DrosophilaMuller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution
Authors: Leung Wilson , Shaffer Christopher D , Reed Laura K , Smith Sheryl T , Barshop William , Dirkes William , Dothager Matthew , Lee Paul , Wong Jeannette , Xiong David , Yuan Han , Bedard James E J , Machone Joshua F , Patterson Seantay D , Price Amber L , Turner Bryce A , Robic Srebrenka , Luippold Erin K , McCartha Shannon R , Walji Tezin A , Walker Chelsea A , Saville Kenneth , Abrams Marita K , Armstrong Andrew R , Armstrong William , Bailey Robert J , Barberi Chelsea R , Beck Lauren R , Blaker Amanda L , Blunden Christopher E , Brand Jordan P , Brock Ethan J , Brooks Dana W , Brown Marie , Butzler Sarah C , Clark Eric M , Clark Nicole B , Collins Ashley A , Cotteleer Rebecca J , Cullimore Peterson R , Dawson Seth G , Docking Carter T , Dorsett Sasha L , Dougherty Grace A , Downey Kaitlyn A , Drake Andrew P , Earl Erica K , Floyd Trevor G , Forsyth Joshua D , Foust Jonathan D , Franchi Spencer L , Geary James F , Hanson Cynthia K , Harding Taylor S , Harris Cameron B , Heckman Jonathan M , Holderness Heather L , Howey Nicole A , Jacobs Dontae A , Jewell Elizabeth S , Kaisler Maria , Karaska Elizabeth A , Kehoe James L , Koaches Hannah C , Koehler Jessica , Koenig Dana , Kujawski Alexander J , Kus Jordan E , Lammers Jennifer A , Leads Rachel R , Leatherman Emily C , Lippert Rachel N , Messenger Gregory S , Morrow Adam T , Newcomb Victoria , Plasman Haley J , Potocny Stephanie J , Powers Michelle K , Reem Rachel M , Rennhack Jonathan P , Reynolds Katherine R , Reynolds Lyndsey A , Rhee Dong K , Rivard Allyson B , Ronk Adam J , Rooney Meghan B , Rubin Lainey S , Salbert Luke R , Saluja Rasleen K , Schauder Taylor , Schneiter Allison R , Schulz Robert W , Smith Karl E , Spencer Sarah , Swanson Bryant R , Tache Melissa A , Tewilliager Ashley A , Tilot Amanda K , VanEck Eve , Villerot Matthew M , Vylonis Megan B , Watson David T , Wurzler Juliana A , Wysocki Lauren M , Yalamanchili Monica , Zaborowicz Matthew A , Emerson Julia A , Ortiz Carlos , Deuschle Frederic J , DiLorenzo Lauren A , Goeller Katie L , Macchi Christopher R , Muller Sarah E , Pasierb Brittany D , Sable Joseph E , Tucci Jessica M , Tynon Marykathryn , Dunbar David A , Beken Levent H , Conturso Alaina C , Danner Benjamin L , DeMichele Gabriella A , Gonzales Justin A , Hammond Maureen S , Kelley Colleen V , Kelly Elisabeth A , Kulich Danielle , Mageeney Catherine M , McCabe Nikie L , Newman Alyssa M , Spaeder Lindsay A , Tumminello Richard A , Revie Dennis , Benson Jonathon M , Cristostomo Michael C , DaSilva Paolo A , Harker Katherine S , Jarrell Jenifer N , Jimenez Luis A , Katz Brandon M , Kennedy William R , Kolibas Kimberly S , LeBlanc Mark T , Nguyen Trung T , Nicolas Daniel S , Patao Melissa D , Patao Shane M , Rupley Bryan J , Sessions Bridget J , Weaver Jennifer A , Goodman Anya L , Alvendia Erica L , Baldassari Shana M , Brown Ashley S , Chase Ian O , Chen Maida , Chiang Scott , Cromwell Avery B , Custer Ashley F , DiTommaso Tia M , El-Adaimi Jad , Goscinski Nora C , Grove Ryan A , Gutierrez Nestor , Harnoto Raechel S , Hedeen Heather , Hong Emily L , Hopkins Barbara L , Huerta Vilma F , Khoshabian Colin , LaForge Kristin M , Lee Cassidy T , Lewis Benjamin M , Lydon Anniken M , Maniaci Brian J , Mitchell Ryan D , Morlock Elaine V , Morris William M , Naik Priyanka , Olson Nicole C , Osterloh Jeannette M , Perez Marcos A , Presley Jonathan D , Randazzo Matt J , Regan Melanie K , Rossi Franca G , Smith Melanie A , Soliterman Eugenia A , Sparks Ciani J , Tran Danny L , Wan Tiffany , Welker Anne A , Wong Jeremy N , Sreenivasan Aparna , Youngblom Jim , Adams Andrew , Alldredge Justin , Bryant Ashley , Carranza David , Cifelli Alyssa , Coulson Kevin , Debow Calise , Delacruz Noelle , Emerson Charlene , Farrar Cassandra , Foret Don , Garibay Edgar , Gooch John , Heslop Michelle , Kaur Sukhjit , Khan Ambreen , Kim Van , Lamb Travis , Lindbeck Peter , Lucas Gabi , Macias Elizabeth , Martiniuc Daniela , Mayorga Lissett , Medina Joseph , Membreno Nelson , Messiah Shady , Neufeld Lacey , Nguyen San Francisco , Nichols Zachary , Odisho George , Peterson Daymon , Rodela Laura , Rodriguez Priscilla , Rodriguez Vanessa , Ruiz Jorge , Sherrill Will , Silva Valeria , Sparks Jeri , Statton Geeta , Townsend Ashley , Valdez Isabel , Waters Mary , Westphal Kyle , Winkler Stacey , Zumkehr Joannee , DeJong Randall J , Hoogewerf Arlene J , Ackerman Cheri M , Armistead Isaac O , Baatenburg Lara , Borr Matthew J , Brouwer Lindsay K , Burkhart Brandon J , Bushhouse Kelsey T , Cesko Lejla , Choi Tiffany Y Y , Cohen Heather , Damsteegt Amanda M , Darusz Jess M , Dauphin Cory M , Davis Yelena P , Diekema Emily J , Drewry Melissa , Eisen Michelle E M , Faber Hayley M , Faber Katherine J , Feenstra Elizabeth , Felzer-Kim Isabella T , Hammond Brandy L , Hendriksma Jesse , Herrold Milton R , Hilbrands Julia A , Howell Emily J , Jelgerhuis Sarah A , Jelsema Timothy R , Johnson Benjamin K , Jones Kelly K , Kim Anna , Kooienga Ross D , Menyes Erika E , Nollet Eric A , Plescher Brittany E , Rios Lindsay , Rose Jenny L , Schepers Allison J , Scott Geoff , Smith Joshua R , Sterling Allison M , Tenney Jenna C , Uitvlugt Chris , VanDyken Rachel E , VanderVennen Marielle , Vue Samantha , Kokan Nighat P , Agbley Kwabea , Boham Sampson K , Broomfield Daniel , Chapman Kayla , Dobbe Ali , Dobbe Ian , Harrington William , Ibrahem Marwan , Kennedy Andre , Koplinsky Chad A , Kubricky Cassandra , Ladzekpo Danielle , Pattison Claire , Ramirez Roman E , Wande Lucia , Woehlke Sarah , Wawersik Matthew , Kiernan Elizabeth , Thompson Jeffrey S , Banker Roxanne , Bartling Justina R , Bhatiya Chinmoy I , Boudoures Anna L , Christiansen Lena , Fosselman Daniel S , French Kristin M , Gill Ishwar S , Havill Jessen T , Johnson Jaelyn L , Keny Lauren J , Kerber John M , Klett Bethany M , Kufel Christina N , May Francis J , Mecoli Jonathan P , Merry Callie R , Meyer Lauren R , Miller Emily G , Mullen Gregory J , Palozola Katherine C , Pfeil Jacob J , Thomas Jessica G , Verbofsky Evan M , Spana Eric P , Agarwalla Anant , Chapman Julia , Chlebina Ben , Chong Insun , Falk I N , Fitzgibbons John D , Friedman