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Authors: Leung, Wilson and Shaffer, Christopher D and Chen, Elizabeth J and Quisenberry, Thomas J and Ko, Kevin and Braverman, John M and Giarla, Thomas C and Mortimer, Nathan T and Reed, Laura K and Smith, Sheryl T and Robic, Srebrenka and McCartha, Shannon R and Perry, Danielle R and Prescod, Lindsay M and Sheppard, Zenyth A and Saville, Ken J and McClish, Allison and Morlock, Emily A and Sochor, Victoria R and Stanton, Brittney and Veysey-White, Isaac C and Revie, Dennis and Jimenez, Luis A and Palomino, Jennifer J and Patao, Melissa D and Patao, Shane M and Himelblau, Edward T and Campbell, Jaclyn D and Hertz, Alexandra L and McEvilly, Maddison F and Wagner, Allison R and Youngblom, James and Bedi, Baljit and Bettincourt, Jeffery and Duso, Erin and Her, Maiye and Hilton, William and House, Samantha and Karimi, Masud and Kumimoto, Kevin and Lee, Rebekah and Lopez, Darryl and Odisho, George and Prasad, Ricky and Robbins, Holly Lyn and Sandhu, Tanveer and Selfridge, Tracy and Tsukashima, Kara and Yosif, Hani and Kokan, Nighat P and Britt, Latia and Zoellner, Alycia and Spana, Eric P and Chlebina, Ben T and Chong, Insun and Friedman, Harrison and Mammo, Danny A and Ng, Chun L and Nikam, Vinayak S and Schwartz, Nicholas U and Xu, Thomas Q and Burg, Martin G and Batten, Spencer M and Corbeill, Lindsay M and Enoch, Erica and Ensign, Jesse J and Franks, Mary E and Haiker, Breanna and Ingles, Judith A and Kirkland, Lyndsay D and Lorenz-Guertin, Joshua M and Matthews, Jordan and Mittig, Cody M and Monsma, Nicholaus and Olson, Katherine J and Perez-Aragon, Guillermo and Ramic, Alen and Ramirez, Jordan R and Scheiber, Christopher and Schneider, Patrick A and Schultz, Devon E and Simon, Matthew and Spencer, Eric and Wernette, Adam C and Wykle, Maxine E and Zavala-Arellano, Elizabeth and McDonald, Mitchell J and Ostby, Kristine and Wendland, Peter and DiAngelo, Justin R and Ceasrine, Alexis M and Cox, Amanda H and Docherty, James E B and Gingras, Robert M and Grieb, 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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. Copyright © 2017 Leung et al.

Journal: G3
DOI: 10.1534/g3.117.040907
Year: 2017

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