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Getting off on the black foot

Black-footed ferrets (Mustela nigripes) once occupied much of the grasslands of the North American Great Plains. Starting in the 19th century, however, this habitat diminished due to its conversion to croplands and pastures for agriculture, which in turn decimated the prey base that the ferrets relied upon, particularly their preferred prey, prairie dogs. In addition, diseases such as sylvatic plague also caused populations of black-footed ferrets to decline. Due to these declines, black-footed ferrets were listed as endangered in the USA in 1967 but then eventually presumed extinct in 1979.

Capone, the black-footed ferret. Photo credits: Paul Marinari (NZCBI). Image provided by Klaus-Peter Koepfli.

Fortunately, in 1981 a single, small population of ferrets was discovered near Meeteetse, Wyoming. The last surviving individuals of this group were used to start an ex-situ captive breeding program through the coordination of the U.S. Fish & Wildlife Service and multiple Association of Zoos & Aquariums (AZA) zoos. As a result of these joint efforts, a species recovery plan was developed and implemented for what continues to be one of the most ambitious conservation breeding and reintroduction program in North America, with more than 10,000 black-footed ferret kits having been born since 1986. Today, about 650 ferrets are living either in captivity or in the wild.


Despite these successes, black-footed ferrets still remain at risk of extinction due to disease susceptibility and multiple genetic challenges that may be related to the small number of founders (only 7) that were used to initiate the conservation breeding program. Previous studies using traditional genetic markers have shown that modern black-footed ferrets have low genetic variation. Further analyses using genomic data will provide a more in-depth view of genetic erosion, inbreeding levels, and mutational load, all of which can affect fitness. Black-footed ferrets are also the focus of ongoing efforts to support the species’ recovery through biotechnology tools such as interspecies somatic cell nuclear transfer, which led to the first female cloned black-footed ferret, ‘Elizabeth Ann’ (Wisely et al., 2015). Such studies are greatly facilitated by generating and using an annotated reference genome assembly (Formenti et al. 2022).


Today, we release the chromosome-length assembly of a male black-footed ferret named ‘Capone’ that came from the ferret conservation breeding colony at the Smithsonian’s National Zoo and Conservation Biology Institute in Front Royal, Virginia. Capone was selected because this animal is partly descended from the last wild-caught male in Meeteetse, WY. The draft assembly was generated using a combination of 10X Genomics linked-reads, done at HudsonAlpha Discovery in Huntsville, Alabama, and optical mapping data generated by Bionano Genomics in San Diego, California. The draft was then upgraded to chromosome-length using Hi-C data generated by the DNA Zoo team. We are already using this assembly for in-depth studies on the conservation genomics of this iconic species.


The assembly contains 19 chromosome-length scaffolds, consistent with the 2n=38 karyotype. This differs from the 2n=40 of a closely related domestic ferret M. putorius furo. The difference is due to the largest chromosome in the black-footed karyotype (HiC_scaffold_1 in the musNig1_HiC assembly) corresponding to two separate chromosomes in the domestic ferret. Browse this chromosomes and and the remaining 18 of them in the interactive Juicebox.js session below, and don't forget to check out the corresponding assembly page.

Blog post by Sergei Kliver, Paul Marinari, and Klaus-Peter Koepfli.

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