Harrison , Ighile Osagie , Kim Andrew J , Knouse Kristin A , Kung Faith , Mammo Danny , Ng Chun Leung , Nikam Vinayak S , Norton Diana , Pham Philip , Polk Jessica W , Prasad Shreya , Rankin Helen , Ratliff Camille D , Scala Victoria , Schwartz Nicholas U , Shuen Jessica A , Xu Amy , Xu Thomas Q , Zhang Yi , Rosenwald Anne G , Burg Martin G , Adams Stephanie J , Baker Morgan , Botsford Bobbi , Brinkley Briana , Brown Carter , Emiah Shadie , Enoch Erica , Gier Chad , Greenwell Alyson , Hoogenboom Lindsay , Matthews Jordan E , McDonald Mitchell , Mercer Amanda , Monsma Nicholaus , Ostby Kristine , Ramic Alen , Shallman Devon , Simon Matthew , Spencer Eric , Tomkins Trisha , Wendland Pete , Wylie Anna , Wolyniak Michael J , Robertson Gregory M , Smith Samuel I , DiAngelo Justin R , Sassu Eric D , Bhalla Satish C , Sharif Karim A , Choeying Tenzin , Macias Jason S , Sanusi Fareed , Torchon Karvyn , Bednarski April E , Alvarez Consuelo J , Davis Kristen C , Dunham Carrie A , Grantham Alaina J , Hare Amber N , Schottler Jennifer , Scott Zackary W , Kuleck Gary A , Yu Nicole S , Kaehler Marian M , Jipp Jacob , Overvoorde Paul J , Shoop Elizabeth , Cyrankowski Olivia , Hoover Betsy , Kusner Matt , Lin Devry , Martinov Tijana , Misch Jonathan , Salzman Garrett , Schiedermayer Holly , Snavely Michael , Zarrasola Stephanie , Parrish Susan , Baker Atlee , Beckett Alissa , Belella Carissa , Bryant Julie , Conrad Turner , Fearnow Adam , Gomez Carolina , Herbstsomer Robert A , Hirsch Sarah , Johnson Christen , Jones Melissa , Kabaso Rita , Lemmon Eric , Vieira Carolina Marques dos Santos , McFarland Darryl , McLaughlin Christopher , Morgan Abbie , Musokotwane Sepo , Neutzling William , Nietmann Jana , Paluskievicz Christina , Penn Jessica , Peoples Emily , Pozmanter Caitlin , Reed Emily , Rigby Nichole , Schmidt Lasse , Shelton Micah , Shuford Rebecca , Tirasawasdichai Tiara , Undem Blair , Urick Damian , Vondy Kayla , Yarrington Bryan , Eckdahl Todd T , Poet Jeffrey L , Allen Alica B , Anderson John E , Barnett Jason M , Baumgardner Jordan S , Brown Adam D , Carney Jordan E , Chavez Ramiro A , Christgen Shelbi L , Christie Jordan S , Clary Andrea N , Conn Michel A , Cooper Kristen M , Crowley Matt J , Crowley Samuel T , Doty Jennifer S , Dow Brian A , Edwards Curtis R , Elder Darcie D , Fanning John P , Janssen Bridget M , Lambright Anthony K , Lane Curtiss E , Limle Austin B , Mazur Tammy , McCracken Marly R , McDonough Alexa M , Melton Amy D , Minnick Phillip J , Musick Adam E , Newhart William H , Noynaert Joseph W , Ogden Bradley J , Sandusky Michael W , Schmuecker Samantha M , Shipman Anna L , Smith Anna L , Thomsen Kristen M , Unzicker Matthew R , Vernon William B , Winn Wesley W , Woyski Dustin S , Zhu Xiao , Du Chunguang , Ament Caitlin , Aso Soham , Bisogno Laura Simone , Caronna Jason , Fefelova Nadezhda , Lopez Lenin , Malkowitz Lorraine , Marra Jonathan , Menillo Daniella , Obiorah Ifeanyi , Onsarigo Eric Nyabeta , Primus Shekerah , Soos Mahdi , Tare Archana , Zidan Ameer , Jones Christopher J , Aronhalt Todd , Bellush James M , Burke Christa , DeFazio