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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. 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...

    Authors: 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…
    Citation: GigaScience 2015 4:4
    Content type: Data Note Published on:

  2. 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...

    Authors: 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
    Citation: Genome Biology 2015 16:21
    Content type: Open letter Published on:

  3. 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...

    Authors: Peter V Lovell, Morgan Wirthlin, Larry Wilhelm, Patrick Minx, Nathan H Lazar, Lucia Carbone, Wesley C Warren and Claudio V Mello
    Citation: Genome Biology 2014 15:565
    Content type: Research Published on:

  5. 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...

    Authors: Zongji Wang, Jilin Zhang, Wei Yang, Na An, Pei Zhang, Guojie Zhang and Qi Zhou
    Citation: BMC Evolutionary Biology 2014 14:250
    Content type: Research article Published on:

  6. 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...

    Authors: Matthew J Greenwold, Weier Bao, Erich D Jarvis, Haofu Hu, Cai Li, M Thomas P Gilbert, Guojie Zhang and Roger H Sawyer
    Citation: BMC Evolutionary Biology 2014 14:249
    Content type: Research article Published on:

  7. 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...

    Authors: Amanda Y Chong, Kenji K Kojima, Jerzy Jurka, David A Ray, Arian F A Smit, Sally R Isberg and Jaime Gongora
    Citation: Retrovirology 2014 11:71
    Content type: Research Published on:

  8. 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...

    Authors: 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…
    Citation: GigaScience 2014 3:27
    Content type: Research Published on:

  9. 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...

    Authors: 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
    Citation: BMC Genomics 2014 15:1060
    Content type: Research article Published on:

  10. 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...

    Authors: 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…
    Citation: Genome Biology 2014 15:557
    Content type: Research Published on:

  11. While effective population size (Ne) and life history traits such as generation time are known to impact substitution rates, their potential effects on base composition evolution are less well understood. GC cont...

    Authors: Claudia C Weber, Bastien Boussau, Jonathan Romiguier, Erich D Jarvis and Hans Ellegren
    Citation: Genome Biology 2014 15:549
    Content type: Research Published on:

  13. 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 ...

    Authors: Jie Cui, Wei Zhao, Zhiyong Huang, Erich D Jarvis, M Thomas P Gilbert, Peter J Walker, Edward C Holmes and Guojie Zhang
    Citation: Genome Biology 2014 15:539
    Content type: Research Published on:

  14. 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...

    Authors: Stephen J OBrien, David Haussler and Oliver Ryder
    Citation: GigaScience 2014 3:32
    Content type: Commentary Published on:

  15. 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...

    Authors: Guojie Zhang, Bo Li, Cai Li, M Thomas P Gilbert, Erich D Jarvis and Jun Wang
    Citation: GigaScience 2014 3:26
    Content type: Data Note Published on: