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.
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 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!