GENOME REPORT: Chromosome-scale genome assembly of the African spiny mouse ( Acomys cahirinus )

Abstract

There is increasing interest in the African spiny mouse ( Acomys cahirinus ) as a model organism because of its ability for regeneration of tissue after injury in skin, muscle, and internal organs such as the kidneys. A high-quality reference genome is needed to better understand these regenerative properties at the molecular level. Here, we present an improved reference genome for A. cahirinus generated from long Nanopore sequencing reads. We confirm the quality of our annotations using RNA sequencing data from four different tissues. Our genome is of higher contiguity and quality than previously reported genomes from this species and will facilitate ongoing efforts to better understand the regenerative properties of this organism.

Figure 1.. Karyotype of Acomys cahirinus and results of Hi-C scaffolding of the assembly.

(A) Representative karyotype of a male A. cahirinus from the same colony that DNA and RNA were obtained from for sequencing and assembly. (B) Hi-C interaction contact heatmap of 19 Acomys pseudo-chromosomes matches the karyotype (bin size is 1 Mb).

Figure 2.

(A) Repeat landscapes for Acomys cahirinus and Mus musculus, visualizing the percent of each genome comprised of different types of repeats according to their divergence from family consensus (DNA, DNA transposon; LINE, long interspersed nuclear element; LTR, long terminal repeat retrotransposon; SINE, short interspersed nuclear element). (B) Venn diagram showing the number of genes per tissue with an RPKM value greater than 1. The majority of genes (2,457; 23%) are expressed at this level in all four tissues, while testis had the highest number of genes (2,148; 20%) with an RPKM greater than 1 not seen in other tissues.