nikam, Duke University
Nicholas U. Schwartz, Duke University
Thomas Q. Xu, Duke University
Martin G. Burg, Grand Valley State University
Spencer M. Batten, Grand Valley State University
Lindsay M. Corbeill, Grand Valley State University
Erica Enoch, Grand Valley State University
Jesse J. Ensign, Grand Valley State University
Mary E. Franks, Grand Valley State University
Breanna Haiker, Grand Valley State University
Judith A. Ingles, Grand Valley State University
Lyndsay D. Kirkland, Grand Valley State University
Josha M. Lorenz-Guertin, Grand Valley State University
Jordan Matthews, Grand Valley State University
Cody M. Mittig, Grand Valley State University
Nicholaus Monsma, Grand Valley State University
Katherine J. Olson, Grand Valley State University
Guillermo Perez-Aragon, Grand Valley State University
Alen Ramic, Grand Valley State University
Jordan R. Ramirez, Grand Valley State University
Christopher Scheiber, Grand Valley State University
Patrick A. Schneider, Grand Valley State University
Devon E. Schultz, Grand Valley State University
Matthew Simon, Grand Valley State University
Eric Spencer, Grand Valley State University
Adam C. Wernette, Grand Valley State University
Maxine E. Wykle, Grand Valley State University
Elizabeth Zavala-Arellano, Grand Valley State University
Mitchell J. McDonald, Grand Valley State University
Kristine Ostby, Grand Valley State University
Peter Wendland, Grand Valley State University
Justin R. DiAngelo, Hofstra University
Alexis M. Ceasrine, Hofstra University
Amanda H. Cox, Hofstra University
James E B Docherty, Hofstra University
Robert M. Gingras, Hofstra University
Stephanie M. Grieb, Hofstra University
Michael J. Pavia, Hofstra University
Casey L. Personius, Hofstra University
Grzegorz L. Polak, Hofstra University
Dale L. Beach, Longwood University
Heaven L. Cerritos, Longwood University
Edward A. Horansky, Longwood University
Karim A. Sharif, Massasoit Community College
Ryan Moran, Massasoit Community College
Susan Parrish, McDaniel College
Kirsten Bickford, McDaniel College
Jennifer Bland, McDaniel College
Juliana Broussard, McDaniel College
Kerry Campbell, McDaniel College
Katelynn E. Deibel, McDaniel College
Richard Forka, McDaniel College
Monika C. Lemke, McDaniel College
Marlee B. Nelson, McDaniel College
Catherine O'Keeffe, McDaniel College
S Mariel Ramey, McDaniel College
Luke Schmidt, McDaniel College
Paola Villegas, McDaniel College
Christopher J. Jones, Moravian College
Stephanie L. Christ, Moravian College
Sami Mamari, Moravian College
Adam S. Rinaldi, Moravian College
Ghazal Stity, Moravian College
Amy T. Hark, Muhlenberg College
Mark Scheuerman, Muhlenberg College
S Catherine Silver Key, North Carolina Central University
Briana D. McRae, North Carolina Central University
Adam S. Haberman, Oberlin College
Sam Asinof, Oberlin College
Harriette Carrington, Oberlin College
Kelly Drumm, Oberlin College
Terrance Embry, Oberlin College
Richard McGuire, Oberlin College
Drew Miller-Foreman, Oberlin College
Stella Rosen, Oberlin College
Nadia Safa, Oberlin College
Darrin Schultz, Oberlin College
Matt Segal, Oberlin College
Yakov Shevin, Oberlin College
Petros Svoronos, Oberlin College
Tam Vuong, Oberlin College
Gary Skuse, Rochester Institute of Technology
Don W. Paetkau, Saint Mary's College
Rachael K. Bridgman, Saint Mary's College
Charlotte M. Brown, Saint Mary's College
Alicia R. Carroll, Saint Mary's College
Francesca M. Gifford, Saint Mary's College
Julie Beth Gillespie, Saint Mary's College
Susan E. Herman, Saint Mary's College
Krystal L. Holtcamp, Saint Mary's College
Misha A. Host, Saint Mary's College
Gabrielle Hussey, Saint Mary's College
Danielle M. Kramer, Saint Mary's College
