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Journal Articles Nature Year : 2007

Evolution of genes and genomes on the Drosophila phylogeny

. Drosophila 12 Genomes Consortium , Andrew G Clark (1) , Michael B Eisen (2, 3) , Douglas R Smith (4) , Casey M Bergman (5) , Brian Oliver (6) , Therese A Markow (7) , Thomas C Kaufman (8) , Manolis Kellis (9, 10) , William Gelbart (10) , Venky N Iyer (3) , Daniel A Pollard (3) , Timothy B Sackton (1, 11) , Amanda M. Larracuente (1) , Nadia D Singh (1) , Jose P Abad (12) , Dawn N Abt (13) , Boris Adryan (14) , Montserrat Aguade (15) , Hiroshi Akashi (16) , Wyatt W Anderson (17) , Charles F Aquadro (1) , David H Ardell (18) , Roman Arguello (19) , Carlo G Artieri (20) , Daniel A Barbash (1) , Daniel Barker (21) , Paolo Barsanti (22) , Phil Batterham (23) , Serafim Batzoglou (24) , Dave Begun (25) , Arjun Bhutkar (26) , Enrico Blanco (27) , Stephanie A Bosak (4) , Robert K Bradley (3) , Adrianne D Brand (4) , Michael R Brent (28) , Angela N Brooks (3) , Randall H Brown (28) , Roger K Butlin (29) , Corrado Caggese (22) , Brian R Calvi (30) , A Bernardo de Carvalho (31) , Anat Caspi (32) , Sergio Castrezana (33) , Susan E Celniker (2) , Jean L Chang (9) , Charles Chapple (27) , Sourav Chatterji (3, 34) , Asif Chinwalla (35) , Alberto Civetta (36) , Sandra W Clifton (35) , Josep M Comeron (37) , James C Costello (38) , Jerry A Coyne (19) , Jennifer Daub (39) , Robert G David (4) , Arthur L Delcher (40) , Kim Delehaunty (35) , Chuong B Do (24) , Heather Ebling (4) , Kevin Edwards (41) , Thomas Eickbush (42) , Jay D Evans (43) , Alan Filipski (44) , Sven Findeiss (44, 45) , Eva Freyhult (18) , Lucinda Fulton (28) , Robert Fulton (28) , Ana C L Garcia (46) , Anastasia Gardiner (21) , David A Garfield (47) , Barry E Garvin (4) , Greg Gibson (48) , Don Gilbert (8) , Sante Gnerre (9) , Jennifer Godfrey (35) , Robert Good (23) , Valer Gotea (16) , Brenton Gravely (49) , Anthony J Greenberg (1) , Sam Griffiths-Jones (5) , Samuel Gross (50) , Roderic Guigo (27) , Erik A Gustafson (4) , Wilfried Haerty (51) , Matthew W Hahn (52) , Daniel L Halligan (53) , Aaron L Halpern (54) , Gillian M Halter (16) , Mira V Han (38) , Andreas Heger (55) , Ladeana Hillier (28) , Angie S Hinrichs (56) , Ian Holmes (32) , Roger A Hoskins , Melissa J Hubisz , Dan Hultmark , Melanie A Huntley , David B Jaffe (9) , Santosh Jagadeeshan , William R Jeck , Justin Johnson , Corbin D Jones , William C Jordan , Gary H Karpen , Eiko Kataoka , Peter D Keightley , Pouya Kheradpour , Ewen F Kirkness , Leonardo B Koerich , Karsten Kristiansen , Dave Kudrna , Rob J Kulathinal , Sudhir Kumar , Roberta Kwok , Eric Lander , Charles H Langley , Richard Lapoint , Brian P Lazzaro , So-Jeong Lee , Lisa Levesque , Ruiqiang Li , Chiao-Feng Lin , Michael F Lin , Kerstin Lindblad-Toh , Ana Llopart , Manyuan Long , Lloyd Low , Elena Lozovsky , Jian Lu , Meizhong Luo , Carlos A Machado , Wojciech Makalowski , Mar Marzo , Muneo Matsuda , Luciano Matzkin , Bryant Mcallister , Carolyn S Mcbride , Brendan Mckernan , Kevin Mckernan , Maria Mendez-Lago , Patrick Minx , Michael U Mollenhauer , Kristi Montooth , Stephen M Mount , Xu Mu , Eugene Myers , Barbara Negre , Stuart Newfeld , Rasmus Nielsen , Mohamed a F Noor , Patrick O'Grady , Lior Pachter , Montserrat Papaceit , Matthew J Parisi , Michael Parisi , Leopold Parts , Jakob S Pedersen , Graziano Pesole , Adam M Phillippy , Chris P Ponting , Mihai Pop , Damiano Porcelli , Jeffrey R Powell , Sonja Prohaska , Kim Pruitt , Marta Puig , Hadi Quesneville (57) , Kristipati Ravi Ram , David Rand , Matthew D Rasmussen , Laura K Reed , Robert Reenan , Amy Reily , Karin A Remington , Tania T Rieger , Michael G Ritchie , Charles Robin , Yu-Hui Rogers , Claudia Rohde , Julio Rozas , Marc J Rubenfield , Alfredo Ruiz , Susan Russo , Steven L