MoG+: a database of genomic variations across three mouse subspecies for biomedical research

Laboratory mouse strains have mosaic genomes derived from at least three major subspecies that are distributed in Eurasia. Here, we describe genomic variations in ten inbred strains: Mus musculus musculus -derived BLG2/Ms, NJL/Ms, CHD/Ms, SWN/Ms, and KJR/Ms; M . m . domesticus -derived PGN2/Ms and B...

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Veröffentlicht in:Mammalian genome 2022-03, Vol.33 (1), p.31-43
Hauptverfasser: Takada, Toyoyuki, Fukuta, Kentaro, Usuda, Daiki, Kushida, Tatsuya, Kondo, Shinji, Kawamoto, Shoko, Yoshiki, Atsushi, Obata, Yuichi, Fujiyama, Asao, Toyoda, Atsushi, Noguchi, Hideki, Shiroishi, Toshihiko, Masuya, Hiroshi
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container_issue 1
container_start_page 31
container_title Mammalian genome
container_volume 33
creator Takada, Toyoyuki
Fukuta, Kentaro
Usuda, Daiki
Kushida, Tatsuya
Kondo, Shinji
Kawamoto, Shoko
Yoshiki, Atsushi
Obata, Yuichi
Fujiyama, Asao
Toyoda, Atsushi
Noguchi, Hideki
Shiroishi, Toshihiko
Masuya, Hiroshi
description Laboratory mouse strains have mosaic genomes derived from at least three major subspecies that are distributed in Eurasia. Here, we describe genomic variations in ten inbred strains: Mus musculus musculus -derived BLG2/Ms, NJL/Ms, CHD/Ms, SWN/Ms, and KJR/Ms; M . m . domesticus -derived PGN2/Ms and BFM/Ms; M . m . castaneus -derived HMI/Ms; and JF1/Ms and MSM/Ms, which were derived from a hybrid between M . m . musculus and M . m . castaneus . These strains were established by Prof. Moriwaki in the 1980s and are collectively named the “Mishima Battery”. These strains show large phenotypic variations in body size and in many physiological traits. We resequenced the genomes of the Mishima Battery strains and performed a comparative genomic analysis with dbSNP data. More than 81 million nucleotide coordinates were identified as variant sites due to the large genetic distances among the mouse subspecies; 8,062,070 new SNP sites were detected in this study, and these may underlie the large phenotypic diversity observed in the Mishima Battery. The new information was collected in a reconstructed genome database, termed MoG+ that includes new application software and viewers. MoG+ intuitively visualizes nucleotide variants in genes and intergenic regions, and amino acid substitutions across the three mouse subspecies. We report statistical data from the resequencing and comparative genomic analyses and newly collected phenotype data of the Mishima Battery, and provide a brief description of the functions of MoG+, which provides a searchable and unique data resource of the numerous genomic variations across the three mouse subspecies. The data in MoG+ will be invaluable for research into phenotype-genotype links in diverse mouse strains.
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The new information was collected in a reconstructed genome database, termed MoG+ that includes new application software and viewers. MoG+ intuitively visualizes nucleotide variants in genes and intergenic regions, and amino acid substitutions across the three mouse subspecies. We report statistical data from the resequencing and comparative genomic analyses and newly collected phenotype data of the Mishima Battery, and provide a brief description of the functions of MoG+, which provides a searchable and unique data resource of the numerous genomic variations across the three mouse subspecies. 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subjects Amino acids
Animal Genetics and Genomics
Animals
Biomedical and Life Sciences
Biomedical Research
Body size
Cell Biology
Databases, Genetic
Genetic distance
Genome
Genomes
Genomic analysis
Genomics
Genotypes
Human Genetics
Inbreeding
Life Sciences
Medical research
Mice
Mice, Inbred Strains - genetics
Nucleotides
Oligodendrocyte-myelin glycoprotein
Phenotypes
Phenotypic variations
Rodents
Single-nucleotide polymorphism
Strains (organisms)
title MoG+: a database of genomic variations across three mouse subspecies for biomedical research
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