Steve , Does Benjamin R , Johnson Todd D , Keysock Nicholas , Knudsen Nelson H , Messler James , Myirski Kevin , Rekai Jade Lea , Rempe Ryan Michael , Salgado Michael S , Stagaard Erica , Starcher Justin R , Waggoner Andrew W , Yemelyanova Anastasia K , Hark Amy T , Bertolet Anne , Kuschner Cyrus E , Parry Kesley , Quach Michael , Shantzer Lindsey , Shaw Mary E , Smith Mary A , Glenn Omolara , Mason Portia , Williams Charlotte , Key S Catherine Silver , Henry Tyneshia C P , Johnson Ashlee G , White Jackie X , Haberman Adam , Asinof Sam , Drumm Kelly , Freeburg Trip , Safa Nadia , Schultz Darrin , Shevin Yakov , Svoronos Petros , Vuong Tam , Wellinghoff Jules , Hoopes Laura L M , Chau Kim M , Ward Alyssa , Regisford E Gloria C , Augustine LaJerald , Davis-Reyes Brionna , Echendu Vivienne , Hales Jasmine , Ibarra Sharon , Johnson Lauriaun , Ovu Steven , Braverman John M , Bahr Thomas J , Caesar Nicole M , Campana Christopher , Cassidy Daniel W , Cognetti Peter A , English Johnathan D , Fadus Matthew C , Fick Cameron N , Freda Philip J , Hennessy Bryan M , Hockenberger Kelsey , Jones Jennifer K , King Jessica E , Knob Christopher R , Kraftmann Karen J , Li Linghui , Lupey Lena N , Minniti Carl J , Minton Thomas F , Moran Joseph V , Mudumbi Krishna , Nordman Elizabeth C , Puetz William J , Robinson Lauren M , Rose Thomas J , Sweeney Edward P , Timko Ashley S , Paetkau Don W , Eisler Heather L , Aldrup Megan E , Bodenberg Jessica M , Cole Mara G , Deranek Kelly M , DeShetler Megan , Dowd Rose M , Eckardt Alexandra K , Ehret Sharon C , Fese Jessica , Garrett Amanda D , Kammrath Anna , Kappes Michelle L , Light Morgan R , Meier Anne C , O’Rouke Allison , Perella Mallory , Ramsey Kimberley , Ramthun Jennifer R , Reilly Mary T , Robinett Deirdre , Rossi Nadine L , Schueler Mary Grace , Shoemaker Emma , Starkey Kristin M , Vetor Ashley , Vrable Abby , Chandrasekaran Vidya , Beck Christopher , Hatfield Kristen R , Herrick Douglas A , Khoury Christopher B , Lea Charlotte , Louie Christopher A , Lowell Shannon M , Reynolds Thomas J , Schibler Jeanine , Scoma Alexandra H , Smith-Gee Maxwell T , Tuberty Sarah , Smith Christopher D , Lopilato Jane E , Hauke Jeanette , Roecklein-Canfield Jennifer A , Corrielus Maureen , Gilman Hannah , Intriago Stephanie , Maffa Amanda , Rauf Sabya A , Thistle Katrina , Trieu Melissa , Winters Jenifer , Yang Bib , Hauser Charles R , Abusheikh Tariq , Ashrawi Yara , Benitez Pedro , Boudreaux Lauren R , Bourland Megan , Chavez Miranda , Cruz Samantha , Elliott GiNell , Farek Jesse R , Flohr Sarah , Flores Amanda H , Friedrichs Chelsey , Fusco Zach , Goodwin Zane , Helmreich Eric , Kiley John , Knepper John Mark , Langner Christine , Martinez Megan , Mendoza Carlos , Naik Monal , Ochoa Andrea , Ragland Nicolas , Raimey England , Rathore Sunil , Reza Evangelina , Sadovsky Griffin , Seydoux Marie-Isabelle B , Smith Jonathan E , Unruh Anna K , Velasquez Vicente , Wolski Matthew W , Gosser Yuying , Govind Shubha , Clarke-Medley Nicole , Guadron Leslie , Lau Dawn , Lu Alvin , Mazzeo Cheryl , Meghdari Mariam , Ng Simon , Pamnani Brad , Plante