Salzberg , Alejandro Sanchez-Gracia , David J Saranga , Hajime Sato , Stephen W Schaeffer , Michael C Schatz , Todd Schlenke , Russell Schwartz , Carmen Segarra , Rama S Singh , Laura Sirot , Marina Sirota , Nicholas B Sisneros , Chris D Smith , Temple F Smith , John Spieth , Deborah E Stage , Alexander Stark , Wolfgang Stephan , Robert L Strausberg , Sebastian Strempel , David Sturgill , Granger Sutton , Granger G Sutton , Wei Tao , Sarah Teichmann , Yoshiko N Tobari , Yoshihiko Tomimura , Jason M Tsolas , Vera L S Valente , Eli Venter , J Craig Venter , Saverio Vicario , Filipe G Vieira , Albert J Vilella , Alfredo Villasante , Brian Walenz , Jun Wang , Marvin Wasserman , Thomas Watts , Derek Wilson , Richard K Wilson , Rod A Wing , Mariana F Wolfner , Alex Wong , Gane Ka-Shu Wong , Chung-I Wu , Gabriel Wu , Daisuke Yamamoto , Hsiao-Pei Yang , Shiaw-Pyng Yang , James A Yorke , Kiyohito Yoshida , Evgeny Zdobnov , Peili Zhang , Yu Zhang , Aleksey V Zimin , Jennifer Baldwin , Amr Abdouelleil , Jamal Abdulkadir , Adal Abebe , Brikti Abera , Justin Abreu , St Christophe Acer , Lynne Aftuck , Allen Alexander , Peter An , Erica Anderson , Scott Anderson , Harindra Arachi , Marc Azer , Pasang Bachantsang , Andrew Barry , Tashi Bayul , Aaron Berlin , Daniel Bessette , Toby Bloom , Jason Blye , Leonid Boguslavskiy , Claude Bonnet , Boris Boukhgalter , Imane Bourzgui , Adam Brown , Patrick Cahill , Sheridon Channer , Yama Cheshatsang , Lisa Chuda , Mieke Citroen , Alville Collymore , Patrick Cooke , Maura Costello , Katie d'Aco , Riza Daza , Georgius de Haan , Stuart Degray , Christina Demaso , Norbu Dhargay , Kimberly Dooley , Erin Dooley , Missole Doricent , Passang Dorje , Kunsang Dorjee , Alan Dupes , Richard Elong , Jill Falk , Abderrahim Farina , Susan Faro , Diallo Ferguson , Sheila Fisher , Chelsea D Foley , Alicia Franke , Dennis Friedrich , Loryn Gadbois , Gary Gearin , Christina R Gearin , Georgia Giannoukos , Tina Goode , Joseph Graham , Edward Grandbois , Sharleen Grewal , Kunsang Gyaltsen , Nabil Hafez , Birhane Hagos , Jennifer Hall , Charlotte Henson , Andrew Hollinger , Tracey Honan , Monika D Huard , Leanne Hughes , Brian Hurhula , M Erii Husby , Asha Kamat , Ben Kanga , Seva Kashin , Dmitry Khazanovich , Peter Kisner , Krista Lance , Marcia Lara , William Lee , Niall Lennon , Frances Letendre , Rosie Levine , Alex Lipovsky , Xiaohong Liu , Jinlei Liu , Shangtao Liu , Tashi Lokyitsang , Yeshi Lokyitsang , Rakela Lubonja , Annie Lui , Pen Macdonald , Vasilia Magnisalis , Kebede Maru , Charles Matthews , William Mccusker , Susan Mcdonough , Teena Mehta , James Meldrim , Louis Meneus , Oana Mihai , Atanas Mihalev , Tanya Mihova , Rachel Mittelman , Valentine Mlenga , Anna Montmayeur , Leonidas Mulrain , Adam Navidi , Jerome Naylor , Tamrat Negash , Thu Nguyen , Nga Nguyen , Robert Nicol , Choe Norbu , Nyima Norbu , Nathaniel Novod , Barry O'Neill , Sahal Osman , Eva Markiewicz , Otero L Oyono , Christopher Patti , Pema Phunkhang , Fritz Pierre , Margaret Priest , Sujaa Raghuraman , Filip Rege , Rebecca Reyes , Cecil Rise , Peter Rogov , Keenan Ross , Elizabeth Ryan , Sampath Settipalli , Terry Shea , Ngawang Sherpa , Lu Shi , Diana Shih , Todd Sparrow , Jessica Spaulding , John Stalker , Nicole Stange-Thomann , Sharon Stavropoulos , Catherine Stone , Christopher Strader , Senait Tesfaye , Talene Thomson , Yama Thoulutsang , Dawa Thoulutsang , Kerri Topham , Ira Topping , Tsamla Tsamla , Helen Vassiliev , Andy Vo , Tsering Wangchuk , Tsering Wangdi , Michael Weiand , Jane Wilkinson , Shailendra Yadav , Geneva Young , Qing Yu , Lisa Zembek , Danni Zhong , Andrew Zimmer , Zac Zwirko , David B Jaffe (9) , Pablo Alvarez , Will Brockman , Jonathan Butler , Cheewhye Chin , Sante Gnerre (9) , Manfred Grabherr , Michael Kleber , Evan Mauceli , Iain Maccallum
