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Pouchies against ouchies

Southern giant pouched rats (Cricetomys ansorgei), referred to as “Pouchies” due to the fact that they are only distantly related to conventional rats, are very large rodents best known for their powerful olfactory senses conferring the ability to reliably detect underground explosives such as TNT. In fact, this species is currently being trained and employed as biodetectors used to clear abandoned landmine fields in the wake of armed conflict.

Southern giant pouched rat, photo by Ehren Bentz [CC]

Notably, in 2020, a Southern giant pouched rat became the first rodent to be awarded the PDSA Gold medal for animal bravery from the British organization the ‘People's Dispensary for Sick Animals’. During his career, ‘Magawa’ (internationally known as the ‘Hero rat’) was responsible for the detection and subsequent removal of at least 71 landmines, as well as dozens of other unexploded ordinance items from extremely dangerous abandoned mine fields in Cambodia. Further, this species’ utility as biodetectors may extend beyond explosives, as they are also able to detect subtle chemical signals indicative of Tuberculosis infection – a condition which is often cryptic and difficult to diagnose.

In addition to their impressive chemosensory prowess, Pouchies also exhibit a unique and interesting reproductive physiology. Similar to some other rodents, females are born lacking a vaginal opening, which typically appears as they reach sexual maturity. In Pouchies, this non-reproductive condition often uniquely persists for years into adulthood, and is even reversible, with adult females exhibiting vaginal openings completely covered by an area of skin, sometimes even after having previously given birth to a litter of pups. The mechanisms governing these unusually plastic reproductive developmental timelines appear to be, at least in part, mediated by pheromonal signals. Pheromonal communication is an important aspect of life for these interesting animals, enabling them to detect subtle differences in chemical social signals used to advertise sex, physiological state, and reproductive status through nothing more than urine.

Today, we release the chromosome-length assembly for the Southern giant pouched rats. This genome assembly was produced by Dr. Ehren Bentz and Dr. Alexander Ophir in the Psychology department at Cornell University in collaboration with DNA Zoo. Whole genome sequencing was performed by the University of Georgia Genomics and Bioinformatics Core using Pacific Biosciences continuous long read sequencing. Reads were error corrected and assembled using Canu (Koren et al., 2017), and contigs were anchored to scaffolds using in situ Hi-C sequencing (Rao, Huntley et al., 2014), 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). The resulting chromosome-level scaffolds were then polished with PacBio long reads using Racon (Vaser, Sović et al., 2017). Check out the interactive JuiceBox.js session exploring the 40 chromosomes below!

The pouched rat’s extremely acute chemosensory abilities, as well as its unique reproductive physiology and social behaviors, provide a powerful, novel model for investigating olfactory communication, reproductive physiology, and development in an exotic rodent species with tremendous potential. This chromosome-length genome assembly surely constitutes an invaluable resource facilitating the development of the Pouched rat as both a research model and as a biodetector.

Funding for this work was provided by the Army Research Office and the National Science Foundation.

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