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.
Highlights
The Mongolian gerbil is susceptible to diabetes (Li et al 2016) and in addition has been a research model for epilepsy (Buckmaster 2006), stroke (Vincent and Rodrick 1979), and hearing loss (Abbas and Rivolta 2015)
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
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
Summary
Moses 1980), or do not recombine (de la Fuente et al 2007). Gerbils have become popular as a medical model for a variety of human diseases. Constructing the fragmented genomes into chromosomelevel assemblies will provide an important link between current large-scale sequencing projects and the classic cytological research on karyotype evolution and genomic rearrangements. Despite having their genomes sequenced, gerbils still lack a published molecular sex-typing assay of the type that has been available for mouse for many years (Lavrovsky et al 1998). One outcome of a chromosomal-level genome assembly is the ability to design a reliable and robust molecular sex-typing PCR assay Such an assay would be less error prone and available to a much wider community of gerbil researchers. Based on sex-linkage we designed a robust and internally controlled PCR assay to determine sex of gerbils
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