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Genome Spotlight: Nile Rat (Avicanthis niloticus)

A reference sequence for this emerging model organism will facilitate research on type 2 diabetes and the health effects of circadian rhythm disruption.

A Nile rat sitting atop fruits
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Christie Wilcox

Christie joined The Scientist's team as newsletter editor in 2021, after more than a decade of science writing. She has a PhD in cell and molecular biology, and her debut book Venomous: How Earth’s Deadliest Creatures Mastered Biochemistry, received widespread acclaim.

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ABOVE: A Nile rat (Avicanthis niloticus) PHOTO COURTESY OF SUSANNE MEYER, THOMSON LAB AT UCSB

It’s no wonder that rodents top the list of model organisms. They’re small and easy to care for, and yet share enough in common with humans that they can provide valuable insights into myriad life science fields, including physiology, neuroscience, and medicine. But the most popular rodent models—house mice (Mus musculus) and Norway rats (Rattus norvegicus)—aren’t ideal choices for studying all human traits. Both species are nocturnal and relatively resistant to diet-induced disorders. And that, researchers say, is where Nile rats (Avicanthis niloticus) come in.

Nile rats follow a much more human-like diurnal schedule, waking at dawn and sleeping through the night, which means they can serve as better models for studies on the health effects of circadian rhythm disruption. And the species is a great model for metabolic disorders too: Unlike its kin, it develops diet-induced diabetes when fed conventional rodent chow. But such work has been hindered by a lack of genomic resources for the species—until now, that is, as a November 8 paper in BMC Biology reports a chromosome-level reference genome for the species.

The 2.5 Gb assembly is part of the Vertebrate Genomes Project, a coalition of scientists who share the goal of generating nearly error-free genome sequences for all 66,000 extant vertebrate species. To assemble the highly contiguous sequence, the team primarily employed PacBio continuous long reads. Meanwhile, scaffolding and genome mapping was accomplished using 10X Genomics linked reads, Bionano optical maps, and Hi-C chromatin capture utilizing Illumina short-read sequencing. And not only did the researchers sequence an individual rat, they also sequenced both its parents, allowing them to separate the original rat’s alleles by parental haplotype. The resulting sequence was estimated to be 99 percent complete by a BUSCO analysis, meaning that the vast majority of expected protein-coding genes were accounted for.

The high-quality sequence allowed the researchers to compare the Nile rat genome with that of the house mouse, in the hopes of spotting genes that may contribute to the rat’s unusual propensity for developing type 2 diabetes. One of their findings is that the Nile rat has fewer genes for producing the enzyme amylase, which helps digest carbohydrates. “We think that the Nile rat is not adapted to eat high carbohydrate foods, which makes sense because they normally eat grass in Africa,” coauthor and University of California, Santa Barbara researcher Huishi Toh says in a press release. “I think this is why they are so susceptible to diabetes.”

Toh adds that the team is now looking to use the genome to study transcriptomic changes associated with diet-induced diabetes and plans to explore epigenetics as well in the future—studies that were all but impossible without a high-quality sequence. In a second press release, Toh also expresses hope that the genome will allow the Nile rat to join its kin as a widely studied model organism.

Runners Up:

          An argonaut tucked in its papery “shell”
A related argonaut (Argonauta hians) tucked in its papery “shell”
© ISTOCK.COM, ATESE

Greater argonaut (Argonauta argo)

Argonauts are sometimes called paper nautiluses, as the fragile protective case females make to help protect their eggs bears a strong resemblance to the shells of their nautiloid cousins. However, a genome for the species, built using Illumina short-reads and published in the November issue of Genome Biology and Evolution, reveals that the argonauts’ mineralized masterpiece uses a whole different set of genes than the ones nautiluses use to build shells. “It tells us that evolution can take many different paths to make similar sorts of things,” Caroline Albertin, a researcher at the Marine Biological Laboratory in Massachusetts who was not involved in the study, tells The New York Times. And “shell” evolution is just one of many insights that can be gleaned from the sequence, according to the Japanese team behind the study. “There are a lot of intriguing questions to be addressed,” coauthors Masa-aki Yoshida from Shimane University and Davin Setiamarga from National Institute of Technology, Wakayama College, note in the journal’s highlight of the paper. “We anticipate that the availability of the genome data of the argonauts will help us to understand not only this species, but also the cephalopods and mollusks in general.”

          A bee louse fly on the head of a honeybee 
A bee louse fly (Braula coeca) on the head of a honeybee (Apis mellifera)
FIG. 1A from Physiological Entomology, 47:83–95, 2021. CC BY 4.0

Bee louse fly (Braula coeca)

The nests of bees and other social insects are often home to specialized parasites known as inquilines. These intruders have evolved traits that both help them adapt to colony life and that help them hide them from their hosts. The genetic basis of such adaptation  is poorly understood, but a genome for an inquiline called the bee louse fly, published as a bioRxiv preprint on November 10, is a step toward rectifying that. The researchers put together the parasite’s 309 Mb genome using Oxford nanopore long-reads combined with Illumina short-reads. And when they compared it to the genome of its host, the honeybee (Apis mellifera), they observed “striking evidence of cross-order genomic parallelism,” the team writes in the paper. Convergent evolution between the two species was seen in genes likely involved in metabolism and immunity, for instance. And like the bees, the flies had lost nearly all genes for bitter taste receptors and odorant receptors. “These results establish a new model for the study of major morphological and neuroethological transitions and indicate that deep genetic convergences between phylogenetically distant organisms can underlie the evolution of social inquilinism,” they conclude.

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Genome Spotlight is a monthly column for The Scientist’s Genetics & Genomics newsletter that highlights recently published genome sequences and the mysteries of life they may reveal.

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