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Nature DOI:10.1038/nature06341

Evolution of genes and genomes on the Drosophila phylogeny.

Publication TypeJournal Article
Year of Publication2007
AuthorsClark, AG, Eisen, MB, Smith, DR, Bergman, CM, Oliver, B, Markow, TA, Kaufman, TC, Kellis, M, Gelbart, W, Iyer, VN, Pollard, DA, Sackton, TB, Larracuente, AM, Singh, ND, Abad, JP, Abt, DN, Adryan, B, Aguade, M, Akashi, H, Anderson, WW, Aquadro, CF, Ardell, DH, Arguello, R, Artieri, CG, Barbash, DA, Barker, D, Barsanti, P, Batterham, P, Batzoglou, S, Begun, D, Bhutkar, A, Blanco, E, Bosak, SA, Bradley, RK, Brand, AD, Brent, MR, Brooks, AN, Brown, RH, Butlin, RK, Caggese, C, Calvi, BR, Bernardo de Carvalho, A, Caspi, A, Castrezana, S, Celniker, SE, Chang, JL, Chapple, C, Chatterji, S, Chinwalla, A, Civetta, A, Clifton, SW, Comeron, JM, Costello, JC, Coyne, JA, Daub, J, David, RG, Delcher, AL, Delehaunty, K, Do, CB, Ebling, H, Edwards, K, Eickbush, T, Evans, JD, Filipski, A, Findeiss, S, Freyhult, E, Fulton, L, Fulton, R, Garcia, ACL, Gardiner, A, Garfield, DA, Garvin, BE, Gibson, G, Gilbert, D, Gnerre, S, Godfrey, J, Good, R, Gotea, V, Gravely, B, Greenberg, AJ, Griffiths-Jones, S, Gross, S, Guigo, R, Gustafson, EA, Haerty, W, Hahn, MW, Halligan, DL, Halpern, AL, Halter, GM, Han, MV, Heger, A, Hillier, LD, Hinrichs, AS, Holmes, I, Hoskins, RA, Hubisz, MJ, Hultmark, D, Huntley, MA, Jaffe, DB, Jagadeeshan, S, Jeck, WR, Johnson, J, Jones, CD, Jordan, WC, Karpen, GH, Kataoka, E, Keightley, PD, Kheradpour, P, Kirkness, EF, Koerich, LB, Kristiansen, K, Kudrna, D, Kulathinal, RJ, Kumar, S, Kwok, R, Lander, E, Langley, CH, Lapoint, R, Lazzaro, BP, Lee, S-J, Levesque, L, Li, R, Lin, C-F, Lin, MF, Lindblad-Toh, K, Llopart, A, Long, M, Low, L, Lozovsky, E, Lu, J, Luo, M, Machado, CA, Makalowski, W, Marzo, M, Matsuda, M, Matzkin, L, McAllister, B, McBride, CS, McKernan, B, McKernan, K, Mendez-Lago, M, Minx, P, Mollenhauer, MU, Montooth, K, Mount, SM, Mu, X, Myers, E, Negre, B, Newfeld, S, Nielsen, R, Noor, MAF, O'Grady, P, Pachter, L, Papaceit, M, Parisi, MJ, Parisi, M, Parts, L, Pedersen, JS, Pesole, G, Phillippy, AM, Ponting, CP, Pop, M, Porcelli, D, Powell, JR, Prohaska, S, Pruitt, K, Puig, M, Quesneville, H, Ram, KRavi, Rand, D, Rasmussen, MD, Reed, LK, Reenan, R, Reily, A, Remington, KA, Rieger, TT, Ritchie, MG, Robin, C, Rogers, Y-H, Rohde, C, Rozas, J, Rubenfield, MJ, Ruiz, A, Russo, S, Salzberg, SL, Sanchez-Gracia, A, Saranga, DJ, Sato, H, Schaeffer, SW, Schatz, MC, Schlenke, T, Schwartz, R, Segarra, C, Singh, RS, Sirot, L, Sirota, M, Sisneros, NB, Smith, CD, Smith, TF, Spieth, J, Stage, DE, Stark, A, Stephan, W, Strausberg, RL, Strempel, S, Sturgill, D, Sutton, G, Sutton, GG, Tao, W, Teichmann, S, Tobari, YN, Tomimura, Y, Tsolas, JM, Valente, VLS, Venter, E, J Venter, C, Vicario, S, Vieira, FG, Vilella, AJ, Villasante, A, Walenz, B, Wang, J, Wasserman, M, Watts, T, Wilson, D, Wilson, RK, Wing, RA, Wolfner, MF, Wong, A, Wong, GKa-Shu, Wu, C-I, Wu, G, Yamamoto, D, Yang, H-P, Yang, S-P, Yorke, JA, Yoshida, K, Zdobnov, E, Zhang, P, Zhang, Y, Zimin, AV, Baldwin, J, Abdouelleil, A, Abdulkadir, J, Abebe, A, Abera, B, Abreu, J, Acer, SChristophe, Aftuck, L, Alexander, A, An, P, Anderson, E, Anderson, S, Arachi, H, Azer, M, Bachantsang, P, Barry, A, Bayul, T, Berlin, A, Bessette, D, Bloom, T, Blye, J, Boguslavskiy, L, Bonnet, C, Boukhgalter, B, Bourzgui, I, Brown, A, Cahill, P, Channer, S, Cheshatsang, Y, Chuda, L, Citroen, M, Collymore, A, Cooke, P, Costello, M, D'Aco, K, Daza, R, De