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

Abstract

We constructed a high-density genetic map for Mongolian gerbils ( Meriones unguiculatus ). We genotyped 137 F2 individuals with a genotype-by-sequencing (GBS) approach at over 10,000 loci and built the genetic map using a two-step approach. First, we chose the highest-quality set of 485 markers to construct a robust map of 1239 cM with 22 linkage groups as expected from the published karyotype. Second, we added an additional 5449 markers onto the map based on their genotype similarity with the original markers. We used the final marker set to assemble 1140 genomic scaffolds (containing ~ 20% of annotated genes) into a chromosome-level assembly. We used both genetic linkage and relative sequencing coverage in males and females to identify X- and Y-chromosome scaffolds and from these we designed a robust and internally-controlled PCR assay to determine sex. This assay will facilitate early stage sex-typing of embryonic and young gerbils which is difficult using current visual methods. Accession ID: Meriones unguiculatus : 10047. Electronic supplementary material The online version of this article (10.1007/s00335-019-09799-z) contains supplementary material, which is available to authorized users.

A chromosome-assigned Mongolian gerbil genome with sequenced centromeres provides evidence of a new chromosome

“…Gerbil genome: approach and summary statistics We sequenced and assembled the genome of the Mongolian gerbil, Meriones unguiculatus into 245 contigs using PacBio HiFi reads and scaffolded OmniC chromatin conformation capture data (Figure S2), Oxford Nanopore long and ultra-long read sequence data, a genetic map (Table S1) (Brekke et al 2019), and BioNano optical mapping. We assigned scaffolds to chromosomes by flow-sorting chromosomes into pools.…”

“…We used a permutation test to show that GC-rich genes are clustered together more than is expected by chance (Figure 4A, observed = 1.71Mbp, mean = 2.89Mbp, n=1,000,000 permutations, p < 0.000001). We used our genetic map (Brekke et al 2019) to locate recombination hotspots which were defined as regions with 5x higher recombination rate than the genome average (as per (Katzer et al 2011). Hotspots were found on 18 of 22 chromosomes (21 autosomes and the X chromosome, we omit the Y chromosome here as it does not recombine) with 2.4+/-2.2(sd) hotspots per chromosome (Figures S11, S12, S13).…”

X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters

“…Expressed genes were then integrated onto the genetic map by comparing captured SNV genotypes to RADtag genotypes. Following Brekke et al . (2019), we counted shared genotypes between each RADtag and each gene across all individuals, placing genes at the location of the RADtag with which they shared the most genotypes.…”

“…Expressed genes were then integrated onto the genetic map by comparing captured SNV genotypes to RADtag genotypes. Following Brekke et al (2019), we counted shared genotypes between each RADtag and each gene across all individuals, placing genes at the location of the RADtag with which they shared the most genotypes. In the event of a tie between multiple RADtags, the gene was placed at the proximal map location and only genes sharing at least 90% of genotypes with at least one RADtag were placed on the map.…”

Shed skin as a source of DNA for genotyping-by-sequencing (GBS) in reptiles

“…We used the coverage from each individual to identify sex-linked genomic contigs as described previously (Brekke et al, 2019; Brekke, Steele, & Mulley, 2018) by first calculating each individuals’ sequencing effort as the sum of aligned reads for that individual. We standardised the contig-level counts by dividing by the sequencing effort of each individual and multiplying by 1,000,000.…”