A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Toh, H.; Yang, C.; Formenti, G.; Raja, K.; Yan, L.; Tracey, A.; Chow, W.; Howe, K.; Bergeron, L. A.; Zhang, G.; Haase, B.; Mountcastle, J.; Fedrigo, O.; Fogg, J.; Kirilenko, B.; Munegowda, C.; Hiller, M.; Jain, A.; Kihara, D.; Rhie, A.; Phillippy, A. M.; Swanson, S. A.; Jiang, P.; Clegg, D. O.; Jarvis, E. D.; Thomson, J. A.; Stewart, R.; Chaisson, M. J. P.; Bukhman, Y. V.

doi:10.1101/2021.12.08.471837

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bioRxiv · 10.1101/2021.12.08.471837

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

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Abstract

The Nile rat (Avicanthis niloticus) is an important animal model for biomedical research, including the study of diurnal rhythms and type 2 diabetes. Here, we report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3,613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including those that affect genes associated with type 2 diabetes and metabolic dysfunctions. These include 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse. Our findings reflect the exceptional level of genomic detail present in this assembly, which will greatly expand the potential of the Nile rat as a model organism for genetic studies.

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Toh, H., Yang, C., Formenti, G., Raja, K., Yan, L., Tracey, A., Chow, W., Howe, K., Bergeron, L. A., Zhang, G., Haase, B., Mountcastle, J., Fedrigo, O., Fogg, J., Kirilenko, B., Munegowda, C., Hiller, M., Jain, A., Kihara, D., Rhie, A., Phillippy, A. M., Swanson, S. A., Jiang, P., Clegg, D. O., Jarvis, E. D., Thomson, J. A., Stewart, R., Chaisson, M. J. P., Bukhman, Y. V.. 2021-12-10. A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes. https://doi.org/10.1101/2021.12.08.471837

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