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!

Locusts: Jekyll & Hyde or the Incredible Hulk of the insect world

In Robert Louis Stevenson’s short novel, “Strange Case of Dr. Jekyll and Mr. Hyde,” the mild-mannered Dr. Jekyll transformed into the evil and violent Mr. Hyde by drinking a serum that he created. The appearances and personalities differed so much between the two that the people who knew Dr. Jekyll would not suspect this incredible transformation. If this story, which was written in 1886, is too unfamiliar to younger folks, we can fast-forward to the 21st century and think about a Marvel character Dr. Bruce Banner who was exposed to gamma radiation and gained the ability to transform into a large green creature known as the Hulk whenever he gets angry.

In both stories, we find a similarity. Both Dr. Jekyll and Dr. Banner have the ability to transform from one form to a very different form in response to a particular stimulus. You might be surprised to learn that this is not only the stuff from fiction. Many organisms on this planet have this amazing and special ability to transform, and this phenomenon is generally known as phenotypic plasticity.

Phenotypic plasticity is formally defined as the ability of a genotype to produce different phenotypes in response to different environmental conditions. Although it is actually a biological phenomenon observed in all living organisms, some organisms show spectacular examples of phenotypic plasticity. Locusts are one such example and this blog post is about our efforts to sequence their genomes. Please check out this episode of a YouTube show Bizarre Beasts, which explains this a bit further.

So, what are locusts? Locusts are a very special type of grasshoppers with a superpower! There are about 7,000 species of grasshoppers described in the world, and only about 20 species have been recognized as locusts. Locust’s superpower? Their ability to form dense migrating swarms through an extreme form of density-dependent phenotypic plasticity, in which cryptically colored, shy individuals transform into conspicuously colored, gregarious individuals in response to increases in population density. The key environmental stimulus for this transformation is local population density. The two density-dependent phenotypes are so different from each other in terms of their color, behavior, morphology, and ecology that people used to think they were different species. In this sense, locusts are truly the Jekyll & Hyde or the Incredible Hulk/Bruce Banner of the insect world.

Schistocerca gregaria nymph, photo by Brandon Woo, Hojun Song lab (Texas A&M)

Of all known locust species, the desert locust (Schistocerca gregaria) is the most intensively studied species. This species is the most destructive locust in the world that can spread into 60 countries and pose a great threat to the livelihoods of 10% of the world’s population. It is so serious a threat, this species has been recognized as a global pest for millennia and even mentioned in the Bible as one of 10 plagues, one would imagine its genome would have already been fully sequenced and characterized. After all, many of the world’s important insect pest species have been among the first to be sequenced, which would pave the way to understand their biology and eventually controls. However, that was not the case for the desert locust. The reason? Its ridiculously large genome size. Among insects, grasshoppers are known to have the largest genome sizes, and the desert locust genome is about 8.8 Gb in size (that’s 8,800,000,000 nucleotides long!). To put into perspective, a human genome is 3.2 Gb in size and the fruit fly Drosophila melanogaster’s genome is about 180 Mb in size. This means that the desert locust genome is 2.75 times larger than the human genome, and a whopping 48.9 times larger than the fruit fly genome! (Of course, the Incredible Hulk of the insect world has to have the largest genome!) A large genome size means that it is more expensive to sequence and more difficult to assemble. So, for many years, it had been simply out of question to sequence the locust genome.

In 2020, at the height of the most recent desert locust upsurge in Eastern Africa, the Biology Integration Institute (BII) program of the U.S. National Science Foundation awarded a $12.5 million grant to establish the Behavioral Plasticity Research Institute (BPRI) to use locusts as a model system to study phenotypic plasticity. Around the same time, the Ag100Pest Initiative of the USDA Agricultural Research Service (ARS) secured funding from the USDA Foreign Agricultural Service (FAS) and the United States Agency for International Development (USAID) to develop genomic resources to study the desert locust. With these unprecedented resources, the BPRI, the USDA and DNA Zoo joined forces to generate the highest quality genomes of locusts and grasshoppers ever produced.

