Captivating callimicos

Found in the upper Amazon rainforests of southern Colombia, eastern Peru, western Brazil, and northern Bolivia, the Goeldi's marmoset or Goeldi's monkey (Callimico goeldii) are one of a kind. They are the only species classified in the genus Callimico and are often referred to as “callimicos”.

Photo Description - Springtamarin (Callimico goeldii) Photo Credit – Matthias Buehler licensed under CC BY-NC-SA 2.0 [source link: https://search.creativecommons.org/photos/c5dd489f-ce18-45e3-8dde-47771b5a279e]

Goeldi’s monkeys are covered in shaggy, black hair, with possible lighter coloration around the face. Longer hairs form a mane draping from the neck and shoulders extending to the base of the tail. They have claw like nails on all digits except their large toe. The average height of these monkeys is 21 to 23 centimeters (25 to 32 centimeters including the tail).

Although the species are part of the Callitrichidae family, which includes marmosets and tamarins, the Goeldi's monkeys have many characteristics to set them apart. For example, they have three molars instead of two, they give birth to single young rather than twins, and males take on less child-rearing roles than other callitrichids.

Callimico goeldii feeds on a diet primarily of fruits, insects and small vertebrates. Unlike any other New World monkey, they also rely on mushrooms during the dry season as their main source of food when fruit is scarce. Although they feed in fruiting trees as groups, they often hunt individually – leaping to the group to find small vertebrates.

Goeldi’s monkey appears on the IUCN list as vulnerable. Potential habitat loss is considered their main threat due to proposed plans for human development and logging in their land areas.

Today, we share a 1K chromosome-length assembly for Goeldi's monkey. The assembly is based on two opportunistic blood samples: one donated by Peach, a Goeldi's monkey at the Houston Zoo, and another one from Ede at the Shedd Aquarium. The first one was used to generate the short-read sequencing draft, and the second one to create a Hi-C library for chromosome-length scaffolding. We thank the animals and their veterinary teams for their help with the samples! We are also grateful to DNA Zoo Australia team at the University of Western Australia and Pawsey Supercomputing Centre and computational support for the assembly.

See below the whole-genome alignment plot for the relationship between the 24 chromosomes in the new assembly and the 23 human chromosomes, as well as the interactive Hi-C contact map visualized using Juicer.js. Check out the assembly page for more details as usual!

Whole-genome alignment plot between the Goeldi's monkey chromosomes from the new assembly (Callimico_goeldii_HiC) and those of human (based on GRCh38 assembly).

Blog by: Ashling Charles and Parwinder Kaur

Not to be sold short

Seba's short-tailed bats (Carollia perspicillata) are a member of the Phyllostomidae family, or New World leaf-nosed bats. Their unique nose structure allows for precise echolocation, although the eyesight and sense of smell are excellent as well [1]. The Seba's short-tailed bat in particular have been shown to have the most directional sonar beams when compared to other echolocating bats [2].

They are also known as the short-tailed fruit bats, their primary food source the many fruit species native to Central and Southern America. Outside of fruiting season, Seba's short-tailed bats supplement their diet with nectar and pollen. Consequentially, the Seba's short-tailed bat play an integral role in the pollination and seed dispersal for a number of plant species in the forests they inhabit [3].

Seba's Short-tailed Bats (Carollia perspicillata) group roosting in old building, photo by Bernard Dupont [CC BY-SA 2.0], via flickr.com

Today, we share the chromosome0-length genome assembly for Seba's short-tailed bat. This is a Hi-C upgrade from the short-read draft (CarPer_v1_BIUU / GCA_004027735.1, cN50=10.3kb; sN50=10.7kb) generated by the Zoonomia Consortium (Genereux et al., Nature, 2020). We thank the Houston Zoo for providing us with the sample for the Hi-C upgrade!

Carollia perspicillata has one of the smallest chromosome numbers reported for bats: in agreement with the assembly, the expected karyotype is 2n=20 for XX females (and 2n=21 for males). This is our 10th Chiroptera species we've released here at the DNA Zoo, giving us an opportunity to finally explore the unusual karyotype of the species as compared to other bats.

Check out below how the 1o assembled chromosomes of the Seba's short-tailed bat relate to those of the straw-colored fruit bat and the large flying fox from among the bat species previously released. We include also the interactive contact map for the chromosomes below!

Whole-genome alignment plots between the 10 chromosomes of Seba's short-tailed bat and those of the straw-colored fruit bat (ASM46528v1_HiC) and large flying fox (Pvam_2.0_HiC).

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!