Population Genomics of Transposable Elements in Drosophila

被引：112

作者：

Barron, Maite G. ^{[1
]}

Fiston-Lavier, Anna-Sophie ^{[2
]}

Petrov, Dmitri A. ^{[3
]}

Gonzalez, Josefa ^{[1
]}

机构：

[1] Univ Pompeu Fabra, CSIC, Inst Evolutionary Biol, Barcelona 08003, Spain

[2] Univ Montpellier 2, CNRS, UMR5554, Inst Sci Evolut ISEM, F-34090 Montpellier, France

[3] Stanford Univ, Dept Biol, Stanford, CA 94305 USA

来源：

ANNUAL REVIEW OF GENETICS, VOL 48 | 2014年 / 48卷

关键词：

evolutionary models; next-generation sequencing; adaptation; CIS-REGULATORY ELEMENTS; ECTOPIC RECOMBINATION; INSECTICIDE RESISTANCE; LTR RETROTRANSPOSONS; NATURAL-POPULATIONS; COPY NUMBER; DNA LOSS; MELANOGASTER; EVOLUTION; SEQUENCE;

D O I：

10.1146/annurev-genet-120213-092359

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Studies of the population dynamics of transposable elements (TEs) in Drosophila melanogaster indicate that consistent forces are affecting TEs independently of their modes of transposition and regulation. New sequencing technologies enable biologists to sample genomes at an unprecedented scale in order to quantify genome-wide polymorphism for annotated and novel TE insertions. In this review, we first present new insights gleaned from high-throughput data for population genomics studies of D. melanogaster. We then consider the latest population genomics models for TE evolution and present examples of functional evidence revealed by genome-wide studies of TE population dynamics in D. melanogaster. Although most of the TE insertions are deleterious or neutral, some TE insertions increase the fitness of the individual that carries them and play a role in genome adaptation.

引用

页码：561 / 581

页数：21

共 117 条

[71] Genomic Variation in Natural Populations of Drosophila melanogaster [J].

Langley, Charles H. ;

Stevens, Kristian ;

Cardeno, Charis ;

Lee, Yuh Chwen G. ;

Schrider, Daniel R. ;

Pool, John E. ;

Langley, Sasha A. ;

Suarez, Charlyn ;

Corbett-Detig, Russell B. ;

Kolaczkowski, Bryan ;

Fang, Shu ;

Nista, Phillip M. ;

Holloway, Alisha K. ;

Kern, Andrew D. ;

Dewey, Colin N. ;

Song, Yun S. ;

Hahn, Matthew W. ;

Begun, David J. .

GENETICS, 2012, 192 (02) :533-+

[72] Long-term evolution of transposable elements [J].

Le Rouzic, Arnaud ;

Boutin, Thibaud S. ;

Capy, Pierre .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (49) :19375-19380

[73] Landscape of Somatic Retrotransposition in Human Cancers [J].

Lee, Eunjung ;

Iskow, Rebecca ;

Yang, Lixing ;

Gokcumen, Omer ;

Haseley, Psalm ;

Luquette, Lovelace J., III ;

Lohr, Jens G. ;

Harris, Christopher C. ;

Ding, Li ;

Wilson, Richard K. ;

Wheeler, David A. ;

Gibbs, Richard A. ;

Kucherlapati, Raju ;

Lee, Charles ;

Kharchenko, Peter V. ;

Park, Peter J. .

SCIENCE, 2012, 337 (6097) :967-971

[74] Transposable elements in natural populations of Drosophila melanogaster [J].

Lee, Yuh Chwen G. ;

Langley, Charles H. .

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2010, 365 (1544) :1219-1228

[75] Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs [J].

Lerat, E. .

HEREDITY, 2010, 104 (06) :520-533

[76] Activation of transposable elements during aging and neuronal decline in Drosophila [J].

Li, Wanhe ;

Prazak, Lisa ;

Chatterjee, Nabanita ;

Grueninger, Servan ;

Krug, Lisa ;

Theodorou, Delphine ;

Dubnau, Josh .

NATURE NEUROSCIENCE, 2013, 16 (05) :529-+

[77] Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster [J].

Linheiro, Raquel S. ;

Bergman, Casey M. .

PLOS ONE, 2012, 7 (02)

[78] Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome [J].

Lipatov, M ;

Lenkov, K ;

Petrov, DA ;

Bergman, CM .

BMC BIOLOGY, 2005, 3 (1)

[79] Revisiting horizontal transfer of transposable elements in Drosophila [J].

Loreto, E. L. S. ;

Carareto, C. M. A. ;

Capy, P. .

HEREDITY, 2008, 100 (06) :545-554

[80] The Drosophila melanogaster Genetic Reference Panel [J].

Mackay, Trudy F. C. ;

Richards, Stephen ;

Stone, Eric A. ;

Barbadilla, Antonio ;

Ayroles, Julien F. ;

Zhu, Dianhui ;

Casillas, Sonia ;

Han, Yi ;

Magwire, Michael M. ;

Cridland, Julie M. ;

Richardson, Mark F. ;

Anholt, Robert R. H. ;

Barron, Maite ;

Bess, Crystal ;

Blankenburg, Kerstin Petra ;

Carbone, Mary Anna ;

Castellano, David ;

Chaboub, Lesley ;

Duncan, Laura ;

Harris, Zeke ;

Javaid, Mehwish ;

Jayaseelan, Joy Christina ;

Jhangiani, Shalini N. ;

Jordan, Katherine W. ;

Lara, Fremiet ;

Lawrence, Faye ;

Lee, Sandra L. ;

Librado, Pablo ;

Linheiro, Raquel S. ;

Lyman, Richard F. ;

Mackey, Aaron J. ;

Munidasa, Mala ;

Muzny, Donna Marie ;

Nazareth, Lynne ;

Newsham, Irene ;

Perales, Lora ;

Pu, Ling-Ling ;

Qu, Carson ;

Ramia, Miquel ;

Reid, Jeffrey G. ;

Rollmann, Stephanie M. ;

Rozas, Julio ;

Saada, Nehad ;

Turlapati, Lavanya ;

Worley, Kim C. ;

Wu, Yuan-Qing ;

Yamamoto, Akihiko ;

Zhu, Yiming ;

Bergman, Casey M. ;

Thornton, Kevin R. .

NATURE, 2012, 482 (7384) :173-178

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