PMMC helps assemble the Guadalupe fur seal

Guadalupe fur seals (Arctocephalus townsendi) are members of the “eared seal” family. Their breeding grounds are almost entirely on Guadalupe Island, off the Pacific coast of Mexico, with recent re-colonization of the islands comprising the San Benito Archipelago. A small number of Guadalupe fur seals have also been reported on the northern Channel Islands off California. [1]

The Guadalupe fur seals were thought to be extinct in the early 1900s. Since their rediscovery in 1954 their population has been steadily increasing (at about 6% rate) thanks to protection by the Mexican government, but Guadalupe fur seals are still listed as threatened under the Endangered Species Act and depleted under the Marine Mammal Protection Act. [1]

Today, together with the Pacific Marine Mammal Center we share the chromosome-length assembly of the Guadalupe fur seal. Read below the story behind the sample used to generate this genome assembly.

Pacific Marine Mammal Center received a call about a very lethargic animal that has stranded itself at the edge of the Wedge Jetty in Newport Beach, CA. As soon as the team saw the photo they knew it was an endangered Guadalupe fur seal and sent a team right away. Two members of the PMMC animal care rescue team responded. As harbor patrol was busy at the time, the team made the mile round trip trek on the jetty rock to rescue the animal (capture was authorized under NOAA Fisheries Permit # 18786-05).

Juni, the Guadalupe fur seal at the Pacific Marine Mammal Center. NOAA Permit # 18786-05.

Once back at the center, the animal, the team names Juni, was examined and determined to be a male, yearling at only 26.7 pounds, emaciated, malnourished and dehydrated.

Over the next few days the animal was under close observation by the veterinary team, tube fed, and given subcutaneous fluids throughout the day. Though he was showing small signs of improvement showing some strength and vocalization, he took a turn and was found dead 5 days after rescue.

PMMC animal care team tube feeding Guadalupe fur seal upon admittance to center. Tube feedings are used to administer nutrients, medicine and other supplements when the patients are too weak to eat on their own. NOAA Permit # 18786-05.

While Juni’s case is an unfortunate one, his story does not end there. We hope that through the collected genomic data from Juni’s tissues samples, his death can provide insight into the intricate lives of this pelagic species. PMMC is dedicated to working with other organizations like the DNA Zoo and Baylor College of Medicine to support collaborative research for ocean and marine mammal conservation.

We thank Hendrik Nollens, Peter Chang, Alissa Deming, Krysta Higuchi and the rest of the team at PMMC for their help with the Guadalupe fur seal sample.

Check out the interactive contact map of the chromosome-length genome assembly comprising 18 chromosomes below. More details are available on the corresponding assembly page!

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).