The first locust species that we sequenced was of course the desert locust, and this effort was led by the USDA scientists, which is described in this press release. Working with scientists at USDA and DNA Zoo, the BPRI has also completed sequencing and assembly of five additional species belonging to the same genus (Schistocerca) as the desert locust. Two locust species that we have sequenced are the Central American locust (Schistocerca piceifrons), a major agricultural pest in Mexico and the Central America, and the South American locust (Schistocerca cancellata), an important pest in Argentina and neighboring countries. We have also sequenced two non-swarming grasshopper species, Schistocerca americana and Schistocerca serialis cubense, which are closely related to the Central American locust and capable of changing color, morphology, and behavior when experimentally crowded in the lab. Finally, we have sequenced Schistocerca nitens, which is a non-swarming grasshopper not related to any locust species and shows very reduced phenotypic plasticity. All five Schistocerca species have equally large genomes, and this genome sequencing project represents a major achievement. Now, by comparing and studying these genomes, we will be able to answer what makes locusts different from grasshoppers, and understand genomic regions and regulatory mechanisms that are important for phenotypic plasticity. In other words, we are one step closer to revealing the secrets behind the amazing transformation for Jekyll and Hyde or the Incredible Hulk of the insect world!

Here we present the genome assemblies of the six Schistocerca species. Our genome sequencing effort was monumental. It took 85 cells or 1.6 Tb of PacBio HiFi data and many months of sequencing run time. We complemented these data with Illumina Hi-C data to assemble chromosome-length scaffolds. These chromosome-length assemblies are huge with some chromosomes a GB each – that’s larger than many entire insect genomes.

The genomic resources that we have developed are available through the following three main outlets.

1. All six Schistocerca genomes have been submitted to NCBI and annotated. These assemblies are available at NCBI:

· BPRI Schistocerca genome BioProject: https://www.ncbi.nlm.nih.gov/bioproject/772722

· Schistocerca gregaria (Desert locust): https://www.ncbi.nlm.nih.gov/bioproject/814718

· Schistocerca piceifrons (Central American locust): https://www.ncbi.nlm.nih.gov/genome/109698

· Schistocerca cancellata (South American locust): https://www.ncbi.nlm.nih.gov/genome/114655

· Schistocerca americana: https://www.ncbi.nlm.nih.gov/genome/109697

· Schistocerca serialis cubense: https://www.ncbi.nlm.nih.gov/genome/115782

· Schistocerca nitens: https://www.ncbi.nlm.nih.gov/genome/114651

2. The genome browsers for all six species are available at USDA’s i5k Workspace@NAL:

· Schistocerca americana: https://i5k.nal.usda.gov/bio_data/1394307 · Schistocerca piceifrons: https://i5k.nal.usda.gov/bio_data/1394321 · Schistocerca gregaria: https://i5k.nal.usda.gov/bio_data/139432 (coming soon) · Schistocerca cancellata: https://i5k.nal.usda.gov/bio_data/1394317 (coming soon) · Schistocerca nitens: https://i5k.nal.usda.gov/bio_data/1394318 (coming soon) · Schistocerca serialis cubense: https://i5k.nal.usda.gov/bio_data/1394319 (coming soon)

3. Hi-C data and contact maps for five Schistocerca species are available here, at DNA Zoo:

· Schistocerca americana: https://www.dnazoo.org/assemblies/Schistocerca_americana · Schistocerca piceifrons: https://www.dnazoo.org/assemblies/Schistocerca_piceifrons · Schistocerca cancellata: https://www.dnazoo.org/assemblies/Schistocerca_cancellata · Schistocerca nitens: https://www.dnazoo.org/assemblies/Schistocerca_nitens · Schistocerca serialis cubense: https://www.dnazoo.org/assemblies/Schistocerca_serialis_cubense

Click on the contact map collage to open an interactive Juicebox.js session and explore the Hi-C contact maps for all the locusts!