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

• DOI: 10.1186/s12915-022-01427-8
• Publication Date: 2022-11-08T01:02:27Z
• Authors: Huishi Toh; Chentao Yang; Giulio Formenti; Kalpana Raja; Lily Yan; Alan Tracey; William Chow; Kerstin Howe; Lucie A. Bergeron; Guojie Zhang; Bettina Haase; Jacquelyn Mountca...; Olivier Fedrigo; John Fogg; Bogdan Kirilenko; Chetan Munegowda; Michael Hiller; Aashish Jain; Daisuke Kihara; Arang Rhie; Adam M. Phillippy; Scott A. Swanson; Peng Jiang; Dennis O. Clegg; Erich D. Jarvis; James A. Thomson; Ron Stewart; Mark J. P. Chaisson; Yury V. Bukhman
• Keywords: Model Organism; Sequence assembly

Abstract Background The Nile rat ( Avicanthis niloticus ) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity humans in these aspects, compared the widely used Mus musculus Rattus norvegicus models, holds promise better translation research findings clinic. Results We report 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated Vertebrate Genomes Project (VGP). highly contiguous, contig N50 11.1 Mb, scaffold 83 95.2% sequence assigned chromosomes. novel workflow identify 3613 segmental duplications quantify duplicated genes. Comparative analyses revealed unique genomic features rat, including some that affect genes associated type 2 metabolic dysfunctions. discuss 14 are heterozygous diverged from house mouse. Conclusions Our reflect exceptional level resolution present this assembly, which will greatly expand potential as organism.