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Evolution of genes and genomes on the Drosophila phylogeny
- Source :
- Clark, A G, Eisen, M B, Smith, D R, Bergman, C M, Oliver, B, Markow, T A, Kaufman, T C, Kellis, M, Gelbart, W, Iyer, V N, Pollard, D A, Sackton, T B, Larracuente, A M, Singh, N D, Abad, J P, Abt, D N, Adryan, B, Aguade, M, Akashi, H, Anderson, W W, Aquadro, C F, Ardell, D H, Arguello, R, Artieri, C G, Barbash, D A, Barker, D, Barsanti, P, Batterham, P, Batzoglou, S, Begun, D, Bhutkar, A, Blanco, E, Bosak, S A, Bradley, R K, Brand, A D, Brent, M R, Brooks, A N, Brown, R H, Butlin, R K, Caggese, C, Calvi, B R, Bernardo de Carvalho, A, Caspi, A, Castrezana, S, Celniker, S E, Chang, J L, Chapple, C, Chatterji, S, Kristiansen, K, Pedersen, J S & Drosophila 12 Genomes Consortium 2007, ' Evolution of genes and genomes on the Drosophila phylogeny ', Nature, vol. 450, no. 7167, pp. 203-18 . https://doi.org/10.1038/nature06341, Nature, Nature, Nature Publishing Group, 2007, 450 (7167), pp.203-18. ⟨10.1038/nature06341⟩, Clark, A G, Eisen, M B, Smith, D R, Bergman, C M, Oliver, B, Markow, T A, Kaufman, T C, Kellis, M, Gelbart, W, Iyer, V N, Pollard, D A, Sackton, T B, Larracuente, A M, Singh, N D, Abad, J P, Abt, D N, Adryan, B, Aguade, M, Akashi, H, Anderson, W W, Aquadro, C F, Ardell, D H, Arguello, R, Artieri, C G, Barbash, D A, Barker, D, Barsanti, P, Batterham, P, Batzoglou, S, Begun, D, Bhutkar, A, Blanco, E, Bosak, S A, Bradley, R K, Brand, A D, Brent, M R, Brooks, A N, Brown, R H, Butlin, R K, Caggese, C, Calvi, B R, Bernardo de Carvalho, A, Caspi, A, Castrezana, S, Celniker, S E, Chang, J L, Chapple, C, Chatterji, S, Chinwalla, A, Civetta, A, Clifton, S W, Comeron, J M, Costello, J C, Coyne, J A, Daub, J, David, R G, Delcher, A L, Delehaunty, K, Do, C B, Ebling, H, Edwards, K, Eickbush, T, Evans, J D, Filipski, A, Findeiss, S, Freyhult, E, Fulton, L, Fulton, R, Garcia, A C L, Gardiner, A, Garfield, D A, Garvin, B E, Gibson, G, Gilbert, D, Gnerre, S, Godfrey, J, Good, R, Gotea, V, Gravely, B, Greenberg, A J, Griffiths-Jones, S, Gross, S, Guigo, R, Gustafson, E A, Haerty, W, Hahn, M W, Halligan, D L, Halpern, A L, Halter, G M, Han, M V, Heger, A, Hillier, L, Hinrichs, A S, Holmes, I, Hoskins, R A, Hubisz, M J, Hultmark, D, Huntley, M A, Jaffe, D B, Jagadeeshan, S, Jeck, W R, Johnson, J, Jones, C D, Jordan, W C, Karpen, G H, Kataoka, E, Keightley, P D, Kheradpour, P, Kirkness, E F, Koerich, L B, Kristiansen, K, Kudrna, D, Kulathinal, R