AsianScientist (Dec. 17, 2014) – The Avian Phylogenomics Consortium has simultaneously published in 28 papers—eight papers in a special issue of Science and 20 more in Genome Biology, GigaScience and other journals. The full set of papers can be accessed at the Avian Phylogenetics Project website.
Although scientists have long known that the birds who survived the mass extinction experienced a rapid burst of evolution, the molecular details of how they arrived at the spectacular biodiversity of more than 10,000 species is poorly understood.
To resolve these fundamental questions, a consortium led by Zhang Guojie of the National Genebank at BGI in China and the University of Copenhagen has sequenced, assembled and compared full genomes of 48 bird species. The species include the crow, duck, falcon, parakeet, crane, ibis, woodpecker, eagle and others, representing all major branches of modern birds.
“BGI’s strong support and four years of hard work by the entire community have enabled us to answer numerous fundamental questions to an unprecedented scale,” said Zhang. “This is the largest whole genomic study across a single vertebrate class to date. The success of this project can only be achieved with the excellent collaboration of all the consortium members.”
The Avian Phylogenomics Consortium has so far involved more than 200 scientists hailing from 80 institutions in 20 countries, including the BGI, the University of Copenhagen, Duke University, the University of Texas at Austin, the Smithsonian Museum, the Chinese Academy of Sciences, Louisiana State University and many others.
This sweeping genome-level comparison of an entire class of life is being powered by frozen bird tissue samples collected over the past 30 years by museums and other institutions around the world. Samples are sent as fingernail-sized chunks of frozen flesh mostly to Duke University and University of Copenhagen for DNA separation. Most of the genome sequencing and critical initial analyses of the genomes have then been conducted by BGI.
The avian genome consortium is now creating a database that will be made publicly available in the future for scientists to study the genetic basis of complex avian traits.
Setting up the pipeline for the large-scale study of whole genomes—collecting and organizing tissue samples, extracting the DNA, analyzing its quality, sequencing and managing torrents of new data—has been a massive undertaking. But the scientists say their work should help inform other major efforts for the comprehensive sequencing of vertebrate classes.
To encourage other researchers to dig through this ‘big data’ and discover new patterns that were not seen in small-scale data before, the avian genome consortium has released the full dataset to the public in GigaScience, and in NCBI, ENSEMBL and CoGe databases.
To maximize the use of this wealth of data, rather than wait until the publication of these papers the project has been a great example in early data release, with unpublished datasets released to the community over a four-year period. Demonstrating the huge interest in birds, the final genomes were released via twitter over the spring, leading to much discussion on social media and a doubling of the number of users of the GigaScience database.
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Source: BGI Shenzhen.
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