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Review
. 2015:3:57-111.
doi: 10.1146/annurev-animal-090414-014900.

The Genome 10K Project: a way forward

Klaus-Peter Koepfli  1 , Benedict Paten; Genome 10K Community of Scientists; Stephen J O'Brien
Collaborators, Affiliations
Review

The Genome 10K Project: a way forward

Klaus-Peter Koepfli et al. Annu Rev Anim Biosci. 2015.

Abstract

The Genome 10K Project was established in 2009 by a consortium of biologists and genome scientists determined to facilitate the sequencing and analysis of the complete genomes of 10,000 vertebrate species. Since then the number of selected and initiated species has risen from ∼26 to 277 sequenced or ongoing with funding, an approximately tenfold increase in five years. Here we summarize the advances and commitments that have occurred by mid-2014 and outline the achievements and present challenges of reaching the 10,000-species goal. We summarize the status of known vertebrate genome projects, recommend standards for pronouncing a genome as sequenced or completed, and provide our present and future vision of the landscape of Genome 10K. The endeavor is ambitious, bold, expensive, and uncertain, but together the Genome 10K Consortium of Scientists and the worldwide genomics community are moving toward their goal of delivering to the coming generation the gift of genome empowerment for many vertebrate species.

Keywords: amphibian; bird; fish; genome; mammal; reptile.

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Figures

Figure 1
Figure 1
Consensus phylogeny of the major lineages of vertebrates. Topology and divergence dates (Ma) are consensus estimates derived from References 1 and 276 and included citations. Following the common names of taxon groups in parentheses are number of living species for that group and number of species with published and/or pending genomes (see Tables 2 and 3).
Figure 2
Figure 2
Consensus phylogeny of the major lineages of fishes. Topology and dates (Ma) are derived from combined data tree reported in Reference 1. On the ends of the limbs is the number of living species for that group. Following the common names of taxon groups is number of species with published and/or pending genomes (see Tables 2 and 3).
Figure 3
Figure 3
Consensus phylogeny of the major lineages of birds. In parentheses are the number of living species as defined by Howard and Moore (277), with the exception of the Passerine species count, which is taken from (1)/number of species with published and/or pending genomes (Tables 2 and 3). Data include both those genomes published to date as listed in Table 2 and those currently undergoing final assembly and annotation as part of the Avian Phylogenomic Consortium (Table 3). The underlying time-calibrated phylogenetic tree is a composite of the Neognath phylogeny published by Jarvis et al. (112) and Palaeognath phylogeny published by Mitchell et al. (278). Illustrations courtesy of Jon Fjeldå.
Figure 4
Figure 4
Consensus phylogeny of the major lineages of mammals. Topology and dates (Ma) are consensus estimates derived from References 1 and 276 and included citations. Following the common names of taxon groups in parentheses are the number of living species for that group and number of species with published and/or pending genomes (see Tables 2 and 3).
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References

    1. Genome 10K Community Sci. Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered. 2009;100(6):659–74. - PMC - PubMed
    1. Hayden EC. 10,000 genomes to come. Nature. 2009;462(7269):21. - PubMed
    1. Pennisi E. No genome left behind. Science. 2009;326(5954):794–95. - PubMed
    1. Wong PB, Wiley EO, Johnson WE, Ryder OA, O’Brien SJ, et al. Tissue sampling methods and standards for vertebrate genomics. GigaScience. 2012;1:8. - PMC - PubMed
    1. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, et al. GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res. 2012;22(3):557–67. - PMC - PubMed

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