Genome spotlight: Nile rat (Avicanthis niloticus)

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

Nile rats follow a much more human-like diurnal schedule, waking at dawn and sleeping through the night, meaning they may serve as better models for studies of the health effects of circadian rhythm disruption. And the species is an excellent model for metabolic disorders too: unlike its brethren, it develops diet-induced diabetes when fed conventional rodent food. But that work has been hampered by a lack of genomic resources for the species — until now, that is, as a Nov. 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 mainly employed long continuous reads of PacBio. Meanwhile, scaffold and genome mapping was accomplished using 10X Genomics linked reads, Bionano optical maps, and Hi-C chromatin acquisition using Illumina short-read sequencing. And not only did the researchers sequence a single rat, but they also sequenced both of its parents, allowing them to separate the original rat’s alleles based on parental haplotype. The resulting sequence was estimated to be 99 percent complete by a BUSCO analysis, meaning that the vast majority of the expected protein-coding genes were accounted for.

The high-quality sequence allowed the researchers to compare the Nile rat’s genome with that of the house mouse, in hopes of pinpointing genes that may contribute to the rat’s unusual propensity to develop type 2 diabetes. One of their findings is that the Nile rat has fewer genes for the production of the enzyme amylase, which helps digest carbohydrates. “We think the Nile rat is not adapted to eating carbohydrate-rich foods, which makes sense because they normally eat grass in Africa,” says co-author and University of California researcher Huishi Toh of Santa Barbara in a news 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 nearly impossible without high-quality sequencing. In a second press release, Toh also expresses hope that the genome will allow the Nile rat to join its relatives as a widely studied model organism.

Runner up:

A related Argonaut (Argonaut hians) slipped into its paper “shell”.

Major Argonaut (Argonaut argus)

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

A louse flies to the head of a bee

A bee louse fly (Braula coeca) on the head of a bee (Apis mellifera)

Bee louse fly (Braula coeca)

The nests of bees and other social insects often harbor specialized parasites known as inquilines. These intruders have developed traits that help them adapt to colony life and that help them hide from their hosts. The genetic basis for that adaptation is poorly understood, but a genome for a tenant called the bee louse fly, published as bioRxiv preprint on November 10, is a step towards fixing this. The researchers pieced together the 309 Mb genome of the parasite using long reads from the Oxford nanopores combined with short reads from Illumina. And when they compared it to the genome of its host, the bee (Apis mellifera), observed “strong evidence for cross-genomic parallelism,” the team writes in the paper. For example, convergent evolution between the two species has been observed in genes likely involved in metabolism and immunity. And like bees, the flies had lost almost all genes for bitter taste receptors and smell receptors. ‘These results establish a new model for studying major morphological and neuroethological transitions and indicate that profound genetic convergences between phylogenetically distant organisms may underlie the evolution of social inquilinism,’ they conclude.

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