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Common side-blotched lizards (Uta stansburiana) are a ubiquitous lizard of the North American deserts. These lizards inhabit an extraordinarily broad range across the United States and northern Mexico from California’s Channel Islands to central Texas, and from the southern tip of Baja California to central Washington state. Throughout this range, these lizards demonstrate a wide variety of colors and patterns on their back, likely to better blend in with the diverse backgrounds where they live. In fact, these lizards are often a critical food source for other desert species and are sometimes referred to as the “food of the desert.”

Female side-blotched lizard (Uta stansburiana) by Samuel Fellows

This species is best known for alternative mating strategies associated with throat color in both male and female lizards in some populations. Orange-throated females lay many small eggs while yellow- and blue-throated females lay fewer but larger eggs. Male lizards, in contrast, demonstrate a “rock-paper-scissors” strategy where orange-throated males singly guard a harem of females, blue-throated males cooperatively guard a small group of females, and yellow-throated males sneak into harems guarded by the orange-throated males to mate. Orange-throated males out-compete blue-throated males, blue-throated males out-compete yellow-throated males, and yellow-throated males out-compete orange-throated males.

These evolutionarily stable strategies make common side-blotched lizards an excellent species in which to begin to understand the ways in which these alternative throat colors, mating strategies, and background-matching patterns can persist within and among populations in the same species. They also can help understand the ways in which these same factors promote speciation. This genome will help reveal the genetic underpinnings for throat color, mating strategy, and the beginning stages of speciation.

Today, we release the chromosome-length assembly for the side-blotched lizards (Uta stansburiana). The draft assembly was generated by Sam Fellows and Dr. Danielle Edwards using long-read sequencing data generated by the University of California Davis DNA Technologies and Expression Analysis core on two Pacific Biosciences Sequel II SMRT-cells, and was assembled with Hifiasm (Cheng et al. 2021). The Hi-C data was generated by DNA Zoo and applied to upgrade the draft to chromosome-length using methods described here.

The sample used for this genome assembly came from an orange-throated male from Wright’s Point, Harney County, Oregon, U.S.A. collected by Dr. Pete Zani. The animal comes from a large population of common side-blotched lizards that occupies sagebrush-steppe habitat in the northern Great Basin. The population persists on a volcanic lava flow surrounded on three sides by the Malheur wetlands national wildlife refuge. This population has been the subject of an 18-year long mark-recapture study which has demonstrated that lizards at this site are much longer-lived than those farther south (up to 7 years, in contrast to 1-2 years elsewhere), and that lizards at this location do not demonstrate the rock-paper-scissors mating behaviors associated with other populations.

Check out the 17 chromosomes (2n=34) of the common side-blotched lizard in the interactive Juicebox.js session below, and find out more information about the new reference on the corresponding assembly page.

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We are excited to report that with our last assembly release we've hit the 325 assemblies mark, which means it's time to do some raw sequencing data upload to NCBI Sequence Read Archive!

Celebratory postcard on the occasion by DNA Zoo junior member Jibreel!

The new data have now been uploaded under our usual BioProject accession PRJNA512907 (some more data can be found under collaborative bioproject accessions like PRJNA679437).

Today, we uploaded data for an additional 18 Hi-C and 12 WGS experiments, in overall the total data covers 325 species, 635 experiments and 43,960,758,871,505 bases!

We thank Illumina, Baylor College of Medicine GARP core, Macrogen, Novogen and the Broad Institute for their help with the data production! And thank you to Jibreel for the celebratory postcard!

As with our previous data releases, we share our bases without restrictions (but don't forget to acknowledge). Please see our data usage policy here! Don't miss on new assemblies, add your email to the mailing list at the bottom of the contact page to subscribe to notifications about new genome assemblies being release or follow us on twitter!

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Off the coast of southern California, there is a group of small islands - Channel Islands. About 7000 years ago, mainland grey foxes (Urocyon cinereoargenteus) got onto these islands (and we still do not know how exactly). The foxes thrived, and are now their own separate species called the island fox (U. littoralis).

Island fox by Christian Schwarz, [CC BY-NC], via

Over the centuries, the foxes got smaller in size; average weight is only about 2 kg (~4 lb) making them the smallest fox in North America! They also lost a few tail vertebrae making their tails shorter. The island foxes are docile and are not afraid of humans. They enjoy life in woods, grasses, and on the beaches of islands by hunting mostly at dawn and dusk on small mammals (deer mice), insects (crickets), lizards, birds (and their eggs), and frogs.

The Santa Catalina Island fox (U. littoralis catalinae) is one of six subspecies of the island gray fox. The Santa Catalina population was almost wiped out in 1999 by the devastating outbreak of canine distemper virus. The epidemic left less than 100 foxes alive. The severe bottleneck has decreased the levels of genetic diversity in the fox population and increased the frequency of potentially deleterious variants. It is likely that these variants are responsible for the unusually high occurrence of ear tumors (ceruminous gland carcinoma) in these foxes after the distemper epidemic (Hendricks et al., 2022).

Over the last two decades enormous conservation efforts of Santa Catalina Island Conservancy together with the National Park Service, The Nature Conservancy, and the Institute for Wildlife Studies brought the number of foxes back to over 2000. Catalina Island fox survival is a remarkable tribute to well-planned science-based conservation strategies: fox vaccinations, captive breeding, radio-collar monitoring, predator control (Golden eagle), strict limits on mainland-derived pets, wildlife, parasites, and human impact monitoring etc. We hope that the genome assembly we share today will contribute to these conservation efforts including long-term monitoring of the carcinoma alleles as well as overall genetic diversity, and provide crucial information for the long-term persistence of the threatened fox population.

The ear sample that was used for this genome assembly was kindly provided by Julie King from the Catalina Island Conservancy and was collected with Winston Vickers. The primary fibroblast cell line ULI-623 was established by Polina Perelman from the biopsy of the 10-year-old female Catalina Island fox #36966 (affected by ceruminous gland carcinoma) at the Laboratory of Genomic Diversity led by Stephen O’Brien. Passage #3 was used to construct the short-read DNA-Seq and Hi-C libraries. We thank Drs. Melody Roelke-Parker, Carlos Driscoll, Christina Barr, and David Goldman for preserving LGD cell line collection.

Browse the 33 chromosomes of the island fox in the interactive Juicebox.js session below, and check out the assembly page for more information about this genome!


Hendricks SA, King JL, Duncan CL, Vickers W, Hohenlohe PA, Davis BW. Genomic Assessment of Cancer Susceptibility in the Threatened Catalina Island Fox (Urocyon littoralis catalinae). Genes (Basel). 2022 Aug 22;13(8):1496. doi: 10.3390/genes13081496.

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