Olivia , Shum Yuki Kwan Wa , Song Roy , Johnson Diana E , Abdelnabi Mai , Archambault Alexi , Chamma Norma , Gaur Shailly , Hammett Deborah , Kandahari Adrese , Khayrullina Guzal , Kumar Sonali , Lawrence Samantha , Madden Nigel , Mandelbaum Max , Milnthorp Heather , Mohini Shiv , Patel Roshni , Peacock Sarah J , Perling Emily , Quintana Amber , Rahimi Michael , Ramirez Kristen , Singhal Rishi , Weeks Corinne , Wong Tiffany , Gillis Aubree T , Moore Zachary D , Savell Christopher D , Watson Reece , Mel Stephanie F , Anilkumar Arjun A , Bilinski Paul , Castillo Rostislav , Closser Michael , Cruz Nathalia M , Dai Tiffany , Garbagnati Giancarlo F , Horton Lanor S , Kim Dongyeon , Lau Joyce H , Liu James Z , Mach Sandy D , Phan Thu A , Ren Yi , Stapleton Kenneth E , Strelitz Jean M , Sunjed Ray , Stamm Joyce , Anderson Morgan C , Bonifield Bethany Grace , Coomes Daniel , Dillman Adam , Durchholz Elaine J , Fafara-Thompson Antoinette E , Gross Meleah J , Gygi Amber M , Jackson Lesley E , Johnson Amy , Kocsisova Zuzana , Manghelli Joshua L , McNeil Kylie , Murillo Michael , Naylor Kierstin L , Neely Jessica , Ogawa Emmy E , Rich Ashley , Rogers Anna , Spencer J Devin , Stemler Kristina M , Throm Allison A , Van Camp Matt , Weihbrecht Katie , Wiles T Aaron , Williams Mallory A , Williams Matthew , Zoll Kyle , Bailey Cheryl , Zhou Leming , Balthaser Darla M , Bashiri Azita , Bower Mindy E , Florian Kayla A , Ghavam Nazanin , Greiner-Sosanko Elizabeth S , Karim Helmet , Mullen Victor W , Pelchen Carly E , Yenerall Paul M , Zhang Jiayu , Rubin Michael R , Arias-Mejias Suzette M , Bermudez-Capo Armando G , Bernal-Vega Gabriela V , Colon-Vazquez Mariela , Flores-Vazquez Arelys , Gines-Rosario Mariela , Llavona-Cartagena Ivan G , Martinez-Rodriguez Javier O , Ortiz-Fuentes Lionel , Perez-Colomba Eliezer O , Perez-Otero Joseph , Rivera Elisandra , Rodriguez-Giron Luke J , Santiago-Sanabria Arnaldo J , Senquiz-Gonzalez Andrea M , delValle Frank R Soto , Vargas-Franco Dorianmarie , Velázquez-Soto Karla I , Zambrana-Burgos Joan D , Martinez-Cruzado Juan Carlos , Asencio-Zayas Lillyann , Babilonia-Figueroa Kevin , Beauchamp-Pérez Francis D , Belén-Rodríguez Juliana , Bracero-Quiñones Luciann , Burgos-Bula Andrea P , Collado-Méndez Xavier A , Colón-Cruz Luis R , Correa-Muller Ana I , Crooke-Rosado Jonathan L , Cruz-García José M , Defendini-Ávila Marianna , Delgado-Peraza Francheska M , Feliciano-Cancela Alex J , Gónzalez-Pérez Valerie M , Guiblet Wilfried , Heredia-Negrón Aldo , Hernández-Muñiz Jennifer , Irizarry-González Lourdes N , Laboy-Corales Ángel L , Llaurador-Caraballo Gabriela A , Marín-Maldonado Frances , Marrero-Llerena Ulises , Martell-Martínez Héctor A , Martínez-Traverso Idaliz M , Medina-Ortega Kiara N , Méndez-Castellanos Sonya G , Menéndez-Serrano Krizia C , Morales-Caraballo Carol I , Ortiz-DeChoudens Saryleine , Ortiz-Ortiz Patricia , Pagán-Torres Hendrick , Pérez-Afanador Diana , Quintana-Torres Enid M , Ramírez-Aponte Edwin G , Riascos-Cuero Carolina , Rivera-Llovet Michelle S , Rivera-Pagán Ingrid T , Rivera-Vicéns Ramón E , Robles-Juarbe