Joan Q. Lawrence, Saint Mary's College
Madeline M. Martin, Saint Mary's College
Ellen N. Niemiec, Saint Mary's College
Ashleigh P. O'Reilly, Saint Mary's College
Olivia A. Pahl, Saint Mary's College
Guadalupe Quintana, Saint Mary's College
Elizabeth A S Rettie, Saint Mary's College
Torie L. Richardson, Saint Mary's College
Arianne E. Rodriguez, Saint Mary's College
Mona O. Rodriguez, Saint Mary's College
Laura Schiraldi, Saint Mary's College
Joanna J. Smith, Saint Mary's College
Kelsey F. Sugrue, Saint Mary's College
Lindsey J. Suriano, Saint Mary's College
Kaitlyn E. Takach, Saint Mary's College
Arielle M. Vasquez, Saint Mary's College
Ximena Velez, Saint Mary's College
Elizabeth J. Villafuerte, Saint Mary's College
Laura T. Vives, Saint Mary's College
Victoria R. Zellmer, Saint Mary's College
Jeanette Hauke, Simmons College
Charles R. Hauser, St. Edward's University
Karolyn Barker, St. Edward's University
Laurie Cannon, St. Edward's University
Perouza Parsamian, St. Edward's University
Samantha Parsons, St. Edward's University
Zachariah Wichman, St. Edward's University
Christopher W. Bazinet, St. John's University
Diana E. Johnson, The George Washington University
Abubakarr Bangura, The George Washington University
Jordan A. Black, The George Washington University
Victoria Chevee, The George Washington University
Sarah A. Einsteen, The George Washington University
Sarah K. Hilton, The George Washington University
Max Kollmer, The George Washington University
Rahul Nadendla, The George Washington University
Joyce Stamm, University of Evansville
Antoinette E. Fafara-Thompson, University of Evansville
Amber M. Gygi, University of Evansville
Emmy E. Ogawa, University of Evansville
Matt Van Camp, University of Evansville
Zuzana Kocsisova, University of Evansville
Judith L. Leatherman, University of Northern Colorado
Cassie M. Modahl, University of Northern Colorado
Michael R. Rubin, University of Puerto Rico - Cayey University College
Susana S. Apiz-Saab, University of Puerto Rico - Cayey University College
Suzette M. Arias-Mejias, University of Puerto Rico - Cayey University College
Carlos F. Carrion-Ortiz, University of Puerto Rico - Cayey University College
Patricia N. Claudio-Vazquez, University of Puerto Rico - Cayey University College
Debbie M. Espada-Green, University of Puerto Rico - Cayey University College
Marium Feliciano-Camacho, University of Puerto Rico - Cayey University College
Karina M. Gonzalez-Bonilla, University of Puerto Rico - Cayey University College
Mariela Taboas-Arroyo, University of Puerto Rico - Cayey University College
Dorianmarie Vargaz-Franco, University of Puerto Rico - Cayey University College
Raquel Montanez-Gonzalez, University of Puerto Rico - Cayey University College
Joseph Perez-Otero, University of Puerto Rico - Cayey University College
Myrielis Rivera-Burgos, University of Puerto Rico - Cayey University College
Francisco J. Rivera-Rosario, University of Puerto Rico - Cayey University College
Heather L. Eisler, University of the Cumberlands
Jackie Alexander, University of the Cumberlands
Samantha K. Begley, University of the Cumberlands
Deana Gabbard, University of the Cumberlands
Robert J. Allen, Washington University in St. Louis
Wint Yan Aung, Washington University in St. Louis
William D. Barshop, Washington University in St. Louis
Amanda Boozalis, Washington University in St. Louis
Vanessa P. Chu, Washington University in St. Louis
Jeremy S. Davis, Washington University in St. Louis
Ryan N. Duggal, Washington University in St. Louis
Robert Franklin, Washington University in St. Louis
Katherine Gavinski, Washington University in St. Louis
Heran Gebreyesus, Washington University in St. Louis
Henry Z. Gong, Washington University in St. Louis
