Reptile profile

The green anole, Anolis carolinensis, is one of over 400 species in the genus Anolis (anoles) and one of over 11,000 species in the group Squamata (squamates). Squamates (lizards and snakes) are the most speciose groups of terrestrial vertebrates on earth. Native to the south-eastern United States, the green anole is known and loved for its vibrant green color and charismatic behavioral displays: during the summer months, male green anoles can be seen walking up walls using their sticky toe-pads, or elsewhere prominently perched in gardens and foliage, furiously doing pushups and extending a flag-like flap of bubblegum pink skin under their chin called a “dewlap.”

Green anole, photo by Bonnie Kircher

These characteristic displays are directed at any males that have invaded their territory, as well as any receptive females that catch their powder-blue eyes. Though males are most likely to be spotted displaying, females also perform these displays. Male and female anoles can be differentiated by differences in overall adult body size but also by the size of their dewlap, (males being larger in both cases). Though named for their gorgeous green hue, green anoles also change color to a silver-y brown. Likely not a camouflage technique, this behavior may correspond instead with environmental or social cues.

Anoles are particularly well studied because of their interesting evolutionary quirks. The genus is often described in textbooks as an example of convergent evolution, a process in which similar traits evolve in different species as a result of similar environmental conditions and not due to evolution from a shared common ancestor. Convergent evolution of morphology, physiology, and behavior has been well characterized in anoles and this group is an important model for understanding evolutionary processes. Anoles thrive in a lab setting, making it easy to adapt modern scientific tools and techniques for use in this system. Recently, CRISPR genome editing was used for the first time in a closely related species, the brown anole (Anolis sagrei), making it the first non-avian reptile to have genome editing capabilities be made available.

The genome for green anole, Anolis carolinensis, was first published in 2011 by Jessica Alföldi et al., and was the first non-avian reptile genome to be sequenced. Since its publication and re-annotation in 2013, the genome has been used widely for studies in evolution, genetics, and development. With over 600 citations, the original publication of this genome transformed the ability of researchers to study the evolution vertebrates.

Today, we share a few tweaks to the existing green anole assembly (AnoCar2.0) including anchoring suggestions for 4 microchromosomes missing in AnoCar2.0. We also share the Hi-C data generated using a fibroblast cell line from a female anole individual, originally frozen back in 1981! 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 sharing this cell line.

This is the 6th member of the Squamata family we've released here on the DNA Zoo Blog, see others here! Browse the 18 chromosomes of the green anole in the interactive JuiceBox.js session below. Note an inversion polymorphism in HiC_scaffold_1: stay tuned for more data to find out if this is a culturing artifact or a primary sample polymorphism.

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!