For goodness saki

The white-faced saki (Pithecia pithecia) are sometimes known as "flying monkeys" as they're able to leap as far as 30 feet between tree branches [1]! These flying monkeys are not native to the land of Oz, but instead can be found inhabiting the rainforests of Brazil and some parts of Venezuela.

Male white-faced saki, photo by Rene Mensen [CC BY-NC 2.0], via flickr.com

The common name of this species is inspired by the distinctive pale mask of fur of male saki (see photo above). However, this species of monkey exhibits strong sexual dimorphism. Female white-faced sakis actually are completely covered in dark brown or black fur with no discernible white patch on the face, despite the name! While both male and female monkeys are similar in appearance at birth, the unique white mask in males forms as they mature over the next 3-4 years [2].

White-faced saki's diets primarily consist of fruits, seeds, and they will occasionally consume small mammals or birds. Due to their diets, the white-faced saki plays a large role in native ecosystems dispersing seeds in their waste miles away from the source [3]. While the wild population of white-faced saki is considered to be of least concern by the IUCN, their population is in a declining trend. White-faced saki's are common in the pet trade due to their charisma and availability. If the wild populations cannot mate fast enough to replace the individuals that are captured, this may lead to fracturing populations [4].

Today, we share the chromosome-length assembly of the white-faced saki named Jolene from the Houston Zoo. This was one of the very fist samples we have collaborated on with the Houston Zoo, and only the 16th sample in our collection! This is a $1K genome assembly (cN50=53kb; sN50=104Mb): for more details see our Methods page.

See below how the 24 chromosomes of the white-faced saki relate to our own 23 chromosomes. Despite the proximity in the chromosome count, the chromosomes appear to be very different, with a lot of rearrangements that have accumulated in the approximately 43M years separating us and the saki monkey [5].

Whole-genome alignment of the white-faced saki chromosomes from the new assembly to those of the human (assembly GRCh38).

See the interactive contact map of the chromosomes below, and don't forget to follow up to the assembly page for more info!

I'm all ears

The bat-eared fox (Otocyon megalotis) is a type of canid native to the African savanna. Bat-eared foxes are not considered true foxes (Vulpes) and instead belong to their own distinct genus (Otocyon). The term 'Otocyon' is derived from the Greek words 'otus' for 'ear' and 'cyon' for 'dog'. Their large ears are used for hunting, and for keeping cool in the sweltering heat.

Photo Description – Bat-eared fox (Otocyon megalotis) at Kgalagadi Transfrontier Park, Northern Cape, South Africa Photo Credits and acknowledgements – Derek Keats from Johannesburg, South Africa, CC BY 2.0, via Wikimedia Commons

Bat-eared foxes are the only canids which are truly insectivorous. They subsist almost entirely on harvester termites and dung beetles. They use their large ears to listen for insects or beetle larvae hatching from dung. Bat-eared foxes are greatly beneficial to farmers. They help control the populations of harvester termite populations, which devastate a variety of crops. If termites are not available, the bat-eared fox will also eat other insects and arthropods, and occasionally, birds and small animals.

A family of bat-eared foxes typically consists of the father, mother, and a litter of pups. Unlike other canids, males take on most of the parental care, protecting, grooming, and playing with the pups while the female is out foraging.

They are currently classified as a species of least-concern. However, as human populations continue to increase, a threat they face is a loss of habitat. In some countries, they are seen as a threat to small livestock. Indigenous peoples in Botswana hunt them for their fur, while they are hunted as game in South Africa.

Today, we share a chromosome-length assembly for the bat-eared fox. This is a Hi-C upgrade to a draft genome assembly published recently by Rémi Allio, Frédéric Delsuc and team at Université de Montpellier (Allio et al., 2021) as part of the ongoing ConvergeAnt project (https://www.convergeant-project.com). The sample for the Hi-C upgrade was donated by the Oklahoma City Zoo. Special thanks also to Pawsey Supercomputing Centre and DNA Zoo Australia team at the University of Western Australia for computational support of the upgrade.

Check out below how the chromosomes of the bat-eared fox relate to those of the dog (Canis lupus familiaris) and explore the interactive contact map for the 36 chromosomes. More data and links related to this assembly can be found on the corresponding assembly page!

Whole-genome alignment plot showing the correspondence between the chromosomes of the dog (2n=78, CanFam3.1) and the new bat-eared fox genome assembly (2n=72, Otocyon_megalotis_TS305_17_09_2019_HiC).

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 flickr.com

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 www.dnazoo.org.

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