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Cloudy with a chance of leopards

It is estimated that fewer than 10,000 clouded leopards (Neofelis nebulosa) remain in the wild [1].

Almost everything we know about clouded leopards comes from research on captive populations, much of it done by the Smithsonian's National Zoo, Khao Kheow Open Zoo in Thailand, The Zoological Parks Organization of Thailand and Nashville Zoo. Read more (and see how you can help) on the Smithsonian’s National Zoo & Conservation Biology Institute website, here!

To help with the ongoing conservation efforts, in collaboration with our colleagues from the Smithsonian Conservation Biology Institute and the Brigham Young University, we share the chromosome-length genome assembly for the clouded leopard. We thank the Houston Zoo for providing the sample used for Hi-C library preparation!

The draft genome assembly for the clouded leopard was generated by Paul Frandsen and Madeline Bursell at Brigham Young University in collaboration with Warren Johnson and Klaus-Peter Koepfli at the Smithsonian Conservation Biology Institute, and Rebecca Dikow from the Smithsonian Institution Data Science Lab. The draft assembly was generated using MaSuRCA.

See below how the 19 chromosomes of the clouded leopard assembly relate to those of domestic cat (from Pontius et al., Genome Res., 2007). A nice illustration of the highly stable felid karyotype across the ~10.8 million years of cat evolution [2]!

It is interesting to note that our scaffolding revealed a huge, 78Mb inversion on one (not both!) of copies of chromosome 2 in the animal whose genomic material was used for scaffolding. (This chromosome corresponds to cat chromosome 8). The zoo keepers believe the animal to be healthy. By contrast, we found no evidence of the inversion in the leopard used for contigging.

While these types of polymorphic rearrangements have been observed in some mammalian species, this is the first time one has been reported in the cat lineage. We hope to look into this rearrangement and its prevalence in the clouded leopard population further, so stay tuned!

Whole-genome alignment between the new clouded leopard genome assembly (Neofelis_nebulosa_HiC) and the genome assembly of the domestic cat (Felis_catus_8.0) (left); rearrangement on one of the copies of chr2 (cat homolog chr8) (right). A leopard may not be able to change its spots, but it sure can change its dot plots!


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