1 Department of Molecular Biology and Genetics
2 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
3 UC Berkeley - University of California [Berkeley]
4 Agencourt Bioscience Corporation
5 Faculty of Life Science
6 LCDB - Laboratory of Cellular and Developmental Biology
7 Department of Ecology and Evolutionary Biology [University of Arizona]
8 Department of Biology
9 MIT - Massachusetts Institute of Technology
10 Harvard University
11 Cornell University [New York]
12 CBMSO - Centro de Biología Molecular Severo Ochoa [Madrid]
13 Department of Ecology and Evolutionary Biology
14 Laboratory of Molecular Biology
15 Departament de Genetica
16 Department of Biology
17 Department of Genetics
18 Uppsala University
19 Department of Ecology and Evolution [Lausanne]
20 Department of Biology
21 School of Biology
22 UNIBA - Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro
23 Department of Genetics
24 Stanford University
25 UC Davis - University of California [Davis]
26 BU - Boston University [Boston]
27 CRG - Centro de Regulación Genómica
28 WUSTL - Washington University in Saint Louis
29 University of Sheffield
30 Department of Biology
31 UFRRJ - Universidade Federal Rural do Rio de Janeiro
32 Department of Bioengineering
33 Tucson Stock Center
34 Genome Center
35 Genome Sequencing Center
36 University of Winnipeg
37 ISU - Iowa State University
38 Indiana University [Bloomington]
39 The Wellcome Trust Sanger Institute [Cambridge]
40 Center for Bioinformatics and Computational Biology
41 Illinois State University
42 Department of Biology
43 USDA - United States Department of Agriculture
44 ASU - Arizona State University [Tempe]
45 Leipzig University / Universität Leipzig
46 UFRGS - Universidade Federal do Rio Grande do Sul [Porto Alegre]
47 Department of Biology
48 Department of Genetics
49 UCONN - University of Connecticut
50 Computer Science Département
51 Mc Master University
52 Indiana University
53 Institute of Evolutionary Biology
54 JCVI - J. Craig Venter Institute [La Jolla, USA]
55 University of Oxford
56 Center for Biomolecular Science and Engineering
57 URGI - Unité de Recherche Génomique Info
Daniel Barker
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Chuong B Do
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Eva Freyhult
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Dan Hultmark
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Xu Mu
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Eugene Myers
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Stuart Newfeld
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Mohamed a F Noor
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Michael Parisi
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Leopold Parts
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Graziano Pesole
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Adam M Phillippy
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Marta Puig
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David Rand
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Robert Reenan
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Amy Reily
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Karin A Remington
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Charles Robin
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Cheewhye Chin
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Abstract

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

Dates and versions

hal-02667683 , version 1 (31-05-2020)

Identifiers

Cite

. Drosophila 12 Genomes Consortium, Andrew G Clark, Michael B Eisen, Douglas R Smith, Casey M Bergman, et al.. Evolution of genes and genomes on the Drosophila phylogeny. Nature, 2007, 450 (7167), pp.203-18. ⟨10.1038/nature06341⟩. ⟨hal-02667683⟩

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