J, Kumar, S, Kwok, R, Lander, E, Langley, C H, Lapoint, R, Lazzaro, B P, Lee, S-J, Levesque, L, Li, R, Lin, C-F, Lin, M F, Lindblad-Toh, K, Llopart, A, Long, M, Low, L, Lozovsky, E, Lu, J, Luo, M, Machado, C A, Makalowski, W, Marzo, M, Matsuda, M, Matzkin, L, McAllister, B, McBride, C S, McKernan, B, McKernan, K, Mendez-Lago, M, Minx, P, Mollenhauer, M U, Montooth, K, Mount, S M, Mu, X, Myers, E, Negre, B, Newfeld, S, Nielsen, R, Noor, M A F, O'Grady, P, Pachter, L, Papaceit, M, Parisi, M J, Parisi, M, Parts, L, Pedersen, J S, Pesole, G, Phillippy, A M, Ponting, C P, Pop, M, Porcelli, D, Powell, J R, Prohaska, S, Pruitt, K, Puig, M, Quesneville, H, Ram, K R, Rand, D, Rasmussen, M D, Reed, L K, Reenan, R, Reily, A, Remington, K A, Rieger, T T, Ritchie, M G, Robin, C, Rogers, Y-H, Rohde, C, Rozas, J, Rubenfield, M J, Ruiz, A, Russo, S, Salzberg, S L, Sanchez-Gracia, A, Saranga, D J, Sato, H, Schaeffer, S W, Schatz, M C, Schlenke, T, Schwartz, R, Segarra, C, Singh, R S, Sirot, L, Sirota, M, Sisneros, N B, Smith, C D, Smith, T F, Spieth, J, Stage, D E, Stark, A, Stephan, W, Strausberg, R L, Strempel, S, Sturgill, D, Sutton, G, Sutton, G G, Tao, W, Teichmann, S, Tobari, Y N, Tomimura, Y, Tsolas, J M, Valente, V L S, Venter, E, Venter, J C, Vicario, S, Vieira, F G, Vilella, A J, Villasante, A, Walenz, B, Wang, J, Wasserman, M, Watts, T, Wilson, D, Wilson, R K, Wing, R A, Wolfner, M F, Wong, A, Wong, G K-S, Wu, C-I, Wu, G, Yamamoto, D, Yang, H-P, Yang, S-P, Yorke, J A, Yoshida, K, Zdobnov, E, Zhang, P, Zhang, Y, Zimin, A V, Baldwin, J, Abdouelleil, A, Abdulkadir, J, Abebe, A, Abera, B, Abreu, J, Acer, S C, 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, C D, Franke, A, Friedrich, D, Gadbois, L, Gearin, G, Gearin, C R, 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, M D, Hughes, L, Hurhula, B, Husby, M 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, O L, 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, D B, Alvarez, P, Brockman, W, Butler, J, Chin, C, Gnerre, S, Grabherr, M, Kleber, M, Mauceli, E & MacCallum, I 2007, ' Evolution of genes and genomes on the Drosophila phylogeny ', Nature, vol. 450, no. 7167, pp. 203-218 . https://doi.org/10.1038/nature06341, Nature, Vol. 450, No 7167 (2007) pp. 203-218, ResearcherID
- Publication Year :
- 2007
- Publisher :
- Nature Publishing Group, 2007.
-
Abstract
- Affiliations des auteurs : cf page 216 de l'article; International audience; 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.
