Genome Spotlight: Nile Rat (Avicanthis niloticus)

INo wonder rodents top the list of model organisms. They are small and easy to maintain, yet share enough in common with humans to provide valuable insight into a myriad of life science fields, including physiology, neuroscience, and medicine. But the most popular rodent models, house mice (Mus musculus) and Norway rats (Rattus norvegicus) – are not ideal choices for studying all human traits. Both species are nocturnal and relatively resistant to food-induced disturbances. And it is there, according to the researchers, that the Nile rats (Avicanthis niloticus) Come in.

Nile rats follow a much more humane diurnal schedule, waking at dawn and sleeping through the night, which means they may serve as better models for studies of the health effects of disruption of circadian rhythm. And the species is also an excellent model for metabolic disorders: unlike its relatives, it develops diet-induced diabetes when fed conventional rodent food. But such work has been hampered by a lack of genomic resources for the species – so far, that is, as a November 8 article in BMC Biology reports a reference genome at the chromosome level for the species.

The 2.5 GB set is part of the Vertebrate Genomes Project, a coalition of scientists who share the goal of generating nearly error-free genomic sequences for all 66,000 extant vertebrate species. To assemble the highly contiguous sequence, the team primarily used PacBio continuous long reads. Meanwhile, genome scaffolding and mapping was done using linked reads 10X Genomics, Bionano optical cardsand Hi-C chromatin capture using Illumina short-read sequencing. And not only did the researchers sequence an individual rat, they also sequenced both of its parents, allowing them to separate the original rat’s alleles by parental haplotype. The resulting sequence was estimated to be 99% complete by 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 hopes of spotting genes that might contribute to the rat’s unusual propensity to develop type 2 diabetes. One of their findings is that the Nile rat has fewer genes to produce the enzyme amylase, which helps digest carbohydrates. “We think the Nile rat is not adapted to eat carbohydrate-rich foods, which makes sense because they normally eat grass in Africa,” said co-author and researcher Huishi Toh. University of California, Santa Barbara. Press release. “I think that’s why they’re 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 plan to also explore epigenetics in the future – studies that were virtually impossible without a high-quality sequence. quality. In a second Press releaseToh also expresses hope that the genome will allow the Nile rat to join its relatives as a widely studied model organism.

Finalists:

Great Argonaut (argonaut argo)

Argonauts are sometimes referred to as paper nautiluses because the flimsy protective case the females make to help protect their eggs bears a strong resemblance to the shells of their nautiloid cousins. However, a genome of the species, constructed using short reads from Illumina and published in the November issue of Biology and evolution of the genome, reveals that the mineralized masterpiece of the argonauts uses an entirely different set of genes than those that nautiluses use to build shells. “This tells us that evolution can take many different paths to create similar things,” said Caroline Albertin, a researcher at the Massachusetts Marine Biological Laboratory, who 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 a lot of intriguing questions to tackle,” note co-authors Masa-aki Yoshida of Shimane University and Davin Setiamarga of Wakayama College’s National Institute of Technology in the paper. underline paper. “We anticipate that the availability of argonaut genomic data will help us understand not only this species, but also cephalopods and molluscs in general.”

Bee louse fly (Braula coeca)

The nests of bees and other social insects often harbor specialized parasites called inquilines. These intruders have evolved traits that both help them adapt to colony life and help them hide from their hosts. The genetic basis for such an adaptation is poorly understood, but the genome of an inquiline called the bee louse fly, published as bioRxiv preprint on November 10, is a step towards rectifying that. The researchers assembled the parasite’s 309MB genome using long reads from Oxford nanopores combined with short reads from Illumina. And when they compared it to the genome of its host, the bee (Apis mellifera), they observed “striking evidence of inter-order genomic parallelism,” the team wrote in the paper. Convergent evolution between the two species has been observed in genes likely involved in metabolism and immunity, for example. And like the bees, the flies had lost almost all the genes for bitter taste receptors and odor 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 may underlie the evolution of social inquilinism,” they conclude.