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.

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!