Genome sequence of a diabetes-prone rodent reveals a mutation hotspot around the ParaHox gene cluster

Abstract

The sand rat Psammomys obesus is a gerbil species native to deserts of North Africa and the Middle East, and is constrained in its ecology because high carbohydrate diets induce obesity and type II diabetes that, in extreme cases, can lead to pancreatic failure and death. We report the sequencing of the sand rat genome and discovery of an unusual, extensive, and mutationally biased GC-rich genomic domain. This highly divergent genomic region encompasses several functionally essential genes, and spans the ParaHox cluster which includes the insulin-regulating homeobox gene Pdx1. The sequence of sand rat Pdx1 has been grossly affected by GC-biased mutation, leading to the highest divergence observed for this gene across the Bilateria. In addition to genomic insights into restricted caloric intake in a desert species, the discovery of a localized chromosomal region subject to elevated mutation suggests that mutational heterogeneity within genomes could influence the course of evolution.

Intrauterine position probabilities in mice, rats and gerbils

“…a model for tissue regeneration (Santos et al, 2016; Seifert et al, 2012)), deer mice ( Peromyscus sp. , models for population genetics and adaptation (Weber et al, 2013; Bedford and Hoekstra, 2015; Bendesky et al, 2017)), sandrats (a model for diet-induced diabetes (Hargreaves et al, 2017; Donath et al, 1999)), hamsters (Brekke et al, 2016; Brekke and Good, 2014) and degus ( Octodon degus (Roff et al, 2017; Correa et al, 2016, 2013)), as well as rabbits (Banszegi et al, 2009) and other mammals.…”

A high-density genetic map and molecular sex-typing assay for gerbils

“…Rodents in the gerbil subfamily (Rodentia, muridae, gerbillinae) have been an important model for a huge range of organismal and evolutionary research. Gerbils inhabit the arid semi-deserts and steppes of Africa, Asia, and the Indian subcontinent and exhibit a wide range of adaptations to low water availability and poor food quality such as increased kidney function (Wilber and Gilchrist 1965), digestive function (Liu and Wang 2007) and altered insulin activity (Hargreaves et al 2017). The extreme environmental pressures and a strong social structure have adapted Mongolian gerbil females to have a high degree of control over the sex ratio, even the ability to skew sex ratio in the left and right uterine horns independently (Clark et al 1994).…”

“…While a great deal of cytological research has been done on various gerbils (Cohen 1970;Benazzou et al 1982), there has been no bridge yet between the new genomics era and these classic karyotype studies. Three gerbil species (Mongolian gerbils, fat sandrats, and great gerbils) have all recently had their genomes sequenced (Hargreaves et al 2017;Zorio et al 2018;Nilsson et al 2018). But as yet, none of these genomes are complete and all assemblies are highly fragmented.…”

“…One example is a missing region approximately five megabases long around the ParaHox cluster of Gsx1, Pdx1 and Cdx2. Due to its high GC-content a great deal of special effort to enrich the libraries for GC-rich DNA was required to successfully sequence the ParaHox region in fat sandrats (Hargreaves et al 2017), and such effort has not been made for the other two gerbil species. Nor has any effort been made to increase contiguity of the gerbil genomes.…”

The complete mitochondrial genome ofPsammomys obesus(Rodentia: Muridae)

“…3, NO. 1, 97-98 https://doi.org/10.1080/23802359.2017.1422396 FichetCalvet et al 1999Shenbrot 2004;Ouadda et al 2009;Hargreaves et al 2017), molecular studies about P. obesus are limited. No mitochondrial genome of P. obesus is available until now.…”