Right off the bat

Affectionately called "sky-puppies" for their puppy-like faces, the Rodrigues flying fox is a member of the Old World mega-bats genus Pteropus. They're one of 60 extant species in this genus, found mainly on the Rodrigues Island in the Indian ocean. Much like other flying foxes, the Rodrigues flying fox is highly sociable species and may live in roosts as large as 500 individuals! Sadly, due to habitat loss and the slow gestation rate of this species, the Rodrigues flying fox is endangered in the wild according to the IUCN red list. Fortunately, breeding programs in zoos and conservation groups have been successful and the species has an upward population trend.

Rodrigues Flying Fox, Pteropus rodricensis by Josh More, [CC BY-NC-ND], via inaturalist.org

Today, we release the chromosome-length assembly for the Rodrigues flying fox, Pteropus rodricensis! This is a $1K-model genome, with a contig n50 = 324 Kb and a scaffold n50 = 113 Mb. For more details on our assembly procedure, please see our Methods page. We graciously thank Moody Gardens for providing the sample used to generate this genome assembly.

This is the 4th Pteropus species we've released here and the 14th bat species overall! For some preliminary analysis, we've aligned the Rodrigues flying fox against the other 3 species in our collection: Large flying fox (P. vampyrus), Madagascan flying fox (P. rufus), and the Indian flying fox (P. giganteus). The karyotype (2n=38) seems to be conserved throughout the genus:

Whole-genome alignment plots between the chromosome-length Rodrigues flying fox and the other flying foxes in the DNA Zoo collection: left to right Pteropus vampyrus, Pteropus rufus, and Pteropus giganteus.

Please check out the 19 chromosomes of the Rodrigues flying fox in the interactive JuiceBox.js session below:

Thumbs up for this genome

The Angolan colobus, Colobus angolensis, is an Old World monkey species found in dense rain forests of the Congo region in Africa. One of the several colobus monkey species, the Angolan colobus is identifiable by their long, glossy black and white hair. The term colobus means "short" or "incomplete" in reference to their small thumbs. This tiny digit is not a hinderance, rather a useful adaptation that allows the colobus monkey to swing from tree brach to tree branch more easily by using their hands like hooks [1].

Angola Colobus Monkey by Ryan Poplin, [CC BY-SA 2.0], via flickr.com

Today, we release the chromosome-length upgrade for the Angolan colobus monkey, Colobus angolensis, based on the draft assembly by the Human Genome Sequencing Center (BCM-HGSC) at the Baylor College of Medicine. We graciously thank the San Antonio Zoo for donating the sample used to generate this upgraded assembly! For details on our assembly procedure, please see our Methods page. Check out the 22 chromosomes of the colobus monkey in the interactive Juicebox.js session below:

We've released chromosome-length genome assemblies for over 20 primate species here on the DNA Zoo website! The Angolan colobus will be the 7th Old World monkey species in our collection. For some preliminary analysis, we've aligned the Angolan colobus (Cang.pa_1.0_HiC) to the Guinea baboon (Papio_papio_HiC), another Old World monkey.

Whole genome alignment of the Angolan colobus (Cang.pa_1.0_HiC) to the Guinea baboon (Papio_papio_HiC).

The mysterious marsupial

The southern marsupial mole (Notoryctes typhlops), also known as the itjaritjari or itjari-itjari, is a mole-like marsupial found in the western central deserts of Australia. It spends the majority of its life tunneling beneath Australia’s vast red deserts. Survival in this unforgiving habitat requires a whole array of specialized traits. For example, the marsupial mole has vestigial eyes that lack both a lens and a pupil hidden beneath delicate, round eyelids with fused lids. To find their way in the perpetual darkness, the mysterious marsupials instead rely on a keen sense of smell and acute hearing.

Southern marsupial mole (Notoryctes typhlops) Photo Credits & acknowledgements – Photograph by Mike Gillam ©2019 California Academy of Sciences

A number of other adaptations like fused neck vertebrae with bulldozer-like rigidity, bony armor protecting the snout and Lobster-like claws on the forelimbs make this ground dweller a powerful digging machine. When doing what it does best, this energetic digger virtually swims through the sand in search of ants and juicy beetle larvae.

Like so many Australian mammals, female marsupial moles have a pouch in which their young complete their development. Interestingly the mole’s pouch opens toward the back, an adaptation that protects young moles from being inundated with sand as the mother burrows.

Despite the physical similarities between marsupial moles and true moles, the two lineages are only very distantly related, having likely diverged during the Mesozoic Era (~160 million years ago). Further, molecular data suggests that Notoryctemorphia separated from other marsupials around 64 million years ago (1). The resemblance between true and marsupial moles is a classic example of convergent evolution, a process by which two distantly related species, or groups, evolve similar traits in response to a similar set of environmental conditions.

DNA Zoo has been working with Prof. Andrew Pask and Dr. Stephen Frankenberg from the University of Melbourne, Australia to develop genomic resources for the species. We combined 3,530,386 Nanopore reads (~9x coverage) provided by the Pask lab, University of Melbourne with 239,676,293 PE Illumina WGS reads and 681,381,650 PE Hi-C reads generated by the DNA Zoo labs to generate a chromosome-length assembly, shared today! The genome was generated using wtdbg2, 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details!

This effort has been supported by Oz Mammals Genomics initiative, a Bioplatforms Australia framework initiative, building genomic resources for conservation through a thorough understanding of the evolution of Australia’s unique mammals that are now under threat, through climate, disease or habitat modifications.

The Hi-C work was supported 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, the Government of Western Australia. The team thanks Zhenzhen Yang from ShanghaiTech, DNA Zoo China, for her help with the contigging of this genome assembly.

Check out the interactive contact map of the southern marsupial mole-rat below, and don't forget to visit the assembly page for more information.

Citations

1. Kirsch, J,A.W.; Springer, Mark S.; Lapointe, François-Joseph (1997). "DNA-hybridization studies of marsupials and their implications for metatherian classification". Australian Journal of Zoology. 45 (3): 211–80. doi:10.1071/ZO96030.