Comparative genomics reveals insights into avian genome evolution and adaptation

American Association for the Advancement of Science (AAAS) - Tập 346 Số 6215 - Trang 1311-1320 - 2014
Guojie Zhang1,2, Cai Li3,2, Qiye Li3,2, Bo Li2, Denis M. Larkin4, Chul Lee5,6, Jay F. Storz7, Agostinho Antunes8,9, Matthew J. Greenwold10, Robert W. Meredith11, Anders Ödeen12, Jie Cui13,14, Qi Zhou15, Luohao Xu2,16, Hailin Pan2, Zongji Wang17, Lijun Jin2, Pei Zhang2, Haofu Hu2, Wei Yang2, Jiang Hu2, Jin Xiao2, Zhi‐Kai Yang2, Jing Wang2, Qiaolin Xie2, Sheng Wang2, Jinmin Lian2, Ping Wen2, Fang Zhang2, Hui Li2, Yongli Zeng2, Zijun Xiong2, Shiping Liu17, Long Zhou2, Zhiyong Huang2, Na An2, Qiumei Zheng2, Yingqi Xiong2, Guangbiao Wang2, Bo Wang2, Jingjing Wang2, Yu Fan18, Rute R. da Fonseca3, Alonzo Alfaro‐Núñez3, Mikkel Schubert3, Ludovic Orlando3, Tobias Mourier3, Jason T. Howard19, Ganeshkumar Ganapathy19, Andreas R. Pfenning19, Osceola Whitney19, Miriam V. Rivas19, Erina Hara19, Julia Smith19, Marta Farré4, Jitendra Narayan20, Gancho Slavov20, Michael N Romanov21, Rui Borges8,9, João Paulo Machado8,22, Imran Khan8,9, Mark S. Springer23, John Gatesy23, Federico G. Hoffmann24,25, Juan C. Opazo26, Olle Håstad27, Roger H. Sawyer10, Heebal Kim5,28,6, Kyu-Won Kim6, Hyeon Jeong Kim5, Seoae Cho5, Ning Li29, Yinhua Huang30,29, Michael W. Bruford31, Xiangjiang Zhan32,31, Andrew Dixon33, Mads F. Bertelsen34, Elizabeth P. Derryberry35,36, Wesley C. Warren37, Richard K. Wilson37, Shengbin Li38, David A. Ray25, Richard E. Green39, Stephen J. O’Brien40,41, Darren Griffin21, Warren E. Johnson42, David Haussler39, Oliver A. Ryder43, Eske Willerslev3, Gary R. Graves44,45, Per Alström46,47, Jon Fjeldså44, David P. Mindell48, Scott V. Edwards49, Edward L. Braun50, Carsten Rahbek44,51, David W. Burt52, Peter Houde53, Yong Zhang2, Huanming Yang2,54, Wei Wang2, Erich D. Jarvis19, M. Thomas P. Gilbert55, Jun Wang2,56,57,58, Chen Ye59, Shaoguang Liang59, Zengli Yan59, M. Lisandra Zepeda59, Paula F. Campos59, Amhed Missael Vargas Velazquez59, José Alfredo Samaniego Castruita59, María C. Ávila‐Arcos59, Michael D. Martin59, Ross Barnett59, Ângela M. Ribeiro59, Claudio V. Mello, Peter V. Lovell, Daniela Almeida59, Emanuel Maldonado59, Joana Pereira, Kartik Sunagar59, Siby Philip59, Maria Gloria Dominguez‐Bello59, Michael Bunce59, David M. Lambert59, Robb T. Brumfield, Frederick H. Sheldon, Edward C. Holmes59, Paul P. Gardner59, Tammy E. Steeves, Peter F. Stadler, Sarah Burge, Eric Lyons59, Jacqueline Smith59, Fiona M. McCarthy59, Frédérique Pitel59, Douglas D. Rhoads59, D. P. Froman
1Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
2China National GeneBank, Beijing Genomics Institute (BGI)–Shenzhen, Shenzhen, 518083, China.
3Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
4Royal Veterinary College, University of London, London, UK
5Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea.
6Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea
7School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
8Centro de Investigación en Ciencias del Mar y Limnología (CIMAR)/Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal.
9Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
10Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
11Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043 USA
12Department of Animal Ecology, Uppsala University, Norbyvägen 18D, S-752 36 Uppsala, Sweden.
13Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
14Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore 169857, Singapore
15Department of Integrative Biology, University of California, Berkeley, CA 94720 USA
16College of Life Sciences, Wuhan University, Wuhan 430072, China
17School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
18Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
19Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.
20Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
21School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
22Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Portugal
23Department of Biology, University of California – Riverside, Riverside, CA 92521, USA
24Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
25Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
26Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
27Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Post Office Box 7011, S-750 07, Uppsala, Sweden.
28Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea
29State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China
30College of Animal Science and Technology, China Agricultural University, Beijing 100094, China
31Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK.
32Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
33International Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK.
34Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark
35Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA
36Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
37The Genome Institute at Washington University, St. Louis, MO 63108, USA.
38College of Medicine and Forensics, Xi’an Jiaotong University Xi’an 710061, China.
39Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
40Nova Southeastern University Oceanographic Center, 8000 N Ocean Drive, Dania, FL, 33004, USA
41Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
42Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA
43Genetics Division, San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, CA 92027, USA.
44Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark.
45Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Post Office Box 37012, Washington, DC 20013-7012, USA.
46Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
47Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, SE-750 07 Uppsala, Sweden
48Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA.
49Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
50Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
51Imperial College London, Grand Challenges in Ecosystems and the Environment Initiative, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK.
52Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The Roslin Institute Building, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK.
53Department of Biology, New Mexico State University, Box 30001 MSC 3AF, Las Cruces, NM 88003, USA.
54Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China.
55Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia
56Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
57Department of Medicine University of Hong Kong, Hong Kong
58Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
59Aberystwyth University ,

