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.

Our two scents on skunk genomics

Spilogale interrupta is one of 4 newly-recognized species of spotted skunks in the United States. The taxonomy of spotted skunk is currently under revision with new analyses of nuclear and mitochondrial DNA suggesting a rapid speciation and expansion of these small carnivores [1, 2]. Until a few decades ago, S. interrupta, or the plains spotted skunk, was abundant and wide-spread from eastern Texas through most of the Great Plains to Canada. The closely related eastern spotted skunk (S. putorius) is found east of the Mississippi River, while the western (S. gracilis) and desert (S. leucoparia) share a boundary to the west. In Texas, Oklahoma, Colorado, Wyoming, and Montana it was possible to find two of the spotted skunks (S. interrupta and S. leucoparia or S. gracilis) on the east and west portions of the state. Despite the recent speciation events, S. interrupta is a true biological species. While it’s close relatives and next door neighbors, S. leucoparia or S. gracilis, exhibit delayed implantation of embryos, the plains spotted skunk shows no such reproductive strategy [3]. The mating seasons of these small carnivores differ, with S. interrupta mating in early spring (March-May) while S. leucoparia and S. gracilis breeding in early fall (August – October). All species give birth in spring. These differing reproductive strategies limit the opportunities for hybridization.

Plains spotted skunk, photo by Robert C. Dowler, Angelo State University [CC]

Spotted skunks are habitat and dietary generalists. They are strictly nocturnal and daytime pictures (like the one below) are usually obtained when releasing an animal after live-capture and handling. Although rare throughout their range, recent motion-activated camera trapping produced hilarious pictures of them performing their famous hand stand.

The plains spotted skunk was petitioned for listing under the Endangered Species Act (ESA) due to large, range-wide declines in abundance [4]. The causes of the decline are unclear, although recent studies suggest that the conversion of much of the Midwest into intensive agriculture may have contributed to their loss [5]. Remnant populations are scattered across much of the previous range, inhabiting abandoned farmland or small protected natural areas [6-8]. A review by the U. S. Fish and Wildlife Service found substantial evidence that listing under ESA may be warranted. The listing process is ongoing and a final decision is expected in 2023.

Today, we release the chromosome-length assembly for the plains spotted skunk. The draft genome for this assembly was generated from an ear punch collected from a male live captured near Polo, South Dakota, by Merav Ben-David, Robert Riotto, and Zachariah Bell from the University of Wyoming, and Samantha Fino from South Dakota State University (under permit SD_DGFP #35). The de novo assembly of the draft genome (including DNA extraction from the ear punch, construction of the long-insert DNA library, and sequencing on PacBio Sequel instrument) was performed by Maggie Weitzman and Douglas Turnbull from the University of Oregon Genomics and Cell Characterization Core Facility, and Vikram Chhatre from the University of Wyoming using high coverage PacBio sequences. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JAKZGT000000000. The version described in this paper is version JAKZGT010000000. DNA Zoo completed the Hi-C analysis to provide chromosome-level information using a sample provided by Robert Dowler from the Angelo State Natural History Collections (sample catalogue number ASNHC 20645). That sample of a male was obtained from a fur trapper (Gerald Herbst under permit 00034475). The animal was harvested near Chamberlain, South Dakota.

Check out the interactive Hi-C contact map of 32 chromosome-length scaffolds from the new assembly below, and follow this link for the assembly page containing the relevant files.

References:

1. McDonough, M. M., A. W. Ferguson, R. C. Dowler, M. E. Gompper, and J. E. Maldonado. 2020. Phylogenomic systematics of the spotted skunks (Carnivora, Mephitidae, Spilogale): Additional species diversity and Pleistocene climate change as a major driver of diversification. bioRxiv 2020.10.23.353045.

2. Bell, Z. H. 2020. Genomic markers reveal four distinct phylogroups of spotted skunks in the United States. Thesis, University of Wyoming, Laramie, USA.

3. Kaplan, J. B., and R. A. Mead. 1994. Seasonal changes in testicular function and seminal characteristics of the male eastern spotted skunk (Spilogale putorius ambarvilus). Journal of Mammalogy 75: 1013–1020.

4. Gompper, M. E., and H. M. Hackett. 2005. The long-term, range-wide decline of a once common carnivore: the eastern spotted skunk (Spilogale putorius). Animal Conservation 8: 195–201.

5. Cheeseman, A. E., B. P. Tanis, and E. J. Finck. 2021. Quantifying temporal variation in dietary niche to reveal drivers of past population declines. Functional Ecology 35:930–941.

6. Fino, S, J.D. Stafford, A.T. Pearse, and J.A. Jenks. 2019. Incidental captures of plains spotted skunks in central South Dakota. The Prairie Naturalist 18: 201-232.

7. Lesmeister, D. B., M. E. Gompper, and J. J. Millspaugh. 2009. Habitat selection and home range dynamics of eastern spotted skunks in the Ouachita Mountains, Arkansas, USA. Journal of Wildlife Management 73: 18–25.

8. Dowler, R. C., C. E. Ebeling, G. I. Guerra, and A. W. Ferguson. 2008. The distribution of spotted skunks, genus Spilogale, in Texas. The Texas Journal of Science 60: 321.