Genetic and genomic architecture in eight strains of the laboratory opossum Monodelphis domestica.

Xiao Xiong,Ana C Leandro,Paul B Samollow,John L Vandeberg,Richard Metz,Wenqi Cao,Xu Wang,Chao Zhang,A Rokas

doi:10.1093/g3journal/jkab389

Abstract

The gray short-tailed opossum (Monodelphis domestica) is an established laboratory-bred marsupial model for biomedical research. It is a critical species for comparative genomics research, providing the pivotal phylogenetic outgroup for studies of derived vs ancestral states of genomic/epigenomic characteristics for eutherian mammal lineages. To characterize the current genetic profile of this laboratory marsupial, we examined 79 individuals from eight established laboratory strains. Double digest restriction site-associated DNA sequencing and whole-genome resequencing experiments were performed to investigate the genetic architecture in these strains. A total of 66,640 high-quality single nucleotide polymorphisms (SNPs) were identified. We analyzed SNP density, average heterozygosity, nucleotide diversity, and population differentiation parameter Fst within and between the eight strains. Principal component and population structure analysis clearly resolve the strains at the level of their ancestral founder populations, and the genetic architecture of these strains correctly reflects their breeding history. We confirmed the successful establishment of the first inbred laboratory opossum strain LSD (inbreeding coefficient F > 0.99) and a nearly inbred strain FD2M1 (0.98 < F < 0.99), each derived from a different ancestral background. These strains are suitable for various experimental protocols requiring controlled genetic backgrounds and for intercrosses and backcrosses that can generate offspring with informative SNPs for studying a variety of genetic and epigenetic processes. Together with recent advances in reproductive manipulation and CRISPR/Cas9 techniques for Monodelphis domestica, the existence of distinctive inbred strains will enable genome editing on different genetic backgrounds, greatly expanding the utility of this marsupial model for biomedical research.

Highlights

The gray short-tailed opossum, Monodelphis domestica, is the world’s predominant laboratory-bred research marsupial species
The RNA-seq single nucleotide polymorphisms (SNPs) set was compared to the ddRAD-seq calls, and we identified 2151 SNP positions in both datasets
We investigated the distribution of SNP density across all chromosomes and found that (1) it is elevated in telomeric relative to non-telomeric regions of the autosomes (Figure 5A), (2) the majority of the X chromosome has less than 1 SNP per kb (Figure 5A), and (3) there is a significant negative correlation between the inbreeding coefficient and the frequency of heterozygous SNPs (Spearman’s correlation coefficient q 1⁄4 À0.67, P-value 1⁄4 2.5 Â 10À10)

Summary

Introduction

The gray short-tailed opossum, Monodelphis domestica ( known as the “laboratory opossum”), is the world’s predominant laboratory-bred research marsupial species. The body length ranges from 70 to 180 mm, and the tail is approximately half the combined head and body length (Costa et al 2003; Voss and Jansa 2003; Cope et al 2012). These animals are maintained in captivity, breed year-round, and reach sexual maturity relatively rapidly (by 6 months of age). Monodelphis domestica serves as a key model for comparative genomics research, providing the pivotal phylogenetic outgroup for studies of derived vs ancestral states of genomic/epigenomic characteristics for all eutherian mammal lineages

Methods

Results

Conclusion