- Subjects :
- melanogaster genome
0106 biological sciences
RNA, Untranslated
[SDV]Life Sciences [q-bio]
Genome, Insect
RNA, Untranslated/genetics
Genes, Insect
01 natural sciences
Genome
Genome, Insect/ genetics
Gene Order
Genome, Mitochondrial/genetics
Drosophila Proteins
Phylogeny
ddc:616
Genetics
0303 health sciences
Multidisciplinary
biology
Reproduction
Genomics
Multigene Family/genetics
Reproduction/genetics
DNA Transposable Elements/genetics
Genes, Insect/ genetics
Multigene Family
dosage compensation
Drosophila
amino-acid substitution
Drosophila Protein
Drosophila Proteins/genetics
Synteny/genetics
fruit-fly
010603 evolutionary biology
Synteny
Drosophila sechellia
Evolution, Molecular
03 medical and health sciences
Phylogenetics
Molecular evolution
Codon/genetics
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Animals
adaptive protein evolution
Codon
030304 developmental biology
Gene Order/genetics
molecular evolution
fungi
Immunity
synonymous codon usage
Sequence Analysis, DNA
Immunity/genetics
biology.organism_classification
Drosophila mojavensis
Evolutionary biology
Genome, Mitochondrial
DNA Transposable Elements
maximum-likelihood
noncoding dna
Drosophila/ classification/ genetics/immunology/metabolism
Sequence Alignment
natural-selection
Drosophila yakuba
Subjects
Details
- Language :
- English
- ISSN :
- 00280836 and 14764679
- Database :
- OpenAIRE
- Journal :
- Clark, A G, Eisen, M B, Smith, D R, Bergman, C M, Oliver, B, Markow, T A, Kaufman, T C, Kellis, M, Gelbart, W, Iyer, V N, Pollard, D A, Sackton, T B, Larracuente, A M, Singh, N D, Abad, J P, Abt, D N, Adryan, B, Aguade, M, Akashi, H, Anderson, W W, Aquadro, C F, Ardell, D H, Arguello, R, Artieri, C G, Barbash, D A, Barker, D, Barsanti, P, Batterham, P, Batzoglou, S, Begun, D, Bhutkar, A, Blanco, E, Bosak, S A, Bradley, R K, Brand, A D, Brent, M R, Brooks, A N, Brown, R H, Butlin, R K, Caggese, C, Calvi, B R, Bernardo de Carvalho, A, Caspi, A, Castrezana, S, Celniker, S E, Chang, J L, Chapple, C, Chatterji, S, Kristiansen, K, Pedersen, J S & Drosophila 12 Genomes Consortium 2007, ' Evolution of genes and genomes on the Drosophila phylogeny ', Nature, vol. 450, no. 7167, pp. 203-18 . https://doi.org/10.1038/nature06341, Nature, Nature, Nature Publishing Group, 2007, 450 (7167), pp.203-18. ⟨10.1038/nature06341⟩, Clark, A G, Eisen, M B, Smith, D R, Bergman, C M, Oliver, B, Markow, T A, Kaufman, T C, Kellis, M, Gelbart, W, Iyer, V N, Pollard, D A, Sackton, T B, Larracuente, A M, Singh, N D, Abad, J P, Abt, D N, Adryan, B, Aguade, M, Akashi, H, Anderson, W W, Aquadro, C F, Ardell, D H, Arguello, R, Artieri, C G, Barbash, D A, Barker, D, Barsanti, P, Batterham, P, Batzoglou, S, Begun, D, Bhutkar, A, Blanco, E, Bosak, S A, Bradley, R K, Brand, A D, Brent, M R, Brooks, A N, Brown, R H, Butlin, R K, Caggese, C, Calvi, B R, Bernardo de Carvalho, A, Caspi, A, Castrezana, S, Celniker, S E, Chang, J L, Chapple, C, Chatterji, S, Chinwalla, A, Civetta, A, Clifton, S W, Comeron, J M, Costello, J C, Coyne, J A, Daub, J, David, R G, Delcher, A L, Delehaunty, K, Do, C