Tóm tắt

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

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Tài liệu tham khảo

F. Gill D. Donsker IOC World Bird List (version 3.5) (2013).

L. M. Chiappe L. M. Witmer Mesozoic Birds: Above the Heads of Dinosaurs (Univ. California Press Berkeley CA 2002).

G. Dyke G. W. Kaiser Living Dinosaurs the Evolutionary History of Modern Birds (Wiley-Blackwell Hoboken NJ 2011).

10.1016/S0169-5347(03)00017-X

10.1126/science.1253451

10.1126/science.1228282

10.1038/nature11631

H. Zeigler P. E. Marler in Behavioral Neurobiology of Birdsong December 2002 Hunter College City University of New York New York NY US

this volume is the result of the aforementioned conference which was one of an annual symposium series sponsored by the Hunter College Gene Center. (2004).

A. J. Stattersfield M. J. Crosby A. J. Long D. C. Wege Endemic Bird Areas of the World: Priorities for Conservation. BirdLife Conservation (BirdLife International Cambridge UK 1998).

10.1016/S0378-1135(00)00160-7

10.1038/nature03154

10.1371/journal.pbio.1000475

10.1038/nature08819

10.1038/ng.2657

10.1038/ng.2588

10.1126/science.1230422

E. Dickinson J. Remsen The Howard and Moore Complete Checklist of the Birds of the World (Aves Press Eastbourne UK 2013).

