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Avian genomes collection

The evolutionary relationships between modern bird lineages are contentious and have been debated for many years. In order to address this point, the Avian Genomes consortium has sequenced the genomes of 45 species of bird representing 36 orders. Together with the three previously sequenced genomes, these data have helped us resolve the phylogeny of the class Aves. As well as specific insights into bird biology, the wealth of data generated has allowed researchers to answer more general questions about evolutionary biology. A number of articles arising from this project have been published in Science, including the two flagship articles (DOI:10.1126/science.1251385 and DOI:10.1126/science.1253451). The following articles have been published in BioMed Central journals, including Genome Biology and GigaScience. The data from the project are available from GigaDB.

The full collection can be viewed at the Avian Genomes Consortium page.

  1. Data Note

    Phylogenomic analyses data of the avian phylogenomics project

    Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genome...

    Erich D Jarvis, Siavash Mirarab, Andre J Aberer, Bo Li, Peter Houde, Cai Li, Simon Y W Ho, Brant C Faircloth, Benoit Nabholz, Jason T Howard, Alexander Suh, Claudia C Weber, Rute R da Fonseca, Alonzo Alfaro-Núñez, Nitish Narula, Liang Liu…

    GigaScience 2015 4:4

    Published on: 12 February 2015

  2. Open letter

    Avianbase: a community resource for bird genomics

    Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements t...

    Lél Eöry, M Thomas P Gilbert, Cai Li, Bo Li, Alan Archibald, Bronwen L Aken, Guojie Zhang, Erich Jarvis, Paul Flicek and David W Burt

    Genome Biology 2015 16:21

    Published on: 29 January 2015

  3. Research

    Conserved syntenic clusters of protein coding genes are missing in birds

    Birds are one of the most highly successful and diverse groups of vertebrates, having evolved a number of distinct characteristics, including feathers and wings, a sturdy lightweight skeleton and unique respir...

    Peter V Lovell, Morgan Wirthlin, Larry Wilhelm, Patrick Minx, Nathan H Lazar, Lucia Carbone, Wesley C Warren and Claudio V Mello

    Genome Biology 2014 15:565

    Published on: 18 December 2014

  4. Research

    Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment

    Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them ha...

    Cai Li, Yong Zhang, Jianwen Li, Lesheng Kong, Haofu Hu, Hailin Pan, Luohao Xu, Yuan Deng, Qiye Li, Lijun Jin, Hao Yu, Yan Chen, Binghang Liu, Linfeng Yang, Shiping Liu, Yan Zhang…

    GigaScience 2014 3:27

    Published on: 12 December 2014

  5. Research article

    Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles

    Vertebrate skin appendages are constructed of keratins produced by multigene families. Alpha (α) keratins are found in all vertebrates, while beta (β) keratins are found exclusively in reptiles and birds. We h...

    Matthew J Greenwold, Weier Bao, Erich D Jarvis, Haofu Hu, Cai Li, M Thomas P Gilbert, Guojie Zhang and Roger H Sawyer

    BMC Evolutionary Biology 2014 14:249

    Published on: 12 December 2014

  6. Research

    Evolution and gene capture in ancient endogenous retroviruses - insights from the crocodilian genomes

    Crocodilians are thought to be hosts to a diverse and divergent complement of endogenous retroviruses (ERVs) but a comprehensive investigation is yet to be performed. The recent sequencing of three crocodilian...

    Amanda Y Chong, Kenji K Kojima, Jerzy Jurka, David A Ray, Arian F A Smit, Sally R Isberg and Jaime Gongora

    Retrovirology 2014 11:71

    Published on: 12 December 2014

  7. Research article

    Temporal genomic evolution of bird sex chromosomes

    Sex chromosomes exhibit many unusual patterns in sequence and gene expression relative to autosomes. Birds have evolved a female heterogametic sex system (male ZZ, female ZW), through stepwise suppression of r...

    Zongji Wang, Jilin Zhang, Wei Yang, Na An, Pei Zhang, Guojie Zhang and Qi Zhou

    BMC Evolutionary Biology 2014 14:250

    Published on: 12 December 2014

  8. Research

    Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species

    Nearly one-quarter of all avian species is either threatened or nearly threatened. Of these, 73 species are currently being rescued from going extinct in wildlife sanctuaries. One of the previously most critic...

    Shengbin Li, Bo Li, Cheng Cheng, Zijun Xiong, Qingbo Liu, Jianghua Lai, Hannah V Carey, Qiong Zhang, Haibo Zheng, Shuguang Wei, Hongbo Zhang, Liao Chang, Shiping Liu, Shanxin Zhang, Bing Yu, Xiaofan Zeng…

    Genome Biology 2014 15:557

    Published on: 11 December 2014

  9. Data Note

    Comparative genomic data of the Avian Phylogenomics Project

    The evolutionary relationships of modern birds are among the most challenging to understand in systematic biology and have been debated for centuries. To address this challenge, we assembled or collected the g...

    Guojie Zhang, Bo Li, Cai Li, M Thomas P Gilbert, Erich D Jarvis and Jun Wang

    GigaScience 2014 3:26

    Published on: 11 December 2014

  10. Research

    Low frequency of paleoviral infiltration across the avian phylogeny

    Mammalian genomes commonly harbor endogenous viral elements. Due to a lack of comparable genome-scale sequence data, far less is known about endogenous viral elements in avian species, even though their small ...

    Jie Cui, Wei Zhao, Zhiyong Huang, Erich D Jarvis, M Thomas P Gilbert, Peter J Walker, Edward C Holmes and Guojie Zhang

    Genome Biology 2014 15:539

    Published on: 11 December 2014

  11. Research article

    Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor

    The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded...

    Michael N Romanov, Marta Farré, Pamela E Lithgow, Katie E Fowler, Benjamin M Skinner, Rebecca O’Connor, Gothami Fonseka, Niclas Backström, Yoichi Matsuda, Chizuko Nishida, Peter Houde, Erich D Jarvis, Hans Ellegren, David W Burt, Denis M Larkin and Darren K Griffin

    BMC Genomics 2014 15:1060

    Published on: 11 December 2014

  12. Commentary

    The birds of Genome10K

    Everyone loves the birds of the world. From their haunting songs and majesty of flight to dazzling plumage and mating rituals, bird watchers – both amateurs and professionals - have marveled for centuries at t...

    Stephen J OBrien, David Haussler and Oliver Ryder

    GigaScience 2014 3:32

    Published on: 11 December 2014