Genome Spotlight: Desert Locust (Schistocerca gregaria)

For farmers in Africa, the Middle East, and Southwest Asia, the desert locust (Schistocerca gregaria) needs no introduction. This notorious pest has periodically devastated agricultural fields for millennia, forming massive swarms that can cover up to 1,200 square kilometers and consume 80 to 100 percent of the crops in their path. According to the Food and Agriculture Organization of the United Nations, a mere 1-square-kilometer swarm containing some 80 million locusts can eat as much food each day as 35,000 people. The swarms that struck East Africa and western Asia in 2019 and 2020 alone are estimated to have resulted in billions of dollars in damages and losses stemming from devastation to crops and pastures that will play out over the coming years.  

These infamous grasshoppers aren’t always ruinous. Most of the time, they live solitary lives. But things change when food scarcity forces them to crowd together around limited resources. They change physical form, become gregarious, and band together into famine-inducing legions. For years, researchers have attempted to sequence the desert locust’s nearly 9-billion-base genome in hopes of understanding “what makes a grasshopper a locust,” as University of Leicester animal biologist Swidbert Ott put it in 2020 when his team first reported a draft genome for the species.

A swarm of locusts covering vegetation

A swarm flies through Samburu National Reserve in Kenya.

Now, thanks to improved sequencing technologies, scientists from the Ag100Pest Initiative have succeeded in generating a high-quality, chromosome-scale assembly—and they did so in less than five months, according to a press release from the US Department of Agriculture’s Agricultural Research Service (ARS). While the work has not yet been peer-reviewed, the sequence has been deposited into the National Center for Biotechnology Information’s BioProject Database.

The Ag100Pest Initiative employs PacBio long-read sequencing as well as HiC chromosome capture—a method that first cross-links nearby DNA sequences to discern their chromosomal arrangement—to generate highly contiguous, chromosome-scale assemblies for important agricultural pests. For the locust, these methods generated an 8.8 Gb genome—one of the largest insect genomes assembled to date—which appears to be split into just 12 chromosomes. For scale, the genome of the fruit fly Drosophila melanogaster is a mere 0.14 Gb in size, an order of magnitude smaller than any one of S. gregaria’s chromosomes.

Much work will need to be done to glean from the sequence the kinds of information that can stop plagues. Still, the researchers express hope that the genome will allow managers to move away from pesticide-based control methods. “Having a high-quality genome is a big step toward finding targeted controls,” Scott Geib, an entomologist with the ARS Tropical Crop and Commodity Protection Research Unit in Hawai‘i and team leader on the project, says in the ARS release. He adds that it may also shed light on aspects of the grasshopper’s biology that are shared with other swarming species, including ones that vex the Americas and Australia.

Runners Up:

Human follicular mite (Demodex folliculorum)

The mites that live and breed on our faces have tiny genomes that are likely getting smaller, finds a study published in Molecular Biology and Evolution on June 21. Their 51.5 Mb genome is almost devoid of transposable elements, with repetitive sequences accounting for just 7.2 percent of the genome, and contains a mere 9,707 protein-coding genes—the fewest of any arthropod sequenced thus far. That may be because the animals are transitioning from being external parasites to internal ones, the authors write. Notably missing are a number of genes involved in DNA repair, leading the researchers to further speculate that the animals may be on a genomic path to extinction (or an “evolutionary dead-end track”) where they are eventually done in by the accumulation of deleterious mutations.

Careful microscopic analyses also revealed that these small genomes are packaged into surprisingly few cells—overall, the animals consist of 500 times fewer cells than D. melanogaster. Still, the researchers reassure us that the critters do have a complete digestive tract, including an anus, so they don’t simply fill with waste until their death (as was previously posited and widely repeated).

Bengal tiger (Panthera tigris tigris)

Bengal tigers are the largest and most genetically diverse subpopulation of tigers (which all technically belong to the same species), and thus are considered key to the animals’ continued survival. Yet, conservation efforts are hampered by a lack of genomic resources. Although there have been a number of efforts to sequence tiger genomes over the years, none have produced high-quality reference genomes, researchers write in a May 17 bioRxiv preprint—that is, until now. The team behind the paper reports the genome assemblies of a pair of wild tigers. By combining long- and short-read sequencing methods with chromosome capture, they were able to generate near-chromosomal assemblies that are 17 times more contiguous than the previously published Amur tiger genome and 1.7 times more contiguous than the reference genome for domesticated cats. Such completeness should facilitate the use of imperfect DNA samples, such as fecal and hair samples, for genomic research, the authors write.


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