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The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex situ conservation breeding and reintroduction into its former range. However, the species remains at risk due to possible inbreeding, disease susceptibility, and multiple fertility challenges. Here, we report the de novo genome assembly of a male black-footed ferret generated through a combination of linked-read sequencing, optical mapping, and Hi-C proximity ligation. In addition, we report the karyotype for this species, which was used to anchor and assign chromosome numbers to the chromosome-length scaffolds. The draft assembly was ~2.5 Gb in length, with 95.6% of it anchored to 19 chromosome-length scaffolds, corresponding to the 2n = 38 chromosomes revealed by the karyotype. The assembly has contig and scaffold N50 values of 148.8 kbp and 145.4 Mbp, respectively, and is up to 96% complete based on BUSCO analyses. Annotation of the assembly, including evidence from RNA-seq data, identified 21,406 protein-coding genes and a repeat content of 37.35%. Phylogenomic analyses indicated that the black-footed ferret diverged from the European polecat/domestic ferret lineage 1.6 million yr ago. This assembly will enable research on the conservation genomics of black-footed ferrets and thereby aid in the further restoration of this endangered species. [ABSTRACT FROM AUTHOR]

Although guanacos (Lama guanicoe) are widely distributed throughout much of their historic range, they are often restricted to small, isolated populations that are at risk of inbreeding and loss of genetic diversity. Here we document and interpret baseline patterns of genetic variation in a guanaco population inhabiting in the Bolivian Chaco that is threatened by hunting and habitat degradation. The region, once open grasslands, is dominated by dense shrubs, the result of livestock grazing. The most-recent census identified only 74 individuals and is designated as at 'risk of extinction' by the Bolivian government. We assessed the population's genetic health and uniqueness from the genetic patterns of 16 microsatellite loci, the Hyper-variable Domain I of the mitochondrial Control Region and SRY gene with 29 fecal samples. We identified 19 male and 10 female unique individuals. Microsatellite variation (Ho = 0.64) was similar to larger, less-isolated populations. However, the estimated effective population size was low and consistent with the continuing loss of allelic variation. The two observed mtDNA haplotypes are common in other L. g. guanicoe populations. Although we documented moderate genetic diversity, gene flow among Bolivian and Paraguayan guanaco Chaco populations should be assessed and integrated into explicit conservation management plans. [ABSTRACT FROM AUTHOR]