• Ruqayya Khan

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).

18 views0 comments

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!

50 views0 comments
  • Ruqayya Khan

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!

25 views0 comments