Genomic variation in captive deer mouse (Peromyscus maniculatus) populations

Creators

Alexander V. Gasparian, Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina
Hao Ji, Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina
Ben Torkian, Research Computing, Division of Information Technology, University of South Carolina
Michael Shtutman, Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina
Diego Altomare, Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina
Robert Doran, Research Computing, Division of Information Technology, University of South Carolina
Joseph Magagnoli, Department of Clinical Pharmacy and Outcomes Sciences, College of Pharmacy, University of South Carolina
Hippokratis Kiaris, Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina
Amanda Havighorst, Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina
Vijay Shankar, Center for Human Genetics, College of Science, Clemson University
Youwen Zhang, Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina
Vimala Kaza, Peromyscus Genetic Stock Center, University of South Carolina
Matthew D. Lucius, Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina

Description

Abstract Background Deer mice (genus Peromyscus) are the most common rodents in North America. Despite the availability of reference genomes for some species, a comprehensive database of polymorphisms, especially in those maintained as living stocks and distributed to academic investigators, is missing. In the present study we surveyed two populations of P. maniculatus that are maintained at the Peromyscus Genetic Stock Center (PGSC) for polymorphisms across their 2.5 × 109 bp genome. Results High density of variation was identified, corresponding to one SNP every 55 bp for the high altitude stock (SM2) or 207 bp for the low altitude stock (BW) using snpEff (v4.3). Indels were detected every 1157 bp for BW or 311 bp for SM2. The average Watterson estimator for the BW and SM2 populations is 248813.70388 and 869071.7671 respectively. Some differences in the distribution of missense, nonsense and silent mutations were identified between the stocks, as well as polymorphisms in genes associated with inflammation (NFATC2), hypoxia (HIF1a) and cholesterol metabolism (INSIG1) and may possess value in modeling pathology. Conclusions This genomic resource, in combination with the availability of P. maniculatus from the PGSC, is expected to promote genetic and genomic studies with this animal model.

Publication Date

1-1-2021

Publisher

figshare Academic Research System

DOI

10.6084/m9.figshare.c.5618665.v1

Document Type

Data Set

Recommended Citation

Gasparian, Alexander V.; Ji, Hao; Torkian, Ben; Shtutman, Michael; Altomare, Diego; Doran, Robert; Magagnoli, Joseph; Kiaris, Hippokratis; Havighorst, Amanda; Shankar, Vijay; Zhang, Youwen; Kaza, Vimala; Lucius, Matthew D. (2021), "Genomic variation in captive deer mouse (Peromyscus maniculatus) populations", figshare Academic Research System, doi: 10.6084/m9.figshare.c.5618665.v1

https://doi.org/10.6084/m9.figshare.c.5618665.v1

Identifier

10.6084/m9.figshare.c.5618665.v1

Related Content

10.1186/s12864-021-07956-w

Embargo Date

1-1-2021