Unbe-leaf-able noses

The Jamaican fruit bat, Artibeus jamaicensis, is a member of the New World leaf-nosed bats, Phyllostomidae. The unique nose shape of the fruit bat plays a role in echo location, modifying and directing echolocation calls. While they are commonly referred to as the Jamaican fruit bat, they are actually widely distributed geographically. One could find the species from Southern Mexico, to northwestern South America. They seem to thrive even despite habitat destruction, and are of least concern for conservation status [1].

Artibeus jamaicensis by Mark Yokoyama, [CC BY-NC-ND 2.0], via flickr.com

Today, we share the chromosome-length upgrade for the Jamaican fruit bat, Artibeus jamaicensis, based on the draft assembly by Wang et. al (2020). The sample used for this upgrade was a primary fibroblast cell line provided by the T.C. Hsu Cryo-Zoo. We thank Drs. Asha Multani, Sen Pathak, Richard Behringer, Liesl Nel-Themaat and Arisa Furuta in the Department of Genetics at the MD Anderson Cancer Center for their help with this sample.

This cell line was originally frozen back in 1974 and was still thriving, see the picture below!

A. jamaicensis primary fibroblast cell line; Magnification: 4X

This is the 13th Chiroptera species we've released here on the DNA Zoo blog! Subscribe below for more weekly releases. While you're here, don't forget to check out the interactive Hi-C contact map for the 15 chromosomes of Artibeus jamaicensis below!

Wonderful wambenger

The wambenger brush-tailed phascogale (Phascogale tapoatafa wambenger), also known by its Noongar name “wambenger”, is a rat-sized arboreal carnivorous marsupial with a characteristic tuft of black silky hairs on the terminal portion of its tail. This phascogale of the family Dasyuridae is one of the thylacine’s close living relatives, last sharing a common ancestor 35-46 million years ago.

Photo Description: Brush-tailed phascogale (Phascogale tapoatafa). Photo credits: Jimmy Lamb

The term Phascogale was coined in 1824 by Coenraad Jacob Temminck in reference to the brush-tailed phascogale, and means "pouched weasel". Phascogales do not have a true pouch that is found in most other marsupials. Instead, they form temporary folds of skin, sometimes called a "pseudo-pouch", around the mammary glands during pregnancy. Young stay in this pseudo-pouch area, nursing for about 7 weeks before being moved to a nest where they stay until they are weaned at about 20 weeks of age.

Phascogales are mostly carnivorous and hunt small mammals, birds, reptiles, insects, spiders, and centipedes. They have been known to kill and eat chickens, and they generally avoid eating carrion. They are mainly arboreal and have been known to feed on the nectar of eucalyptus flowers. Brush-tailed phascogale is considered effective at helping to control insect and rodent pest populations since it is a natural predator of these animals.

The brush-tailed phascogale has a widespread but fragmented distribution throughout all states of Australia, excluding Tasmania. As a result of habitat destruction and predation by the red fox and feral cat, they are believed to have disappeared from roughly half of their former range. The species is considered very vulnerable to localised extinction.

Wambenger is listed as ‘near threatened’ on the Red List of the International Union for the Conservation of Nature and Natural Resources.

Today we share the chromosome-length assembly for the brush-tailed phascogale. The assembly was generated using the sample provided by Dr Kenny J. Travouillon from the Western Australian Museum in collaboration with Dr Renee Catullo from the University of Western Australia. This is a short-read Illumina assembly, see our Methods page for more detail on the assembly procedure, and check out the interactive map of the phascogale chromosomes below!

The work was enabled by resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

Aye-aye captain

Perhaps one of the most peculiar species of primates, the aye-aye (Daubentonia madagascariensis) is a nocturnal, arboreal insectivore is found only in Madagascar. It is believed that the common name for this species came from the "exclaim of surprise and astonishment" by the French naturalist Pierre Sonnerat at the sight of the animal. However, it was later pointed out that the name is quite similar to the Malagasy name for the animal "hai hai" [1].

Aye-aye by nomis-simon, [CC BY 2.0], via wikimedia.org

Aye-ayes spend the majority of their lives in solitude in the canopies of the forests. The most notable characteristic of the aye-aye is their long, skeletal middle finger which is used to tap into trees to unearth larvae using a method called "tap foraging". The aye-aye is the only primate to use echo-location, and it's middle digit serves as it's primary sensory organ. Their odd appearance may have contributed to the superstition by some natives of Madagascar that they are an incredibly unlucky omen. Unfortunately this has led to many being killed onsite [3]. Coupled with deforestasion this has led to the aye-aye becoming endangered (see IUCN).

Today we share the genome assembly for the aye-aye, Daubentonia madagascariensis. This is a $1K genome assembly, with a contig N50 = 215 Kb and a scaffold N50 = 211 Mb. For assembly procedure details, please see our Methods page. We graciously thank the Duke Lemur Center for providing the sample used to generate this chromosome-length assembly. Please check out the interactive Juicbox.js session below to explore the 15 chromosomes of the aye-aye:

Upon its initial classification, the aye-aye was believed to be a kind of rodent. This was a understandable presumption, as the aye-aye has ever growing incisors that are characteristic of the order Rodentia. Their cat-like face also led to some debate whether the aye-aye should be a a felid. Eventually, it was established that aye-ayes are lemurs! For some preliminary analysis, we aligned the new chromosome-length aye-aye reference, Daubentonia_madagascariensis_HiC (2n=30) against the collared lemur assembly Eulemur_collaris_HiC (2n=50), see the dot plot below. There are a large number of rearrangements between the two genomes underlying the different chromosome count.

Whole genome alignment plot between the aye-aye, (Daubentonia_madagascariensis_HiC) (2n=30) against the collared lemur, (Eulemur_collaris_HiC).

We're not monkeying around here, this is the 6th Lemuroidea species we've released so far and the 20th primate overall! Check out these other $1K assemblies for the Guinea baboon (P. papio), the golden lion tamarin (L. rosalia), and the Patas monkey (E. patas). Remember to follow us on Twitter @thednazoo and subscribe to our mailing list below to keep up to date on our latest releases!