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J is for jaguarundi

According to the Cat Classification Task Force of the IUCN Cat Specialist Group jaguarundi (Puma yagouaroundi) is a monotypic species (Kitchener et al., 2017) and one of the three living representatives of Puma lineage diverged from the last common ancestor around 5 million years ago. Historically, jaguarundi was included in the genus Herpailurus, but recently, phylogenetic and phylogenomic studies have positioned it among the Puma lineage together with the African cheetah (Acinonyx jubatus) and the mountain lion (Puma concolor) (Johnson, et al., 2006; Li, et al., 2016; O'Brien, et al., 2008; O'Brien and Johnson, 2007).

Jaguarundi by Cloudtail the Snow Leopard, [CC BY-NC-ND 2.0], via

Jaguarundi displays a very unique appearance among other cats - slender, elongated body, short legs, a small flattened head, long “otter-like” tail, and a sleek, unmarked coat. Coats occur in two main color variations: gray/dark or reddish. Color variants showed significant association with specific habitats, where gray/dark variants are common within moist and dense forests while reddish variants are more prevalent for open and arid areas (da Silva, et al., 2016).

Although jaguarundi is listed as Least Concern on the IUCN Red List they still suffer from population decline due to habitat fragmentation and habitat loss. They are also affected by persecution for killing poultry in local areas. Puma yagouaroundi species is protected over much of its range and hunting is prohibited in Argentina, Belize, Bolivia, Colombia, Costa Rica, French Guiana, Guatemala, Honduras, Mexico, Panama, Paraguay, Suriname, Uruguay, U.S. and Venezuela. In Peru hunting is regulated. They are not legally protected in Brazil, Ecuador, El Salvador, Guyana or Nicaragua.

The first jaguarundi whole genome assembly became publicly available in 2021 (Tamazian et al, 2021). A genome of a male jaguarundi specimen was sequenced with 10X Genomics linked reads and assembled with supernova2. The assembled genome contains series of scaffolds that reach the length of chromosome arms and is similar in scaffold contiguity to the genome assemblies of African cheetah and mountain lion, with a contig N50 = 100.2 kbp and a scaffold N50 = 49.27 Mbp. This assembly was used as a draft for HiC-scaffolding, shared today on

The primary fibroblast cell line (HYA-1) at passage 10 was used to make the Hi-C library. The skin biopsy was collected by Dr. Mitchell Bush (Smithsonian National Zoological Park, Washington DC) in 1981 in Blijdorp Zoo (Rotterdam, Netherlands) from a 9-year old captive breeding male jaguarundi originally from Mexico. The cell line was established by Mary Thompson in December 1981 and stored at the Laboratory of Genomic Diversity headed by Dr. Stephen O’Brien (LGD, Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD) and later the LGD cryo collection was preserved by Drs. Melody Roelke, Carlos Driscoll, Christina Barr and David Goldman. The cells of the primary fibroblast cell line at passage 10 were used for high-molecular weight DNA extraction for 10X Genomics by Nataliya Serdyukova at the (Dr. Grafodatsky’s Laboratory of Animal Cytogenetics at the Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia). This four decades old jaguarundi sample story shows the worthiness of wildlife samples cryopreservation.

Browse the interactive Hi-C contact map showing how the 19 chromosomes of the jaguarundi fold in 3D below and on the corresponding assembly page!

Blog post by Pasha Dobrynin, Polina Perelman, and Sergei Kliver


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