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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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Happy Year of the Rabbit everyone! To celebrate, we share the chromosome-length assembly of the New England cottontail, Sylvilagus transitionalis, the only rabbit native to parts of New England and eastern New York.

The New England cottontail, Sylvilagus transitionalis, was once a widespread rodent across the North East. However, as their preferred habitat of forest thickets declined due to urban development, so did the wild population of the New England Cottontail. Today, biologists believe there are only around 13,000 New England cottontails left. Read more about efforts to restore the New England cottontail on

New England cottontail rabbit by Steve McDonald, [CC BY 2.0], via

New England cottontails are medium-sized rabbits that look a lot like eastern cottontails except for the fact that they have black hair on the front side of the ears and between their ears (appropriate for the Year of the Black Rabbit!). Females are larger than males. And it was a female sample that we received via the T.C. Hsu CryoZoo from the M.D. Anderson Cancer Center, originally frozen back in 1979! Using the sample, we generated a short-read genome assembly (contig N50 = 24Kb, scaffold N50 = 79Mb).

Browse the 23 chromosomes of the New England cottontail, Sylvilagus transitionalis in the interactive Juicebox session below, and find more information and links on the corresponding assembly page!

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African elephants of which there are two species (the savanna elephant Loxodonta africana, and its smaller cousin, the forest elephant Loxodonta cyclotis), are the largest terrestrial animals on Earth. African savanna elephants, for which we provide an upgraded chromosome-level genome assembly, are found in 24 sub-Saharan African countries and occur in a variety of habitats from open and wooded savanna to desert (Gobush et al. 2021). Along with the lion, leopard, black rhinoceros and African buffalo, the African savanna elephants are part of the Big Five, a term used to describe the most iconic of Africa's large mammals.

A group of elephants at the Addo Elephant National Park, South Africa. This population is known for the high number of tuskless females (Whitehouse, 2002). RJ van Aarde, Conservation Ecology Research Unit, University of Pretoria (South Africa).

Afrotheria phylogeny

Afrotheria (from Latin Afro- "of Africa" + theria "wild beast") represents one of the most eutherian mammals’ ancient clades that includes six mammalian orders all with an Afro-Arabian origin. The group comprises golden moles, elephant shrews, tenrecs, aardvarks, hyraxes, elephants and sea cows (dugongs and manatees). The afrotherian species exhibit extreme morphological diversity and niche preference, which is thought to result from the long period of isolation when Africa was an island continent 105-125 mya (Meredith et al., 2011). Genome organization within Afrotheria is diverse, with diploid numbers ranging from 2n = 54 in the African and Asian elephants to 2n = 20 in the aardvark (Robinson and Seiffert, 2004; Ruiz-Herrera et al. 2012).


Concerns about Africa’s elephant numbers have led to savanna elephants being categorized as Endangered, and forest elephants as Critically Endangered by the IUCN (International Union for Conservation of Nature) (Gobush et al. 2021a and 2021b). The greatest threat to Africa’s elephants is ivory poaching and habitat loss, primarily through agriculture, often leading to human-elephant conflict (Borchert 2022). The increasing fragmentation of suitable elephant habitat due to altered land-use led to suggestions that ~70% of their current distribution may fall outside of protected areas, and that savanna elephants may persist in only 15 percent of their historic pre-agricultural range (Chase et al. 2016).

The effects of habitat alteration and poaching extend beyond the threat of possible elephant extinction. Elephants play a significant role in savanna ecosystems by altering the physical environment, facilitating seed dispersal and though the creation of microhabitats¾it seems inescapable that declining elephant densities will result in a cascade of consequences for other savanna species (Robson et al. 2017).


Today, we share the upgraded chromosome-level genome for the savanna elephant Loxodonta africana! This genome assembly was based on the Loxafr3.0 draft genome assembly generated by the Broad Institute (Di Palma, F., Heiman, D., Young,S., Johnson,J., Lander, E.S. and Lindblad-Toh, K.). The Hi-C data was generated from cryopreserved fibroblast cell cultures that form part of the South African National Biodiversity Institute Biobank collection (Alvarez-Gonzalez et al. 2022). For more details on our assembly procedure, please see our Methods page. Finally, don't forget to check out the interactive Juicebox.js session below featuring the chromosomes (2n=54) of the African savanna elephant below!


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