10.1186/2047-217X-3-26

G. Ganapathy et al . GigaScience 3 11 (2013).

T. R. Gregory in The Animal Genome Size Database (2005); available at www.genomesize.com.

10.1126/science.1246338

10.1038/35057062

10.1126/science.1254449

10.1038/377391a0

10.1093/gbe/evp007

10.1016/S0168-9525(01)02414-3

10.1086/342079

10.1023/A:1016072014259

10.1146/annurev.genet.40.110405.090448

10.1023/A:1022696612931

10.1186/gb-2010-11-6-r59

10.1007/s10577-007-1202-6

10.1093/gbe/evs070

10.1038/nature05621

10.1093/molbev/msn207

10.1159/000103166

10.1186/2047-217X-2-10

10.1073/pnas.1220349110

10.1093/molbev/msr207

10.1093/molbev/msn004

10.1074/jbc.M112.375600

10.1038/nrg2158

10.1016/j.tree.2009.06.010

10.1101/gr.3715005

10.1038/nature10530

10.1186/1471-2148-9-54

10.1083/jcb.111.6.2939

10.1038/nrg733

10.1038/nature05295

10.1038/nature11247

10.1101/gr.6031907

10.1101/gr.3021305

10.1038/ncomms1448

10.1196/annals.1298.038

10.1126/science.1256780

10.1126/science.1256846

10.1002/cne.23443

10.1093/bib/bbq072

10.1098/rspb.2010.0117

10.1002/ar.22691

10.1016/j.resp.2004.07.020

10.1016/j.resp.2006.12.005

F. Gill Ornithology (W.H. Freeman and Company New York 1995).

10.1016/0012-1606(84)90240-9

10.1086/380606

10.1038/326803a0

10.1016/j.tree.2011.09.004

10.1111/j.1096-3642.2006.00293.x

10.1093/sysbio/31.1.35

10.1126/science.1254390

10.1093/molbev/msh054

10.1126/science.182.4118.1271

10.1371/journal.pone.0027114

10.1093/molbev/msq286

10.1111/j.1365-294X.2012.05617.x

10.1098/rspb.2007.0976

10.1007/BF00610668

10.1186/1471-2148-11-313

10.1007/BF01142181

S. S. Guraya Ovarian Follicles in Reptiles and Birds (Springer-Verlag Berlin Germany 1989).

10.1038/nature11985

10.1095/biolreprod.104.031823

10.1210/jc.2006-2600

T. R. Birkhead A. P. Møller Sperm competition and sexual selection. (Academic Press 1998).

C. Darwin The Descent of Man and Selection in Relation to Sex (J. Murray London 1871).

10.1016/S0003-3472(05)80312-4

10.1006/anbe.1997.0516

10.1016/j.tig.2011.10.002

10.1016/j.ympev.2012.07.013

10.1093/molbev/msp325

10.1046/j.1365-294x.1998.00389.x

10.1371/journal.pbio.0020312

C. Li D. Lambert S. Subramanian C. D. Millar C. P. Ponting L. Kong C. M. Rands M. K. Fujita S. Meader H. Ellegren K. Nam T. A. Castoe D. D. Pollock W. Gu M. J. Greenwold S. Y. W. Ho D. W. Burt E. D. J. Jarvis T. P. Gilbert Y. Zhang J. Li H. Hu H. Pan L. Xu Y. Deng H. Yu Q. Li L. Jin Y. Chen B. Liu L. Yang S. Liu Y. Zhang Y. Lang J. Xia W. He Q. Shi J. Wang G. Zhang J. Jian Wang H. Yang Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment.  GigaScience   (2014).10.1186/2047-217X-3-27

Li S., et al.., Rapid decline of genomic diversity in restored population of almost-extinct Crested Ibis. Xxxxxxxxxxxxxx XX, XXXX (2014).

10.1101/gr.097261.109

10.1038/nature08696

10.1093/nar/gkl842

10.1093/nar/gkr991

10.1093/nar/gkq963

10.1093/nar/25.17.3389

10.1101/gr.082081.108

10.1101/gr.1865504

10.1093/nar/gkh340

10.1038/ng.2615

10.1186/gb-2012-13-1-415

10.1038/nature10390

A. F. A. Smit R. Hubley P. Green RepeatMasker Open-3.0 (1996); available at www.repeatmasker.org.

A. F. A. Smit R. Hubley RepeatModeler Open-1.0 (2008); available at www.repeatmasker.org.

10.1038/nature10532

10.1093/bioinformatics/btp120

10.1038/nbt.1621

10.1093/nar/gkm391

10.1261/rna.2536111

10.1038/ncomms2416

10.1038/nature10533

10.1126/science.1230835

10.1101/gr.6380007

10.1038/nature11622

R. S. Harris thesis Pennsylvania State University (2007).

10.1073/pnas.1932072100

10.1101/gr.1933104

10.1038/75556

10.1093/bioinformatics/btq102

10.1186/1756-0500-2-148

10.1101/gr.5383506

10.1101/gr.086546.108

10.1111/j.2041-210X.2011.00169.x

10.1186/1471-2105-10-421

10.1186/1748-7188-5-25

10.1006/jmbi.1997.0951

10.1111/j.1574-6968.1999.tb13575.x

10.1101/gr.3567505

10.1093/bioinformatics/btl097

10.1093/molbev/mst100

10.1126/science.1211028

10.1126/science.1183670

10.1038/nature05634

10.1093/bioinformatics/btm538

10.1093/bioinformatics/btg412

R. C. Team R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing Vienna Austria 2012).

J. Fox S. Weisberg An R Companion to Applied Regression (Sage Los Angeles CA 2011).

10.1186/1471-2105-8-374

10.1093/bioinformatics/btg1080

10.1093/nar/gkq1138

10.1016/j.cell.2011.11.055

10.1093/nar/gkg599

10.1093/molbev/msm088

10.1093/oxfordjournals.molbev.a026334

10.1371/journal.pone.0003440

10.1002/cne.20201

D. T. Whitaker Differential gene expression in the anterior forebrain pathway nucleus area X during rapid vocal learning: Honors and undergraduate research; available at http://hdl.handle.net/1969.1/1487501 (2010).

10.1038/nprot.2008.211

10.1186/1471-2105-8-426

10.1006/bbrc.2001.4512

10.1016/j.febslet.2009.10.044

10.1093/bioinformatics/btp536

10.1093/molbev/msp259

10.1186/gb-2007-8-9-r183

10.1093/molbev/msr269

10.1101/gr.229202. Article published online before March 2002

10.1186/1471-2148-10-148

10.1002/jez.b.21306

10.1093/bioinformatics/btl446

10.1093/bioinformatics/btm404

10.1093/bioinformatics/bts199

10.1101/gr.2289704

10.1093/nar/gki198

10.1093/molbev/msr121

10.1016/j.tig.2004.09.005

10.1093/bioinformatics/bts091

10.1073/pnas.082666399

10.1093/bioinformatics/bti037

10.1021/bi992776m

10.1073/pnas.97.13.7366

10.1098/rspb.2007.0174

10.1016/j.tig.2010.02.002

10.1098/rspb.2011.0765

10.1016/j.semcdb.2013.05.005

J. J. Bull Evolution of Sex Determining Mechanisms (Benjamin/Cummings Publishing Company San Francisco 1983).

10.1242/jeb.013094

10.1371/journal.pone.0001768

10.1186/gb-2009-10-4-r42

10.1126/science.1178158

10.1038/nature10842

10.1126/science.1139247

10.1038/nature05805

10.1038/nature01262

10.1038/nature06936

10.1038/nature04072

10.1038/nature09687

10.1038/nature02426