Space poddity

The short-beaked common dolphin, Delphinus delphis, is one of the most wide spread and abundant dolphin species in the world. They're known to be especially social, energetic, and may live in large groups (pods) of a few hundred individuals. The common dolphin will sometimes form "mega-pods", in which thousands of individual dolphins will band together for a time [1]. The short-beaked common dolphin is known to go "bow-riding" alongside waves made by boats, and even some large whales [2].

Short-beaked common dolphin (Delphinus delphis) in Portugal by Alexandre Roux, [CC BY-NC-ND 2.0], via flickr.com

Today we share the chromosome-length genome assembly for the short-beaked common dolphin, Delphinus delphis! This genome assembly was generated using the $1K strategy with a contig N50=50Kb and a scaffold N50=89Mb. The sample for this genome assembly was provided to us by Barbie Halaska, from The Marine Mammal Center in Sausalito, California. As the world’s largest marine mammal hospital, the Center prides itself on gathering and providing open research data that is free to access, reuse, repurpose and redistribute in service to ocean conservation and marine mammal health. Learn more about the impact of The Marine Mammal Center’s scientific research by visiting the Center's website.

This sample was collected by The Marine Mammal Center under the Marine Mammal Health and Stranding Program (MMHSPR) Permit No. 18786-04 issued by the National Marine Fisheries Service (NMFS) in accordance with the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The work at DNA Zoo was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03.

Browse the 22 chromosomes, (2n=44), of the common dolphin in the interactive Juicebox.js session below. This is the 15th dolphin species we've released here on the DNA Zoo, check out our other assemblies here!

Don't you phoget about me

The Weddell seal (Leptonychotes weddellii) is a true seal and one of the largest members of the Phocidae family, with adults measuring 2.5 to 3.5 m (8 ft 2 in–11 ft 6 in) in length and weighing from 400 to 600 kg (880–1,320 lb). The species has a circumpolar distribution around Antarctica. Unlike the three other Antarctic seal species (leopard, crabeater, and Ross seals) that inhabit the broken and circulating pack ice extending northward from the continent into the southern ocean, Weddell seals are associated with the fast ice frozen to the continent. They are predators near the top of the food chain and are exceptional divers, capable of holding their breath for up to an hour and diving to depths up to 600 m. Their primary prey are the herring-like Antarctic silverfish, the large Antarctic toothfish, cephalopods, and a variety of smaller fishes. Leopard seals prey on their pups as do Orcas that also prey on adults.

Photo of Weddell seals courtesy of William A. Link, U.S. Geological Survey Patuxent Wildlife Research Center (used with permission).

During the Austral spring, Weddell seals are found in colonies hauled out on the ice in localized areas where cracks due to tides and glacier pressures provide ready access to the ice surface. The females give birth to a single pup and closely attend the pup, with nursing lasting for 30-40 days. Mothers feed very little, if at all, while nursing and lose up to 40% of their body mass. Pups are actively encouraged by mothers to enter the water, with most pups beginning to swim at 10-12 days of age. During the pup-rearing period, adult males establish underwater territories associated with the colonies and compete aggressively to breed females when they become receptive at about the time pups are weaned. Copulation occurs underwater. Maximum life span is approximately 30 years.

Weddell seals are docile when hauled out on the sea ice, with no fear of man, and were exploited for food and fuel during the era of exploration in the late 1800s and early 1900s, with local populations depleted in areas where expeditions were concentrated. All Antarctic seals are currently protected by the international Antarctic Treaty (1961) and the Convention for the Conservation of Antarctic Seals (1978). Weddell seals are the most studied of the Antarctic seal species due to their mild temperament and because researchers have ready access to the animals when the seals are hauled out on the fast ice. The species is considered secure, but there is no reliable estimate of their abundance. Because Weddell seals are closely associated with sea ice and their primary prey are ice-obligates there is concern that global climate change may impact the distribution and abundance of the species in the future. The recent development of commercial fisheries in some portions of the seal’s range also has the potential to impact food resources.

Today, we release the genome assembly for the Weddell seal, Leptonychotes weddellii! The sample used for this experiment was provided by Robert Garrott, Montana State University. Field work for the project was supported by the National Science Foundation, Division of Polar Programs under grant numbers ANT 1141326 and ANT 1640481 to Jay J. Rotella, Robert A. Garrott, and Donald B. Siniff and prior NSF Grants to Robert A. Garrott, Jay J. Rotella, D. B. Siniff, and J. Ward Testa. Browse the 17 chromosomes of the Weddell seal below in the interactive Juicebox.js session below, and visit the assembly page for more data and links.

This is our 7th Phocidae genome assembly, check out the rest here!

The dragonfly effect

The Black Petaltail (Tanypteryx hageni) is one of eleven dragonfly species in the family Petaluridae. The family’s name recognizes the large, wide claspers at the end of the male abdomen (resembling the petals of a flower), which are used to clasp the female while mating. The Black Petaltail is found in western North America, from British Columbia in Canada to southern California in the US, but other species of petaltail are found in Australia, New Zealand, Chile, eastern North America and Japan. Like other dragonflies petaltails have an aquatic juvenile stage (a larva or nymph), but these are not found in ponds or streams like the majority of dragonfly species; petaltails live in fens and bogs, places near springs and small streams where the soils are consistently saturated with water.

Adult Tanypteryx hageni, courtesy of Carey Kerst, AMNS (used with permission)

Most species of petaltail construct and maintain a burrow in these fens—the ‘Hobbits’ of the dragonfly world, living in a hole in the ground. The burrow fills with water, and the petaltail nymphs live in these burrows for multiple years before emerging as adults—the Black Petaltail is thought to take five years to develop. Black petaltail fens are usually found in mountain valleys, in large meadows surrounded by forests. As such habitats can be quite isolated, and are also subject to increasing risk from wildfires in these areas. Understanding how these dragonflies are adapted to these unique habitats, and how their long development times influence their populations genetics, will be some of the questions that can be addressed with a quality genome assembly.

Today, we share the chromosome-length assembly for the black petaltail (Tanypteryx hageni). The draft assembly was generated by Ethan Tolman, Paul Frandsen, Jessica Ware, Christopher Beatty and colleagues at the American Museum of Natural History colleagues at the American Museum of Natural History. Data from two PacBio Sequel II SMRT cells generated at the BYU sequencing center was assembled with Hifiasm (Cheng et al., 2021). We upgraded the draft to chromosome-length using Hi-C data from a hemolymph sample from a juvenile petaltail not unlike the one you can see in the photo below, collected by Christopher Beatty in 2022 in the Lassen National Forest in California.

Juvenile nymph Tanypteryx hageni courtesy of Christopher Beatty (AMNS)

Funding for this project was provided by the College Undergraduate Research Award from the College of Life Sciences at Brigham Young University. We are also grateful for Grant #8709-09 from the National Geographic Society Committee for Research and Exploration.

We are also very proud to announce that Chirag Maheshwari, the DNA Zoo team member who helped bring this genome assembly to it's chromosome-length glory, has just been awarded the Atlas Fellowship for outstanding high school students. Congratulations!

Check out the interactive Juicebox.js instance below for a contact map of the 9 chromosomes of T. hageni. And don't forget to visit the assembly page for more info and links!