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Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element.

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Date
2017-08-07
Authors
Leung, Wilson
Shaffer, Christopher D
Chen, Elizabeth J
Quisenberry, Thomas J
Ko, Kevin
Braverman, John M
Giarla, Thomas C
Mortimer, Nathan T
Reed, Laura K
Smith, Sheryl T
Robic, Srebrenka
McCartha, Shannon R
Perry, Danielle R
Prescod, Lindsay M
Sheppard, Zenyth A
Saville, Ken J
McClish, Allison
Morlock, Emily A
Sochor, Victoria R
Stanton, Brittney
Veysey-White, Isaac C
Revie, Dennis
Jimenez, Luis A
Palomino, Jennifer J
Patao, Melissa D
Patao, Shane M
Himelblau, Edward T
Campbell, Jaclyn D
Hertz, Alexandra L
McEvilly, Maddison F
Wagner, Allison R
Youngblom, James
Bedi, Baljit
Bettincourt, Jeffery
Duso, Erin
Her, Maiye
Hilton, William
House, Samantha
Karimi, Masud
Kumimoto, Kevin
Lee, Rebekah
Lopez, Darryl
Odisho, George
Prasad, Ricky
Robbins, Holly Lyn
Sandhu, Tanveer
Selfridge, Tracy
Tsukashima, Kara
Yosif, Hani
Kokan, Nighat P
Britt, Latia
Zoellner, Alycia
Spana, Eric P
Chlebina, Ben T
Chong, Insun
Friedman, Harrison
Mammo, Danny A
Ng, Chun L
Nikam, Vinayak S
Schwartz, Nicholas U
Xu, Thomas Q
Burg, Martin G
Batten, Spencer M
Corbeill, Lindsay M
Enoch, Erica
Ensign, Jesse J
Franks, Mary E
Haiker, Breanna
Ingles, Judith A
Kirkland, Lyndsay D
Lorenz-Guertin, Joshua M
Matthews, Jordan
Mittig, Cody M
Monsma, Nicholaus
Olson, Katherine J
Perez-Aragon, Guillermo
Ramic, Alen
Ramirez, Jordan R
Scheiber, Christopher
Schneider, Patrick A
Schultz, Devon E
Simon, Matthew
Spencer, Eric
Wernette, Adam C
Wykle, Maxine E
Zavala-Arellano, Elizabeth
McDonald, Mitchell J
Ostby, Kristine
Wendland, Peter
DiAngelo, Justin R
Ceasrine, Alexis M
Cox, Amanda H
Docherty, James EB
Gingras, Robert M
Grieb, Stephanie M
Pavia, Michael J
Personius, Casey L
Polak, Grzegorz L
Beach, Dale L
Cerritos, Heaven L
Horansky, Edward A
Sharif, Karim A
Moran, Ryan
Parrish, Susan
Bickford, Kirsten
Bland, Jennifer
Broussard, Juliana
Campbell, Kerry
Deibel, Katelynn E
Forka, Richard
Lemke, Monika C
Nelson, Marlee B
O'Keeffe, Catherine
Ramey, S Mariel
Schmidt, Luke
Villegas, Paola
Jones, Christopher J
Christ, Stephanie L
Mamari, Sami
Rinaldi, Adam S
Stity, Ghazal
Hark, Amy T
Scheuerman, Mark
Silver Key, S Catherine
McRae, Briana D
Haberman, Adam S
Asinof, Sam
Carrington, Harriette
Drumm, Kelly
Embry, Terrance
McGuire, Richard
Miller-Foreman, Drew
Rosen, Stella
Safa, Nadia
Schultz, Darrin
Segal, Matt
Shevin, Yakov
Svoronos, Petros
Vuong, Tam
Skuse, Gary
Paetkau, Don W
Bridgman, Rachael K
Brown, Charlotte M
Carroll, Alicia R
Gifford, Francesca M
Gillespie, Julie Beth
Herman, Susan E
Holtcamp, Krystal L
Host, Misha A
Hussey, Gabrielle
Kramer, Danielle M
Lawrence, Joan Q
Martin, Madeline M
Niemiec, Ellen N
O'Reilly, Ashleigh P
Pahl, Olivia A
Quintana, Guadalupe
Rettie, Elizabeth AS
Richardson, Torie L
Rodriguez, Arianne E
Rodriguez, Mona O
Schiraldi, Laura
Smith, Joanna J
Sugrue, Kelsey F
Suriano, Lindsey J
Takach, Kaitlyn E