Fabiola , Rodríguez-Bonilla Lorraine , Rodríguez-Echevarría Brian O , Rodríguez-García Priscila M , Rodríguez-Laboy Abneris E , Rodríguez-Santiago Susana , Rojas-Vargas Michael L , Rubio-Marrero Eva N , Santiago-Colón Albeliz , Santiago-Ortiz Jorge L , Santos-Ramos Carlos E , Serrano-González Joseline , Tamayo-Figueroa Alina M , Tascón-Peñaranda Edna P , Torres-Castillo José L , Valentín-Feliciano Nelson A , Valentín-Feliciano Yashira M , Vargas-Barreto Nadyan M , Vélez-Vázquez Miguel , Vilanova-Vélez Luis R , Zambrana-Echevarría Cristina , MacKinnon Christy , Chung Hui-Min , Kay Chris , Pinto Anthony , Kopp Olga R , Burkhardt Joshua , Harward Chris , Allen Robert , Bhat Pavan , Chang Jimmy Hsiang-Chun , Chen York , Chesley Christopher , Cohn Dara , DuPuis David , Fasano Michael , Fazzio Nicholas , Gavinski Katherine , Gebreyesus Heran , Giarla Thomas , Gostelow Marcus , Greenstein Rachel , Gunasinghe Hashini , Hanson Casey , Hay Amanda , He Tao Jian , Homa Katie , Howe Ruth , Howenstein Jeff , Huang Henry , Khatri Aaditya , Kim Young Lu , Knowles Olivia , Kong Sarah , Krock Rebecca , Kroll Matt , Kuhn Julia , Kwong Matthew , Lee Brandon , Lee Ryan , Levine Kevin , Li Yedda , Liu Bo , Liu Lucy , Liu Max , Lousararian Adam , Ma Jimmy , Mallya Allyson , Manchee Charlie , Marcus Joseph , McDaniel Stephen , Miller Michelle L , Molleston Jerome M , Diez Cristina Montero , Ng Patrick , Ngai Natalie , Nguyen Hien , Nylander Andrew , Pollack Jason , Rastogi Suchita , Reddy Himabindu , Regenold Nathaniel , Sarezky Jon , Schultz Michael , Shim Jien , Skorupa Tara , Smith Kenneth , Spencer Sarah J , Srikanth Priya , Stancu Gabriel , Stein Andrew P , Strother Marshall , Sudmeier Lisa , Sun Mengyang , Sundaram Varun , Tazudeen Noor , Tseng Alan , Tzeng Albert , Venkat Rohit , Venkataram Sandeep , Waldman Leah , Wang Tracy , Yang Hao , Yu Jack Y , Zheng Yin , Preuss Mary L , Garcia Angelica , Juergens Matt , Morris Robert W , Nagengast Alexis A , Azarewicz Julie , Carr Thomas J , Chichearo Nicole , Colgan Mike , Donegan Megan , Gardner Bob , Kolba Nik , Krumm Janice L , Lytle Stacey , MacMillian Laurell , Miller Mary , Montgomery Andrew , Moretti Alysha , Offenbacker Brittney , Polen Mike , Toth John , Woytanowski John , Kadlec Lisa , Crawford Justin , Spratt Mary L , Adams Ashley L , Barnard Brianna K , Cheramie Martin N , Eime Anne M , Golden Kathryn L , Hawkins Allyson P , Hill Jessica E , Kampmeier Jessica A , Kern Cody D , Magnuson Emily E , Miller Ashley R , Morrow Cody M , Peairs Julia C , Pickett Gentry L , Popelka Sarah A , Scott Alexis J , Teepe Emily J , TerMeer Katie A , Watchinski Carmen A , Watson Lucas A , Weber Rachel E , Woodard Kate A , Barnard Daron C , Appiah Isaac , Giddens Michelle M , McNeil Gerard P , Adebayo Adeola , Bagaeva Kate , Chinwong Justina , Dol Chrystel , George Eunice , Haltaufderhyde Kirk , Haye Joanna , Kaur Manpreet , Semon Max , Serjanov Dmitri , Toorie Anika , Wilson Christopher , Riddle Nicole C , Buhler Jeremy , Mardis Elaine R , Elgin Sarah C R 
Published: March 2015

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.