The Genome 10K Project: A Way Forward

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.

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

“…Recently greater than 50 de novo mammalian assemblies have been produced (more are inevitable); these, however, at best, are collections of subchromosomal-sized scaffolds. Moreover, several hundred are currently being assembled to scaffold level by individual projects or consortia such as Genome10K (Koepfli et al 2015). Building a mammalian universal BAC set would be a greater challenge than in birds as mammalian genomes have more repetitive sequences and are about three times larger; thus, more BACs would be needed to achieve the same level of mapping resolution.…”

“…The ability to sequence complex animal genomes quickly and inexpensively has initiated numerous genome projects beyond those of agricultural/medical importance (e.g., Hu et al 2009;Groenen et al 2012) and inspired ambitious undertakings to sequence thousands of species (Zhang et al 2014a;Koepfli et al 2015). De novo genome assembly efforts ultimately aim to create a series of contigs, each representing a single chromosome, from p-to q-terminus ("chromosome-level" assembly).…”

Did sex chromosome turnover promote divergence of the major mammal groups?

“…Complete genome sequencing of non‐model vertebrates promoted by Genome 10 K 87 may reveal many more systems that are in the process of sex chromosome change, and which we can exploit to determine under what conditions sex chromosome turnover leads to reproductive isolation, and how this translates into speciation.…”

From sauropsids to mammals and back: New approaches to comparative cortical development

“…This phylogenetic tree is not time‐calibrated. More details about GenBank accession can be found at Koepfli et al (2015; table 2) and/or https://genome10k.soe.ucsc.edu. Abbreviations in the avian brain: A, arcopallium; DP, dorsal pallium; DVR, dorsal ventricular ridge; d, dorsal tier of the mesopallium; E, entopallium; H, hyperpallium; HA, hyperpallium apicale; HAl, hyperpallium apicale lateral; HAm, hyperpallium apicale medial; HD, hyperpallium densocellulare; Hp, hippocampus; IH, intercalated hyperpallium; IHA, interstitial nucleus of hyperpallium apicale; IZ, intermediate zone; lCx, lateral cerebral cortex; LMI, lamina mesopallium intermediate; LP, lateral pallium; LS, lateral striatum; lv, lateral ventricle; MP, medial pallium; M, mesopallium; MS, medial striatum; N, nidopallium; P, pallidum; Pir, piriform cortex; ps, pial surface; S, striatum; v, ventral tier of the mesopallium; VPa, ventral pallidum; VZ, ventricular zone.…”