Totally ratical

The giant white-tailed rat, Uromys caudimaculatus, aka the giant rat, the white-tailed rat, and the giant naked-tailed rat is a rodent species endemic to Australia. (They are found mostly in the rain forests of Queensland.) They are one of the largest rodents in Australia, weighing up to 1 kilogram. They are covered in a gray-brown fur with a white underbelly and white paws. White-tailed rats are part of the Uromyini group known as known as the mosaic tiled rats. This is because the scales on their hairless tails are arranged in an interlocking pattern, with very little overlap, rather like tiles in a mosaic. [1] Like other rodent species, the front incisors of the white-tailed rat are ever growing. Their teeth size is maintained by frequent chewing on nuts, branches, and other materials [2]. Much to their chagrin, a group of researchers from James Cook University working at the Daintree Rainforest Observatory in northern Queensland found that the white-tailed rats enjoyed the taste of the building's internet cables. Here's a quote from Professor Ian Atkinson in an interview to Diginomica: "The giant white tailed rat is a particular nuisance in Far North Queensland with its love of chewing through plastic, rubber and electrical wires. It also turns out ethernet and fibre optic cables are a tasty treat as well which it will happily climb up trees to nibble on as well." [3]

White-tailed Giant Rat by Steve Dew (aussiecreature), [CC-BY-NC], via inaturalist.org

Today, we release the genome assembly of the giant white-tailed rat. This is a $1K genome assembly that has a contig n50 = 50 KB and a scaffold n50 = 99 MB (see Dudchenko et al., 2018 for procedure details). The genome was generated using a sample from the T.C. Hsu Cryo-Zoo at the University of Texas MD Anderson Cancer Center stored all the way back in 1977! 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 is the 16th species from the order Rodentia and the third Australian rodent we've released here on the DNAZoo Blog! Learn more about the rodents from down-under by checking out these blog posts by Dr. Parwinder Kaur on the broad-toothed rat and the brown desert mouse.

This seal hits the spot

The spotted seal gets its name from its coat pattern: dark spots on a silvery-gray to light gray background. They can weigh between 140 and 250 pounds (63 to 113 kilograms) and reach 4.5 to 5.5 feet (1.4 to 1.7 meters) in length. They prefer arctic to sub-arctic waters, often on the outer margins of ice floes. Specifically in U.S. waters, they migrate through the Bering Strait from the Chukchi Sea in the fall, spending the winter in the annual pack ice over the continental shelf there. In the spring, following the retreat of sea ice, they migrate to coastal habitats from Siberia and Alaska to coastal Japan and the northern Yellow Sea. During summer months they can be found in the open ocean or hauled out on shore.

Photo Credit: Dave Withrow (NOAA); Marine Mammal Permit: 15126

In contrast to notorious deep divers like the Weddell or elephant seal, spotted seals feed almost exclusively over the continental shelf in waters less than 650 feet (200 meters) deep. Though their global population is estimated at more than 500,000 individuals, they are sensitive to changes in the environment that affect the annual timing and extent of sea ice formation and breakup since they rely on sea ice during reproduction and to some extent during molting.

Spotted seals are also big on family time. Though unusual among true seals, spotted seals form annual family groups consisting of an annually monogamous male, a female and a pup during the breeding season. Gestation lasts just over 10 months and pups are born with a white coat. Pups are then nursed for 3 to 6 weeks as they triple in weight, and usually shed their white coat for a spotted coat when they are weaned.

Today we release the genome assembly for the spotted seal! This is a $1K genome assembly with a contig n50 = 56 KB and scaffold n50 = 142 MB, strategy described in (Dudchenko et al., 2018). See our Methods page for more details.

This is the 5th Phocidae species that the DNA Zoo has released! Check out these posts on the Hawaiian monk seal, Northern elephant seal, the bearded seal and the harbor seal. In places that harbor seals and spotted seals co-habit such as Bristol Bay, they can be confused with each other due to their similar appearance.

This work was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03 issued by the National Marine Fisheries Service (NMFS) under the authority of the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The spotted seal (Phoca largha) specimen used in this study was collected from Kotzebue Sound, AK by James Jones and Sherman Anderson. The specimen was provided by the National Marine Mammal Tissue Bank, which is maintained by the National Institute of Standards and Technology (NIST) in the NIST Biorepository, which is operated under the direction of NMFS with the collaboration of USGS, USFWS, MMS, and NIST through the Marine Mammal Health and Stranding Response Program and the Alaska Marine Mammal Tissue Archival Project.

Check out the interactive Juicebox.js map with the 16 chromosomes of the new assembly below!

The mane attraction

Is it a fox? Is it a wolf? Though its name or fur coloring may imply it, the maned wolf is actually neither. It belongs to a genus all of its own, Chrysocyon, the full binomial being Chrysocyon brachyurus. The maned wolf stands about 3ft tall, with long graceful legs suited the grasslands, savannas, and wetlands it inhabits in South America. Their large ears help them locate small animals, fruits, and insects hidden in the grasses. The jaws and teeth of the maned are small and ill-suited to hunt large animals and livestock.

The maned wolf is not a pack animal, instead they prefer the solitary life. The one exception is their mate, with which they maintain a monogamous lifestyle [1]. The maned wolf does not howl, rather it emits a loud, roar-bark to warn others to stay away or to locate it's mate. They also mark their territory with their strong smelling urine.

Like many forest-dwelling animals, the maned wolf is victim to habitat loss and poaching and is listed as near threatened by the IUCN.

Maned wolf by Cloudtail the Snow Leopard, [CC BY-NC-ND 2.0], via flickr.com

Today, we release the genome assembly for the maned wolf. This is another $1K genome assembly, with a contig n50 = 91KB and a scaffold n50 = 61MB. For procedure details see Dudchenko et al., 2018 and our Methods page.

Many thanks to Seis, the maned wolf from the Houston Zoo for donating the sample to make this assembly possible! Check out this post featuring Seis about unconventional pollinators by the Houston Zoo.

This is our 9th Canidae in the collection, after the red fox, several dog breeds including the German shepherd, golden retriever and the Basenji, the African wild dog and 3 dingo assemblies (here, here and here)!

P.S.: If you were wondering, like we did, were's the mane, it is on the neck. It stands erect when the maned wolf scents danger!