Vasquez, Arielle M
Velez, Ximena
Villafuerte, Elizabeth J
Vives, Laura T
Zellmer, Victoria R
Hauke, Jeanette
Hauser, Charles R
Barker, Karolyn
Cannon, Laurie
Parsamian, Perouza
Parsons, Samantha
Wichman, Zachariah
Bazinet, Christopher W
Johnson, Diana E
Bangura, Abubakarr
Black, Jordan A
Chevee, Victoria
Einsteen, Sarah A
Hilton, Sarah K
Kollmer, Max
Nadendla, Rahul
Stamm, Joyce
Fafara-Thompson, Antoinette E
Gygi, Amber M
Ogawa, Emmy E
Van Camp, Matt
Kocsisova, Zuzana
Leatherman, Judith L
Modahl, Cassie M
Rubin, Michael R
Apiz-Saab, Susana S
Arias-Mejias, Suzette M
Carrion-Ortiz, Carlos F
Claudio-Vazquez, Patricia N
Espada-Green, Debbie M
Feliciano-Camacho, Marium
Gonzalez-Bonilla, Karina M
Taboas-Arroyo, Mariela
Vargas-Franco, Dorianmarie
Montañez-Gonzalez, Raquel
Perez-Otero, Joseph
Rivera-Burgos, Myrielis
Rivera-Rosario, Francisco J
Eisler, Heather L
Alexander, Jackie
Begley, Samatha K
Gabbard, Deana
Allen, Robert J
Aung, Wint Yan
Barshop, William D
Boozalis, Amanda
Chu, Vanessa P
Davis, Jeremy S
Duggal, Ryan N
Franklin, Robert
Gavinski, Katherine
Gebreyesus, Heran
Gong, Henry Z
Greenstein, Rachel A
Guo, Averill D
Hanson, Casey
Homa, Kaitlin E
Hsu, Simon C
Huang, Yi
Huo, Lucy
Jacobs, Sarah
Jia, Sasha
Jung, Kyle L
Wai-Chee Kong, Sarah
Kroll, Matthew R
Lee, Brandon M
Lee, Paul F
Levine, Kevin M
Li, Amy S
Liu, Chengyu
Liu, Max Mian
Lousararian, Adam P
Lowery, Peter B
Mallya, Allyson P
Marcus, Joseph E
Ng, Patrick C
Nguyen, Hien P
Patel, Ruchik
Precht, Hashini
Rastogi, Suchita
Sarezky, Jonathan M
Schefkind, Adam
Schultz, Michael B
Shen, Delia
Skorupa, Tara
Spies, Nicholas C
Stancu, Gabriel
Vivian Tsang, Hiu Man
Turski, Alice L
Venkat, Rohit
Waldman, Leah E
Wang, Kaidi
Wang, Tracy
Wei, Jeffrey W
Wu, Dennis Y
Xiong, David D
Yu, Jack
Zhou, Karen
McNeil, Gerard P
Fernandez, Robert W
Menzies, Patrick Gomez
Gu, Tingting
Buhler, Jeremy
Mardis, Elaine R
Elgin, Sarah CR
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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.
Type
Journal article
Subject
Chromosomes
Animals
Drosophila
Wolbachia
Histones
Retroelements
Codon
Gene Expression Profiling
Protein Processing, Post-Translational
Base Composition
Base Sequence
Genes, Insect
Female
Permalink
https://hdl.handle.net/10161/23708
Published Version (Please cite this version)
10.1534/g3.117.040907
Publication Info
Leung, Wilson; Shaffer, Christopher D; Chen, Elizabeth J; Quisenberry, Thomas J; Ko, Kevin; Braverman, John M; ... Elgin, Sarah CR (2017). Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element. G3 (Bethesda, Md.), 7(8). pp. 2439-2460. 10.1534/g3.117.040907. Retrieved from https://hdl.handle.net/10161/23708.
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.
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Scholars@Duke

Ceasrine

Alexis Ceasrine

Postdoctoral Scholar
Spana

Eric P. Spana

Associate Professor of the Practice of Biology

Leah Esther Waldman

Assistant Professor in the Department of Radiology
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