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

sMartening up

The yellow-throated marten (Martes flavigula) is a flamboyant oddball in the genus Martes, which also includes the sable, pine marten, stone marten, Japanese marten, and American martens. Unlike any other marten species, yellow-throated martens hunt in packs, usually made up of siblings, and are frighteningly good at that: they successfully take down much bigger animals, such as water deer and macaques. In fact, they appear to be much more advanced socially than their loner relatives – while the overall color of their coat is an olive-tinged agouti-to-black gradient, providing good camouflage in lush foliage, some markings almost definitely serve the purpose of biocommunication: the contrasting black head and white chin, bright yellow chest, and long, black tail are amazingly similar to patterns seen in highly social simians, such as squirrel monkeys.

Martes flavigula, yellow-throated marten by Rushen, [CC BY-SA 2.0], via flickr.com

As of now, the yellow-throated marten is listed as LC (Least Concern) by the IUCN due to wide distribution and considerable numbers, as well as its presence in a number of protected territories. However, like most other martens, it prefers large continuous stretches of old-growth primeval forests, and uncontrolled logging and consequent habitat fragmentation and loss are causing an ongoing decline of its numbers in some parts of its range, which stretches from Pakistan in the west to the Russian Far East in the east and the island of Borneo in the south. In the Russian Far East, the yellow throated-marten, locally known as kharza, coexists with another member of the genus - the sable (Martes zibellina), albeit not always peacefully.

The unusual for martens combination of morphological, genetic and behavioral differences has led some researchers to believe that Martes flavigula, together with its sister species, the Nilgiri marten (Martes gwatkinsii) should be assigned a genus of their own. Further genomic research will help to assess whether this suggestion is founded. Moreover, the species as a whole is poorly studied, and there are reasons to believe that some of the isolated patches that make up its range may in fact host distinct subspecies or even separated species.

Today, we present the chromosome-length assembly for the third marten species of this year. All C-scaffolds of the yellow-throated marten were assigned to the corresponding chromosomes via a Zoo-FISH experiment with the stone marten chromosomes used as probes. In contrast to other marten species, Martes flavigula have more chromosomes: 2n=40 instead of 2n=38. (Fig. 1): you can see the chromosome corresponding to chr8 in the stone marten into two chromosomes (chr9 and 19) in the yellow-throated marten in the whole-genome alignment plot below!

Figure 1. Dotplot for whole genome alignment of yellow-throated marten genome to stone marten assembly

We thank Dr. Rogell Powell (North Carolina State University) for funding 10x Genomics linked-read sequencing for the draft assembly and Dr. Klaus Koepfli and Dr. Alexander Graphodatsky for organizing this sequencing and bringing all of the collaborators together. Also we thank Olga Shilo (deputee director), Rosa Solovyova (head of carnivore department) and Svetlana Verkholantseva (veterinarian) from Rostislav Shilo Novosibirsk Zoo (Russia, Novosibirsk) who provided samples for a cell line. Samples were collected postmortem from a 15-year old male individual called Dixi. These cells were used for both DNA extraction for linked read sequencing and for the Hi-C experiment. DNA extraction and Zoo-FISH experiments were performed by Natalia Serdyukova and Dr Violetta Beklemisheva. The initial assembly was performed by Sergei Kliver. Hi-C experiments and scaffolding to chromosomes were done by Dr. Polina Perelman, Ruqayya Khan and Dr. Olga Dudchenko. The genome annotation and a paper describing this research is in progress.