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

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.

A high-quality blue whale genome, segmental duplications, and historical demography

“…However, the total bases of resolved SD sequence may reflect the sequencing depth used: 50-60× coverage in blue whale versus 121× in vaquita and ~80× in cow. Contrary to patterns of recent bursts of SD in primate (40) as well as muroid genomes (38,41), SDs represent a smaller fraction of genomes in cetartiodactyla. Between 0.7-3.4% of cetartiodactyl genomes are duplicated regions, compared to 4-14% in rodent and primate genomes.…”

“…High-quality genomes from long-read assemblies have been shown to resolve more duplicated sequences than short-read assemblies (32), indicating this study enables comparative analysis of repetitive DNA and gene copy numbers in cetacean genomes. We applied a computational pipeline recently developed to analyze duplicated genes in rodentia (38) to assess if there are duplications that could be associated with size differences in cetacea. The vaquita, the world's smallest cetacean, provides a comparison point to the blue whale in terms of body size, while the cow is a terrestrial relative of both species.…”

“…See our OSF repository (169) for a more detailed description in wiki/1_body_size_and_development and the R script 1_body_size_and_development/body_size_and_development_genes.R. See also (38) for a more detailed description of our literature mining methodology.…”