• The Genome 10K Project: A Way Forward

      Koepfli, Klaus-Peter; Benedict, Paten; The Genome 10K Community of Scientists; Antunes, Agostinho; Belov, Kathy; Bustamante, Carlos; Castoe, Todd A.; Clawson, Hiram; Crawford, Andrew J.; Diekhans, Mark; et al. (2015)
      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....
    • Whole genome sequencing and re-sequencing of the sable antelope (Hippotragus niger): A resource for monitoring diversity in ex situ and in situ populations

      Koepfli, Klaus-Peter; Tamazian, Gaik; Wildt, David; Dobrynin, Pavel; Kim, Changhoon; Frandsen, Paul B.; Godinho, Raquel; Yurchenko, Andrey A.; Komissarov, Aleksey; Krasheninnikova, Ksenia; et al. (2019)
      Genome-wide assessment of genetic diversity has the potential to increase the ability to understand admixture, inbreeding, kinship and erosion of genetic diversity affecting both captive (ex situ) and wild (in situ) populations of threatened species. The sable antelope (Hippotragus niger), native to the savannah woodlands of sub-Saharan Africa, is a species that is being managed ex situ in both public (zoo) and private (ranch) collections in the United States. Our objective was to develop whole genome sequence resources that will serve as a foundation for characterizing the genetic status of ex situ populations of sable antelope relative to populations in the wild. Here we report the draft genome assembly of a male sable antelope, a member of the subfamily Hippotraginae (Bovidae, Cetartiodactyla, Mammalia). The 2.926 Gb draft genome consists of 136,532 contigs with an N50 of 45.5 Kbp and 16,931 scaffolds with an N50 of 4.59 Mbp. De novo annotation identified 21,276 protein-coding genes and repetitive sequences encompassing 46.97% of the genome. The discovery of single nucleotide variants (SNVs) was assisted by the re-sequencing of seven additional captive and wild individuals, representing two different subspecies, leading to the identification of 1,987,710 bi-allelic SNVs. Assembly of the mitochondrial genomes revealed that each individual was defined by a unique haplotype and these data were used to infer the mitochondrial gene tree relative to other hippotragine species. The sable antelope genome constitutes a valuable resource for assessing genome-wide diversity and evolutionary potential, thereby facilitating long-term conservation of this charismatic species.