Haan, G, DeGray, S, DeMaso, C, Dhargay, N, Dooley, K, Dooley, E, Doricent, M, Dorje, P, Dorjee, K, Dupes, A, Elong, R, Falk, J, Farina, A, Faro, S, Ferguson, D, Fisher, S, Foley, CD, Franke, A, Friedrich, D, Gadbois, L, Gearin, G, Gearin, CR, Giannoukos, G, Goode, T, Graham, J, Grandbois, E, Grewal, S, Gyaltsen, K, Hafez, N, Hagos, B, Hall, J, Henson, C, Hollinger, A, Honan, T, Huard, MD, Hughes, L, Hurhula, B, M Husby, ii, E, Kamat, A, Kanga, B, Kashin, S, Khazanovich, D, Kisner, P, Lance, K, Lara, M, Lee, W, Lennon, N, Letendre, F, Levine, R, Lipovsky, A, Liu, X, Liu, J, Liu, S, Lokyitsang, T, Lokyitsang, Y, Lubonja, R, Lui, A, MacDonald, P, Magnisalis, V, Maru, K, Matthews, C, McCusker, W, McDonough, S, Mehta, T, Meldrim, J, Meneus, L, Mihai, O, Mihalev, A, Mihova, T, Mittelman, R, Mlenga, V, Montmayeur, A, Mulrain, L, Navidi, A, Naylor, J, Negash, T, Nguyen, T, Nguyen, N, Nicol, R, Norbu, C, Norbu, N, Novod, N, O'Neill, B, Osman, S, Markiewicz, E, Oyono, OL, Patti, C, Phunkhang, P, Pierre, F, Priest, M, Raghuraman, S, Rege, F, Reyes, R, Rise, C, Rogov, P, Ross, K, Ryan, E, Settipalli, S, Shea, T, Sherpa, N, Shi, L, Shih, D, Sparrow, T, Spaulding, J, Stalker, J, Stange-Thomann, N, Stavropoulos, S, Stone, C, Strader, C, Tesfaye, S, Thomson, T, Thoulutsang, Y, Thoulutsang, D, Topham, K, Topping, I, Tsamla, T, Vassiliev, H, Vo, A, Wangchuk, T, Wangdi, T, Weiand, M, Wilkinson, J, Wilson, A, Yadav, S, Young, G, Yu, Q, Zembek, L, Zhong, D, Zimmer, A, Zwirko, Z, Jaffe, DB, Alvarez, P, Brockman, W, Butler, J, Chin, CW, Gnerre, S, Grabherr, M, Kleber, M, Mauceli, E, MacCallum, I
Corporate AuthorsDrosophila 12 Genomes Consortium
JournalNature
Volume450
Issue7167
Pages203-18
Date Published2007 Nov 08
ISSN1476-4687
KeywordsAnimals, Codon, DNA Transposable Elements, Drosophila, Drosophila Proteins, Evolution, Molecular, Gene Order, Genes, Insect, Genome, Insect, Genome, Mitochondrial, Genomics, Immunity, Multigene Family, Phylogeny, Reproduction, RNA, Untranslated, Sequence Alignment, Sequence Analysis, DNA, Synteny
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.

URLhttp://dx.doi.org/10.1038/nature06341
DOI10.1038/nature06341
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/17994087?dopt=Abstract

Alternate JournalNature
PubMed ID17994087
Grant ListZ01 DK015600-12 / / Intramural NIH HHS / United States
R01 GM036431 / GM / NIGMS NIH HHS / United States
R01 HG004037 / HG / NHGRI NIH HHS / United States
MC_U137761446 / / Medical Research Council / United Kingdom
MC_U105161047 / / Medical Research Council / United Kingdom
R01 LM006845-08 / LM / NLM NIH HHS / United States
F32 GM067504 / GM / NIGMS NIH HHS / United States
R01 HG002779-06 / HG / NHGRI NIH HHS / United States
R01 LM006845-09 / LM / NLM NIH HHS / United States
R01 HD038921 / HD / NICHD NIH HHS / United States
R01 HG002779-05 / HG / NHGRI NIH HHS / United States
R01 GM074813-04 / GM / NIGMS NIH HHS / United States
R01 HG000747 / HG / NHGRI NIH HHS / United States
R01 HG000747-16 / HG / NHGRI NIH HHS / United States