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Genomic variation in captive deer mouse (Peromyscus maniculatus) populations

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...

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Autores principales: Lucius, Matthew D., Ji, Hao, Altomare, Diego, Doran, Robert, Torkian, Ben, Havighorst, Amanda, Kaza, Vimala, Zhang, Youwen, Gasparian, Alexander V., Magagnoli, Joseph, Shankar, Vijay, Shtutman, Michael, Kiaris, Hippokratis
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8438655/
https://www.ncbi.nlm.nih.gov/pubmed/34521341
http://dx.doi.org/10.1186/s12864-021-07956-w
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author Lucius, Matthew D.
Ji, Hao
Altomare, Diego
Doran, Robert
Torkian, Ben
Havighorst, Amanda
Kaza, Vimala
Zhang, Youwen
Gasparian, Alexander V.
Magagnoli, Joseph
Shankar, Vijay
Shtutman, Michael
Kiaris, Hippokratis
author_facet Lucius, Matthew D.
Ji, Hao
Altomare, Diego
Doran, Robert
Torkian, Ben
Havighorst, Amanda
Kaza, Vimala
Zhang, Youwen
Gasparian, Alexander V.
Magagnoli, Joseph
Shankar, Vijay
Shtutman, Michael
Kiaris, Hippokratis
author_sort Lucius, Matthew D.
collection PubMed
description 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 × 10(9) 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07956-w.
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spelling pubmed-84386552021-09-14 Genomic variation in captive deer mouse (Peromyscus maniculatus) populations Lucius, Matthew D. Ji, Hao Altomare, Diego Doran, Robert Torkian, Ben Havighorst, Amanda Kaza, Vimala Zhang, Youwen Gasparian, Alexander V. Magagnoli, Joseph Shankar, Vijay Shtutman, Michael Kiaris, Hippokratis BMC Genomics Research 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 × 10(9) 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07956-w. BioMed Central 2021-09-14 /pmc/articles/PMC8438655/ /pubmed/34521341 http://dx.doi.org/10.1186/s12864-021-07956-w Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Lucius, Matthew D.
Ji, Hao
Altomare, Diego
Doran, Robert
Torkian, Ben
Havighorst, Amanda
Kaza, Vimala
Zhang, Youwen
Gasparian, Alexander V.
Magagnoli, Joseph
Shankar, Vijay
Shtutman, Michael
Kiaris, Hippokratis
Genomic variation in captive deer mouse (Peromyscus maniculatus) populations
title Genomic variation in captive deer mouse (Peromyscus maniculatus) populations
title_full Genomic variation in captive deer mouse (Peromyscus maniculatus) populations
title_fullStr Genomic variation in captive deer mouse (Peromyscus maniculatus) populations
title_full_unstemmed Genomic variation in captive deer mouse (Peromyscus maniculatus) populations
title_short Genomic variation in captive deer mouse (Peromyscus maniculatus) populations
title_sort genomic variation in captive deer mouse (peromyscus maniculatus) populations
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8438655/
https://www.ncbi.nlm.nih.gov/pubmed/34521341
http://dx.doi.org/10.1186/s12864-021-07956-w
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