Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution.

Journal: G3 (Bethesda, Md.)
Published:
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.

Authors
Wilson Leung, Christopher Shaffer, Laura Reed, Sheryl Smith, William Barshop, William Dirkes, Matthew Dothager, Paul Lee, Jeannette Wong, David Xiong, Han Yuan, James E Bedard, Joshua Machone, Seantay Patterson, Amber Price, Bryce Turner, Srebrenka Robic, Erin Luippold, Shannon Mccartha, Tezin Walji, Chelsea Walker, Kenneth Saville, Marita Abrams, Andrew Armstrong, William Armstrong, Robert Bailey, Chelsea Barberi, Lauren Beck, Amanda Blaker, Christopher Blunden, Jordan Brand, Ethan Brock, Dana Brooks, Marie Brown, Sarah Butzler, Eric Clark, Nicole Clark, Ashley Collins, Rebecca Cotteleer, Peterson Cullimore, Seth Dawson, Carter Docking, Sasha Dorsett, Grace Dougherty, Kaitlyn Downey, Andrew Drake, Erica Earl, Trevor Floyd, Joshua Forsyth, Jonathan Foust, Spencer Franchi, James Geary, Cynthia Hanson, Taylor Harding, Cameron Harris, Jonathan Heckman, Heather Holderness, Nicole Howey, Dontae Jacobs, Elizabeth Jewell, Maria Kaisler, Elizabeth Karaska, James Kehoe, Hannah Koaches, Jessica Koehler, Dana Koenig, Alexander Kujawski, Jordan Kus, Jennifer Lammers, Rachel Leads, Emily Leatherman, Rachel Lippert, Gregory Messenger, Adam Morrow, Victoria Newcomb, Haley Plasman, Stephanie Potocny, Michelle Powers, Rachel Reem, Jonathan Rennhack, Katherine Reynolds, Lyndsey Reynolds, Dong Rhee, Allyson Rivard, Adam Ronk, Meghan Rooney, Lainey Rubin, Luke Salbert, Rasleen Saluja, Taylor Schauder, Allison Schneiter, Robert Schulz, Karl Smith, Sarah Spencer, Bryant Swanson, Melissa Tache, Ashley Tewilliager, Amanda Tilot, Eve Vaneck, Matthew Villerot, Megan Vylonis, David Watson, Juliana Wurzler, Lauren Wysocki, Monica Yalamanchili, Matthew Zaborowicz, Julia Emerson, Carlos Ortiz, Frederic Deuschle, Lauren Dilorenzo, Katie Goeller, Christopher Macchi, Sarah Muller, Brittany Pasierb, Joseph Sable, Jessica Tucci, Marykathryn Tynon, David Dunbar, Levent Beken, Alaina Conturso, Benjamin Danner, Gabriella Demichele, Justin Gonzales, Maureen Hammond, Colleen Kelley, Elisabeth Kelly, Danielle Kulich, Catherine Mageeney, Nikie Mccabe, Alyssa Newman, Lindsay Spaeder, Richard Tumminello, Dennis Revie, Jonathon Benson, Michael Cristostomo, Paolo Dasilva, Katherine Harker, Jenifer Jarrell, Luis Jimenez, Brandon Katz, William Kennedy, Kimberly Kolibas, Mark Leblanc, Trung Nguyen, Daniel Nicolas, Melissa Patao, Shane Patao, Bryan Rupley, Bridget Sessions, Jennifer Weaver, Anya Goodman, Erica Alvendia, Shana Baldassari, Ashley Brown, Ian Chase, Maida Chen, Scott Chiang, Avery Cromwell, Ashley Custer, Tia Ditommaso, Jad El Adaimi, Nora Goscinski, Ryan Grove, Nestor Gutierrez, Raechel Harnoto, Heather Hedeen, Emily Hong, Barbara Hopkins, Vilma Huerta, Colin Khoshabian, Kristin Laforge, Cassidy Lee, Benjamin Lewis, Anniken Lydon, Brian Maniaci, Ryan Mitchell, Elaine Morlock, William Morris, Priyanka Naik, Nicole Olson, Jeannette Osterloh, Marcos Perez, Jonathan Presley, Matt Randazzo, Melanie Regan, Franca Rossi, Melanie Smith, Eugenia Soliterman, Ciani Sparks, Danny Tran, Tiffany Wan, Anne Welker, Jeremy Wong, Aparna Sreenivasan, Jim Youngblom, Andrew Adams, Justin Alldredge, Ashley Bryant, David Carranza, Alyssa Cifelli, Kevin Coulson, Calise Debow, Noelle Delacruz, Charlene Emerson, Cassandra Farrar, Don Foret, Edgar Garibay, John Gooch, Michelle Heslop, Sukhjit Kaur, Ambreen Khan, Van Kim, Travis Lamb, Peter Lindbeck, Gabi Lucas, Elizabeth Macias, Daniela Martiniuc, Lissett Mayorga, Joseph Medina, Nelson Membreno, Shady Messiah, Lacey Neufeld, San Nguyen, Zachary Nichols, George Odisho, Daymon Peterson, Laura Rodela, Priscilla Rodriguez, Vanessa Rodriguez, Jorge Ruiz, Will Sherrill, Valeria Silva, Jeri Sparks, Geeta Statton, Ashley Townsend, Isabel Valdez, Mary Waters, Kyle Westphal, Stacey Winkler, Joannee Zumkehr, Randall Dejong, Arlene Hoogewerf, Cheri Ackerman, Isaac Armistead, Lara Baatenburg, Matthew Borr, Lindsay Brouwer, Brandon Burkhart, Kelsey Bushhouse, Lejla Cesko, Tiffany Choi, Heather Cohen, Amanda Damsteegt, Jess Darusz, Cory Dauphin, Yelena Davis, Emily Diekema, Melissa Drewry, Michelle E Eisen, Hayley Faber, Katherine Faber, Elizabeth Feenstra, Isabella Felzer Kim, Brandy Hammond, Jesse Hendriksma, Milton Herrold, Julia Hilbrands, Emily Howell, Sarah Jelgerhuis, Timothy Jelsema, Benjamin Johnson, Kelly Jones, Anna Kim, Ross Kooienga, Erika Menyes, Eric Nollet, Brittany Plescher, Lindsay Rios, Jenny Rose, Allison Schepers, Geoff Scott, Joshua Smith, Allison Sterling, Jenna Tenney, Chris Uitvlugt, Rachel Vandyken, Marielle Vandervennen, Samantha Vue, Nighat Kokan, Kwabea Agbley, Sampson Boham, Daniel Broomfield, Kayla Chapman, Ali Dobbe, Ian Dobbe, William Harrington, Marwan Ibrahem, Andre Kennedy, Chad Koplinsky, Cassandra Kubricky, Danielle Ladzekpo, Claire Pattison, Roman Ramirez, Lucia Wande, Sarah Woehlke, Matthew Wawersik, Elizabeth Kiernan, Jeffrey Thompson, Roxanne Banker, Justina Bartling, Chinmoy Bhatiya, Anna Boudoures, Lena Christiansen, Daniel Fosselman, Kristin French, Ishwar Gill, Jessen Havill, 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