B, Ebling, H, Edwards, K, Eickbush, T, Evans, J D, Filipski, A, Findeiss, S, Freyhult, E, Fulton, L, Fulton, R, Garcia, A C L, Gardiner, A, Garfield, D A, Garvin, B E, Gibson, G, Gilbert, D, Gnerre, S, Godfrey, J, Good, R, Gotea, V, Gravely, B, Greenberg, A J, Griffiths-Jones, S, Gross, S, Guigo, R, Gustafson, E A, Haerty, W, Hahn, M W, Halligan, D L, Halpern, A L, Halter, G M, Han, M V, Heger, A, Hillier, L, Hinrichs, A S, Holmes, I, Hoskins, R A, Hubisz, M J, Hultmark, D, Huntley, M A, Jaffe, D B, Jagadeeshan, S, Jeck, W R, Johnson, J, Jones, C D, Jordan, W C, Karpen, G H, Kataoka, E, Keightley, P D, Kheradpour, P, Kirkness, E F, Koerich, L B, Kristiansen, K, Kudrna, D, Kulathinal, R J, Kumar, S, Kwok, R, Lander, E, Langley, C H, Lapoint, R, Lazzaro, B P, Lee, S-J, Levesque, L, Li, R, Lin, C-F, Lin, M F, Lindblad-Toh, K, Llopart, A, Long, M, Low, L, Lozovsky, E, Lu, J, Luo, M, Machado, C A, Makalowski, W, Marzo, M, Matsuda, M, Matzkin, L, McAllister, B, McBride, C S, McKernan, B, McKernan, K, Mendez-Lago, M, Minx, P, Mollenhauer, M U, Montooth, K, Mount, S M, Mu, X, Myers, E, Negre, B, Newfeld, S, Nielsen, R, Noor, M A F, O'Grady, P, Pachter, L, Papaceit, M, Parisi, M J, Parisi, M, Parts, L, Pedersen, J S, Pesole, G, Phillippy, A M, Ponting, C P, Pop, M, Porcelli, D, Powell, J R, Prohaska, S, Pruitt, K, Puig, M, Quesneville, H, Ram, K R, Rand, D, Rasmussen, M D, Reed, L K, Reenan, R, Reily, A, Remington, K A, Rieger, T T, Ritchie, M G, Robin, C, Rogers, Y-H, Rohde, C, Rozas, J, Rubenfield, M J, Ruiz, A, Russo, S, Salzberg, S L, Sanchez-Gracia, A, Saranga, D J, Sato, H, Schaeffer, S W, Schatz, M C, Schlenke, T, Schwartz, R, Segarra, C, Singh, R S, Sirot, L, Sirota, M, Sisneros, N B, Smith, C D, Smith, T F, Spieth, J, Stage, D E, Stark, A, Stephan, W, Strausberg, R L, Strempel, S, Sturgill, D, Sutton, G, Sutton, G G, Tao, W, Teichmann, S, Tobari, Y N, Tomimura, Y, Tsolas, J M, Valente, V L S, Venter, E, Venter, J C, Vicario, S, Vieira, F G, Vilella, A J, Villasante, A, Walenz, B, Wang, J, Wasserman, M, Watts, T, Wilson, D, Wilson, R K, Wing, R A, Wolfner, M F, Wong, A, Wong, G K-S, Wu, C-I, Wu, G, Yamamoto, D, Yang, H-P, Yang, S-P, Yorke, J A, Yoshida, K, Zdobnov, E, Zhang, P, Zhang, Y, Zimin, A V, Baldwin, J, Abdouelleil, A, Abdulkadir, J, Abebe, A, Abera, B, Abreu, J, Acer, S C, 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, C D, Franke, A, Friedrich, D, Gadbois, L, Gearin, G, Gearin, C R, 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, M D, Hughes, L, Hurhula, B, Husby, M 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, O L, 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, D B, Alvarez, P, Brockman, W, Butler, J, Chin, C, Gnerre, S, Grabherr, M, Kleber, M, Mauceli, E & MacCallum, I 2007, ' Evolution of genes and genomes on the Drosophila phylogeny ', Nature, vol. 450, no. 7167, pp. 203-218 . https://doi.org/10.1038/nature06341, Nature, Vol. 450, No 7167 (2007) pp. 203-218, ResearcherID
- Accession number :
- edsair.doi.dedup.....185fcef84a75fcef336e3156b9953635
- Full Text :
- https://doi.org/10.1038/nature06341