Rachel A. Greenstein, Washington University in St. Louis
Averill D. Guo, Washington University in St. Louis
Casey Hanson, Washington University in St. Louis
Kaitlin E. Homa, Washington University in St. Louis
Simon C. Hsu, Washington University in St. Louis
Yi Huang, Washington University in St. Louis
Lucy Huo, Washington University in St. Louis
Sarah Jacobs, Washington University in St. Louis
Sasha Jia, Washington University in St. Louis
Kyle L. Jung, Washington University in St. Louis
Sarah Wai-Chee Kong, Washington University in St. Louis
Matthew R. Kroll, Washington University in St. Louis
Brandon M. Lee, Washington University in St. Louis
Paul F. Lee, Washington University in St. Louis
Kevin M. Levine, Washington University in St. Louis
Amy S. Li, Washington University in St. Louis
Chengyu Liu, Washington University in St. Louis
Max Mian Liu, Washington University in St. Louis
Adam P. Lousararian, Washington University in St. Louis
Peter B. Lowery, Washington University in St. Louis
Allyson P. Mallya, Washington University in St. Louis
Joseph E. Marcus, Washington University in St. Louis
Patrick C. Ng, Washington University in St. Louis
Hien P. Nguyen, Washington University in St. Louis
Ruchik Patel, Washington University in St. Louis
Hashini Precht, Washington University in St. Louis
Suchita Rastogi, Washington University in St. Louis
Jonathan M. Sarezky, Washington University in St. Louis
Adam Schefkind, Washington University in St. Louis
Michael B. Schultz, Washington University in St. Louis
Delia Shen, Washington University in St. Louis
Tara Skorupa, Washington University in St. Louis
Nicholas C. Spies, Washington University in St. Louis
Gabriel Stancu, Washington University in St. Louis
Hiu Man Vivian Tsang, Washington University in St. Louis
Alice L. Turski, Washington University in St. Louis
Rohit Venkat, Washington University in St. Louis
Leah E. Waldman, Washington University in St. Louis
Kaidi Wang, Washington University in St. Louis
Tracy Wang, Washington University in St. Louis
Jeffrey W. Wei, Washington University in St. Louis
Dennis Y. Wu, Washington University in St. Louis
David D. Xiong, Washington University in St. Louis
Jack Yu, Washington University in St. Louis
Karen Zhou, Washington University in St. Louis
Gerard P. McNeil, York College
Robert W. Fernandez, York College
Patrick Gomez Menzies, York College
Tingting Gu, Washington University in St. Louis
Jeremy Buhler, Washington University in St. Louis
Elaine R. Mardis, Washington University School of Medicine
Sarah C R Elgin, Washington University in St. Louis

Keywords

Drosophila, genome size, heterochromatin, retrotransposons, Wolbachia

Disciplines

Genetics and Genomics

Abstract

The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (>18.7 Mb) in D. ananassae. To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes (e.g., larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in D. ananassae. Compared to D. melanogaster, the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 5′ ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains.

Comments

Originally published in G3: Genes | Genomes | Genetics, Oxford University Press.

Original Citation

Leung, W., Shaffer, C. D., Chen, E. J., Quisenberry, T. J., Ko, K., Braverman, J. W., Giarla, T. C., Mortimer, N. T., Reed, L. K., Smith, S. T., Srebrenka, R., McCartha, S. R., Perry, D. R., Prescod, L. M., Sheppard, Z. A., Saville, K. J., McClish, A., Morlock, E. A., Sochor, V. … Elgin, S. C. R. (2017). Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element. G3: Genes, Genomes, Genetics, 7(8), 2439–2460. https://doi.org/10.1534/g3.117.040907

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