B10K - Toward decoding all bird genomes – University of Copenhagen

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02 June 2015

B10K - Toward decoding all bird genomes

evolution

Today (3rd June, 2015) we formally announce the launch of the Bird 10,000 genomes (B10K) project (http://b10k.genomics.cn/), an initiative to generate representative draft genome sequences from all extant bird species within the next five years. In addition to contributing a large public genomic resource that will benefit the entire research community and human society, this project will include extensive collections of the morphological, physiological, ecological and behavioral traits of all species and will address a number of fundamental questions in evolution, ecology, and biodiversity. This will be the first attempt to sequence the genomes of all living species of a vertebrate class.

The establishment of this project is built on the success of the previous ordinal level project, which provided the first proof of concept for carrying out large-scale sequencing of multiple representative species across a vertebrate class and a window into the types of discoveries that can be made with such genomes (1). The announcement of the B10K project is published online today in Nature.

Figure 1. The new avian family tree based on whole genomes of 48 bird species representing all 30 neoavian orders and two galloanserae orders and two palaeognathae orders. For more detail, see ref (4) and other studies at http://avian.genomics.cn/en/index.html. Painting by Jon Fjeldså.

Figure 1. The new avian family tree based on whole genomes of 48 bird species representing all 30 neoavian orders and two galloanserae orders and two palaeognathae orders. For more detail, see ref (4) and other studies at http://avian.genomics.cn/en/index.html. Painting by Jon Fjeldså.

The phylogeny of birds has been one of the most challenging vertebrate groups to decipher. Recently, the ordinal level project, led by Guojie Zhang from Department of Biology in University of Copenhagen and BGI, Tom Gilbert from National History Museum of Denmark, and Erich Jarvis from Duke University (2), and including investigators from more than 20 countries, sequenced and/or collected the genomes from 48 bird species representing nearly all orders and covering a broad range of evolutionary diversity (3). The consortium was able to resolve much of the contested phylogenetic history of modern avian orders (4) (Fig. 1). This project also addressed an extensive array of questions regarding avian evolution, diversity and behavior (1).

Due to this success, the researchers decided to expand the understanding and exploration of this unique class of vertebrates and extend these findings into multiple disciplines. To do so, the consortium has expanded and been reinforced through the addition of three more institutes as part of the leadership board: Carsten Rahbek from the Center of Macroecology, Evolution and Climate in Denmark, Gary Grave from the Smithsonian Institution in the USA, and Fumin Lei from the Institute of Zoology of Chinese Academy of Science in Beijing. These other contributing institutions and collaborators are listed in the B10K project website. 

The B10K project will allow the completion of a genomic level tree of life of the entire living avian class, decode the link between genetic variation and phenotypic variation, uncover the correlation of genetic evolutionary and biogeographical and biodiversity patterns across a wide-range of species, evaluate the impact of various ecological factors and human influence on species evolution, and unveil the demographic history of an entire class of organisms.

Given all these aims, the consortium is carrying out the project in three phases. Each phase focuses on the completion of milestones at hierarchical levels of avian classification (Fig. 2). This project will have significant scientific and public impact that will change our understanding of avian biology and evolution, which in turn will affect our understanding of other organisms and open doors to new areas of research.

Figure 2. The B10K plan in four phases. We are carrying out the project in phases based on the hierarchical levels of avian classification. The ordinal level phase of about 34 orders has been accomplished (1), while the genomic data collection for representative species of about 240 families is ongoing right now. The specimen collection for the phase 3 of 2250 genera and phase 4 of the remaining 8000 species is under way.

Figure 2. The B10K plan in four phases. We are carrying out the project in phases based on the hierarchical levels of avian classification. The ordinal level phase of about 34 orders has been accomplished (1), while the genomic data collection for representative species of about 240 families is ongoing right now. The specimen collection for the phase 3 of 2250 genera and phase 4 of the remaining 8000 species is under way.

1.
G. Zhang, E. D. Jarvis, M. T. Gilbert, Avian genomes. A flock of genomes. Introduction. Science 346, 1308-1309 (2014); published online EpubDec 12 (10.1126/science.346.6215.1308).

2.
http://biome.biomedcentral.com/how-bird-genomes-got-their-wings/.

