Gibbon take

The agile gibbon, Hylobates agilis, is a species of Old-World primate also known as the black-handed gibbon. It is found in Sumatra southeast of Lake Toba and Singkil River, in a small area on the Malay Peninsula, and south Thailand near the Malaysian border. They predominantly live in rainforests where their long arms help them swing from branch to branch with ease.

By Julielangford - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=7428342

Gibbon pairs are monogamous, whereby mated pairs stay together until one mate dies. The species becomes sexually mature around 8 years of age. The gestation period is around 7 months. Agile gibbons give birth to a single offspring per pregnancy, and around 5-6 offspring during their lifetime. The female gibbons care for their offspring until they are around 2 years old. Males participate in parental care grooming offspring and helping defend them.

Agile gibbons are highly vocal, using their vocalizations to defend their territories from other mated pairs. This is known as “singing” where in the early morning great calls can be heard, often as duets, as a way of claiming home territory. When singing is not enough the pairs will chase intruders away.

Hylobates agilis is listed as "endangered" by IUCN, the key reasons being deforestation leading to loss of habitat. Conservation measures such as breeding programs and reserve game parks have been implemented to combat the species decline, but it is yet to be seen if the measures are to be effective.

Today we share a $1K chromosome-length assembly for the agile gibbon (cN50=36kb; sN50=94Mb), generated using samples donated by Susie, an agile gibbon from the Houston Zoo. Check out this photo of her created by Joel Sartore for the National Geographic Photo Ark!

Check out below how the 22 chromosomes of the new assembly relate to those of humans. The whole-genome alignment plot suggests multiple rearrangements, in agreement with the previously noted propensity for unusually high number of large-scale chromosomal rearrangements in gibbons in comparison to the inferred ancestral ape karyotype [1]. Given the relatively recent differentiation of these genera (4–6 million years ago (Myr ago), this constitutes an extraordinarily fast rate of karyotype change. Check out the exciting work by Carbone et al., Nature 2014 for the investigation of possible causes in the white-cheeked gibbon Nomascus leucogenys. We look forward to using the agile gibbon genome assembly to investigate the question further.

Whole-genome alignment of the new agile gibbon genome assembly (Hylobates_agilis_HiC) to the human chromosomes (GRCh38 assembly). A great many rearrangements are visible on the plot, in agreement with the suggested fast karyotype evolution of gibbons seen previously, e.g. for the white-cheeked gibbon (Carbone et al., 2014).

Browse below the interactive contact map for the agile gibbon and don't forget to visit the corresponding assembly page for more information and details!

We gratefully acknowledge Houston Zoo for providing the sample for this work. We also thank the DNA Zoo Australia team at the University of Western Australia and Pawsey Supercomputing Centre for the computational support for this genome assembly.

Blog by: Ashling Charles, Olga Dudchenko, Parwinder Kaur

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).