Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity inex Situandin SituPopulations

Abstract

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 2.596 Gb draft genome consists of 136,528 contigs with an N50 of 45.5 Kbp and 16,927 scaffolds with an N50 of 4.59 Mbp. De novo annotation identified 18,828 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.

Chromosomal‐level genome assembly of the scimitar‐horned oryx: Insights into diversity and demography of a species extinct in the wild

“…to 100.4 Mb. This is more than 20 times the scaffold N50 reported for the sable antelope (~4.6 Mb, Koepfli et al, 2019) and almost double that of the N50 reported for gemsbok (47 Mb, Farré et al, 2019).…”

“…Chromium sequencing and Hi-C contact mapping. The total assembly length was 2.7 Gb, similar to the hippotragine sable antelope (Hippotragus niger; Koepfli et al, 2019) and gemsbok (Oryx gazella;…”

An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi)

“…Gene and repeat annotation of the assembly identified a similar number of genes and transposable elements as found in other ruminant species. Following the example of the sable antelope [41] and the California condor [42], the new giraffe genome assembly will foster research into conservation of this charismatic species, serving as a foundation for characterizing the genetic diversity of wild and captive populations. Furthermore, the high-quality, chromosome-scale assembly described in this report contributes to the goals of the Genome 10K Project [43] and the Earth BioGenome Project [44].…”

A Single Nucleotide Mutation in Adenylate Cyclase Affects Vegetative Growth, Sclerotial Formation and Virulence of Botrytis cinerea

“…During saprotrophic culture, fungi may also exhibit natural phenotypic variation due to various environmental factors [33]. With the development of high-throughput sequencing technology, genome-wide resequencing has been widely used to reveal the genetic diversity of species and to identify novel candidate genes associated with phenotypes in different organisms [34]. In our study, a phenotypic variant strain, B05.10 M , was derived from the sequenced wild-type strain B05.10 of B. cinerea during culture; it showed significant differences in mycelial growth, reproductive differentiation and virulence compared to B05.10 (Figures 1 and 2; Figure S1).…”