3.
G. Zhang, C. Li, Q. Li, B. Li, D. M. Larkin, C. Lee, J. F. Storz, A. Antunes, M. J. Greenwold, R. W. Meredith, A. Odeen, J. Cui, Q. Zhou, L. Xu, H. Pan, Z. Wang, L. Jin, P. Zhang, H. Hu, W. Yang, J. Hu, J. Xiao, Z. Yang, Y. Liu, Q. Xie, H. Yu, J. Lian, P. Wen, F. Zhang, H. Li, Y. Zeng, Z. Xiong, S. Liu, L. Zhou, Z. Huang, N. An, J. Wang, Q. Zheng, Y. Xiong, G. Wang, B. Wang, J. Wang, Y. Fan, R. R. da Fonseca, A. Alfaro-Nunez, M. Schubert, L. Orlando, T. Mourier, J. T. Howard, G. Ganapathy, A. Pfenning, O. Whitney, M. V. Rivas, E. Hara, J. Smith, M. Farre, J. Narayan, G. Slavov, M. N. Romanov, R. Borges, J. P. Machado, I. Khan, M. S. Springer, J. Gatesy, F. G. Hoffmann, J. C. Opazo, O. Hastad, R. H. Sawyer, H. Kim, K. W. Kim, H. J. Kim, S. Cho, N. Li, Y. Huang, M. W. Bruford, X. Zhan, A. Dixon, M. F. Bertelsen, E. Derryberry, W. Warren, R. K. Wilson, S. Li, D. A. Ray, R. E. Green, S. J. O'Brien, D. Griffin, W. E. Johnson, D. Haussler, O. A. Ryder, E. Willerslev, G. R. Graves, P. Alstrom, J. Fjeldsa, D. P. Mindell, S. V. Edwards, E. L. Braun, C. Rahbek, D. W. Burt, P. Houde, Y. Zhang, H. Yang, J. Wang, C. Avian Genome, E. D. Jarvis, M. T. Gilbert, J. Wang, Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346, 1311-1320 (2014); published online EpubDec 12 (10.1126/science.1251385).

4.
E. D. Jarvis, S. Mirarab, A. J. Aberer, B. Li, P. Houde, C. Li, S. Y. Ho, B. C. Faircloth, B. Nabholz, J. T. Howard, A. Suh, C. C. Weber, R. R. da Fonseca, J. Li, F. Zhang, H. Li, L. Zhou, N. Narula, L. Liu, G. Ganapathy, B. Boussau, M. S. Bayzid, V. Zavidovych, S. Subramanian, T. Gabaldon, S. Capella-Gutierrez, J. Huerta-Cepas, B. Rekepalli, K. Munch, M. Schierup, B. Lindow, W. C. Warren, D. Ray, R. E. Green, M. W. Bruford, X. Zhan, A. Dixon, S. Li, N. Li, Y. Huang, E. P. Derryberry, M. F. Bertelsen, F. H. Sheldon, R. T. Brumfield, C. V. Mello, P. V. Lovell, M. Wirthlin, M. P. Schneider, F. Prosdocimi, J. A. Samaniego, A. M. Vargas Velazquez, A. Alfaro-Nunez, P. F. Campos, B. Petersen, T. Sicheritz-Ponten, A. Pas, T. Bailey, P. Scofield, M. Bunce, D. M. Lambert, Q. Zhou, P. Perelman, A. C. Driskell, B. Shapiro, Z. Xiong, Y. Zeng, S. Liu, Z. Li, B. Liu, K. Wu, J. Xiao, X. Yinqi, Q. Zheng, Y. Zhang, H. Yang, J. Wang, L. Smeds, F. E. Rheindt, M. Braun, J. Fjeldsa, L. Orlando, F. K. Barker, K. A. Jonsson, W. Johnson, K. P. Koepfli, S. O'Brien, D. Haussler, O. A. Ryder, C. Rahbek, E. Willerslev, G. R. Graves, T. C. Glenn, J. McCormack, D. Burt, H. Ellegren, P. Alstrom, S. V. Edwards, A. Stamatakis, D. P. Mindell, J. Cracraft, E. L. Braun, T. Warnow, W. Jun, M. T. Gilbert, G. Zhang, Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320-1331 (2014); published online EpubDec 12 (10.1126/science.1253451).