Comparative genomics reveals insights into avian genome evolution and adaptation-Reference-Cited by-同舟云学术

Comparative genomics reveals insights into avian genome evolution and adaptation

Published:2014-12-12 Issue:6215 Volume:346 Page:1311-1320
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Zhang Guojie¹²,Li Cai¹³,Li Qiye¹³,Li Bo¹,Larkin Denis M.⁴,Lee Chul⁵⁶,Storz Jay F.⁷,Antunes Agostinho⁸⁹,Greenwold Matthew J.¹⁰,Meredith Robert W.¹¹,Ödeen Anders¹²,Cui Jie¹³¹⁴,Zhou Qi¹⁵,Xu Luohao¹¹⁶,Pan Hailin¹,Wang Zongji¹¹⁷,Jin Lijun¹,Zhang Pei¹,Hu Haofu¹,Yang Wei¹,Hu Jiang¹,Xiao Jin¹,Yang Zhikai¹,Liu Yang¹,Xie Qiaolin¹,Yu Hao¹,Lian Jinmin¹,Wen Ping¹,Zhang Fang¹,Li Hui¹,Zeng Yongli¹,Xiong Zijun¹,Liu Shiping¹¹⁷,Zhou Long¹,Huang Zhiyong¹,An Na¹,Wang Jie¹¹⁸,Zheng Qiumei¹,Xiong Yingqi¹,Wang Guangbiao¹,Wang Bo¹,Wang Jingjing¹,Fan Yu¹⁹,da Fonseca Rute R.³,Alfaro-Núñez Alonzo³,Schubert Mikkel³,Orlando Ludovic³,Mourier Tobias³,Howard Jason T.²⁰,Ganapathy Ganeshkumar²⁰,Pfenning Andreas²⁰,Whitney Osceola²⁰,Rivas Miriam V.²⁰,Hara Erina²⁰,Smith Julia²⁰,Farré Marta⁴,Narayan Jitendra²¹,Slavov Gancho²¹,Romanov Michael N²²,Borges Rui⁸⁹,Machado João Paulo⁸²³,Khan Imran⁸⁹,Springer Mark S.²⁴,Gatesy John²⁴,Hoffmann Federico G.²⁵²⁶,Opazo Juan C.²⁷,Håstad Olle²⁸,Sawyer Roger H.¹⁰,Kim Heebal⁵⁶²⁹,Kim Kyu-Won⁵,Kim Hyeon Jeong⁶,Cho Seoae⁶,Li Ning³⁰,Huang Yinhua³⁰³¹,Bruford Michael W.³²,Zhan Xiangjiang³²³³,Dixon Andrew³⁴,Bertelsen Mads F.³⁵,Derryberry Elizabeth³⁶³⁷,Warren Wesley³⁸,Wilson Richard K³⁸,Li Shengbin³⁹,Ray David A.²⁶,Green Richard E.⁴⁰,O’Brien Stephen J.⁴¹⁴²,Griffin Darren²²,Johnson Warren E.⁴³,Haussler David⁴⁰,Ryder Oliver A.⁴⁴,Willerslev Eske³,Graves Gary R.⁴⁵⁴⁶,Alström Per⁴⁷⁴⁸,Fjeldså Jon⁴⁶,Mindell David P.⁴⁹,Edwards Scott V.⁵⁰,Braun Edward L.⁵¹,Rahbek Carsten⁴⁶⁵²,Burt David W.⁵³,Houde Peter⁵⁴,Zhang Yong¹,Yang Huanming¹⁵⁵,Wang Jian¹,Jarvis Erich D.²⁰,Gilbert M. Thomas P.³⁵⁶,Wang Jun¹⁵⁵⁵⁷⁵⁸⁵⁹,Ye Chen,Liang Shaoguang,Yan Zengli,Zepeda M. Lisandra,Campos Paula F.,Velazquez Amhed Missael Vargas,Samaniego José Alfredo,Avila-Arcos María,Martin Michael D.,Barnett Ross,Ribeiro Angela M.,Mello Claudio V.,Lovell Peter V.,Almeida Daniela,Maldonado Emanuel,Pereira Joana,Sunagar Kartik,Philip Siby,Dominguez-Bello Maria Gloria,Bunce Michael,Lambert David,Brumfield Robb T.,Sheldon Frederick H.,Holmes Edward C.,Gardner Paul P.,Steeves Tammy E.,Stadler Peter F.,Burge Sarah W.,Lyons Eric,Smith Jacqueline,McCarthy Fiona,Pitel Frederique,Rhoads Douglas,Froman David P.,

Affiliation:

1. China National GeneBank, Beijing Genomics Institute (BGI)–Shenzhen, Shenzhen, 518083, China.

2. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.

3. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.

4. Royal Veterinary College, University of London, London, UK.

5. Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea.

6. Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea.

7. School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA.

8. Centro 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.

9. Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.

10. Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.

11. Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, USA.

12. Department of Animal Ecology, Uppsala University, Norbyvägen 18D, S-752 36 Uppsala, Sweden.

13. Marie 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.

14. Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore 169857, Singapore.

15. Department of Integrative Biology University of California, Berkeley, CA 94720, USA.

16. College of Life Sciences, Wuhan University, Wuhan 430072, China.

17. School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China.

18. BGI Education Center,University of Chinese Academy of Sciences,Shenzhen, 518083, China.

19. Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China.

20. Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.

21. Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK.

22. School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK.

23. Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Portugal.

24. Department of Biology, University of California Riverside, Riverside, CA 92521, USA.

25. Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA.

26. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.

27. Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.

28. Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Post Office Box 7011, S-750 07, Uppsala, Sweden.

29. Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea.

30. State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China.

31. College of Animal Science and Technology, China Agricultural University, Beijing 100094, China.

32. Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK.

33. Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 China.

34. International Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK.

35. Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark.

36. Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA.

37. Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.

38. The Genome Institute at Washington University, St. Louis, MO 63108, USA.

39. College of Medicine and Forensics, Xi’an Jiaotong University, Xi’an, 710061, China.

40. Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.

41. Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia.

42. Nova Southeastern University Oceanographic Center 8000 N Ocean Drive, Dania, FL 33004, USA.

43. Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA.

44. Genetics Division, San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, CA 92027, USA.

45. Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Post Office Box 37012, Washington, DC 20013-7012, USA.

46. Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark.

47. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China.

48. Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, SE-750 07 Uppsala, Sweden.

49. Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA.

50. Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.

51. Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA.

52. Imperial College London, Grand Challenges in Ecosystems and the Environment Initiative, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK.

53. Division 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.

54. Department of Biology, New Mexico State University, Box 30001 MSC 3AF, Las Cruces, NM 88003, USA.

55. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China.

56. Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, 6102, Australia.

57. Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.

58. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia.

59. Department of Medicine, University of Hong Kong, Hong Kong.

Abstract

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.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

Reference192 articles.

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