Ruff day

The black and white ruff lemur, Varecia variegata, are one of the largest pollinators in world [1]! Their diet consists mostly of fruit and nectar, which they can eat thanks to their especially long tongues. When eating the nectar of flowers, pollen sticks to their fluffy neck fur and faces, allowing cross-pollination to occur [1]. Found only in Madagascar, the black and white ruffed lemur is critically endangered.

Today, we share the genome assembly for the black and white ruff lemur, Varecia variegata. This is a $1K genome assembly with a contig N50 = 40 Kb and a scaffold N50 = 129 Mb (browse the chromosomes in the interactive map below). For assembly procedure details, please see our Methods page. Many thanks to the Duke Lemur Center for providing the sample used for this genome assembly! Consider symbolically adopting a lemur here, to support animal care at the Duke Lemur Center as well as conservation programs in Madagascar.

This is the 7th lemur species we've released here on the DNA Zoo! Check out the assembly pages for these fascinating primates, Blue-eyed black lemur (E. flavifrons), Mongoose lemur (E. mongoz), Gray mouse lemur (M. murinus), and finally the Coquerel's sifaka (P. coquereli). For some preliminary analysis, we've aligned the assembly of the black and white ruff lemur, Varecia_variegata_HiC against the collared lemur, Eulemur_collaris_HiC.

Whole genome alignment plot of the black-and-white ruffed lemur (Varecia_variegata_HiC) against the collared lemur (Eulemur_collaris_HiC)

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.