Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species

Abstract

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16,203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60,000 living species). In this proposal, we present precise counts for these 16,203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

Figure 1

Consensus phylogeny of the major lineages of vertebrates. Topology and divergence dates (Ma) are consensus estimates derived from Hedges and Kumar (2009) and included citations and amended per Benton and Donoghue (2007), Janvier (2006), Maisey (2000), and Sansom et al. (1996). Following the common names of taxon groups in parentheses is the number of living species for that group followed by the number of G10K species with specific biospecimens nominated for G10K whole-genome sequence.

Figure 2

Consensus phylogeny of the major lineages of mammals. Topology and dates (Ma) are consensus estimates derived from Hedges and Kumar (2009) and included citations. Following the common names of taxon groups in parentheses is the number of living species for that group, followed by the number of G10K species with specific biospecimens nominated for G10K whole-genome sequence.

Figure 3

Consensus phylogeny of the major lineages of birds. Topology and dates (Ma) are derived from combined-data tree reported in Hackett et al. (2008), rendered ultrametric by nonparametric rate-smoothing (Sanderson 1997) and scaled to a root age of 119 Ma based on an average of multiple dating studies (van Tuinen et al. 2006). Following the common names of taxon groups in parentheses is the number of living species for that group followed by the number of G10K species with specific biospecimens nominated for G10K whole-genome sequence.

Figure 4

Consensus phylogeny of the major lineages of nonavian reptiles. Topology and dates (Ma) are consensus estimates derived from Hedges and Kumar (2009) and included citations. Following the common names of taxon groups in parentheses is the number of living species for that group followed by the number of G10K species with specific named biospecimens nominated for G10K whole-genome sequence.

Figure 5

Consensus phylogeny of the major lineages of amphibians. Topology and dates (Ma) are consensus estimates derived from Hedges and Kumar (2009) and included citations. Following the common names of taxon groups in parentheses is the number of living species for that group followed by the list of G10K species with specific named biospecimens nominated for G10K whole-genome sequence.