Chromosome 1 Sequence Analysis of C57BL/6J-Chr1KM Mouse Strain
The Chinese Kunming (KM) mouse is a widely used outbred mouse stock in China. However, its genetic structure remains unclear. In this study, we sequenced the genome of the C57BL/6J-Chr1KM (B6-Chr1KM) strain, the chromosome 1 (Chr 1) of which was derived from one KM mouse. With 36.6× average coverage...
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| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2017-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2017/1712530 |
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| author | Fuyi Xu Tianzhu Chao Yiyin Zhang Shixian Hu Yuxun Zhou Hongyan Xu Junhua Xiao Kai Li |
| author_facet | Fuyi Xu Tianzhu Chao Yiyin Zhang Shixian Hu Yuxun Zhou Hongyan Xu Junhua Xiao Kai Li |
| author_sort | Fuyi Xu |
| collection | DOAJ |
| description | The Chinese Kunming (KM) mouse is a widely used outbred mouse stock in China. However, its genetic structure remains unclear. In this study, we sequenced the genome of the C57BL/6J-Chr1KM (B6-Chr1KM) strain, the chromosome 1 (Chr 1) of which was derived from one KM mouse. With 36.6× average coverage of the entire genome, 0.48 million single nucleotide polymorphisms (SNPs) and 96,679 indels were detected on Chr 1 through comparison with reference strain C57BL/6J. Moreover, 46,590 of them were classified as novel mutations. Further functional annotation identified 155 genes harboring potentially functional variants, among which 27 genes have been associated with human diseases. We then performed sequence similarity and Bayesian concordance analysis using the SNPs identified on Chr 1 and their counterparts in three subspecies, Mus musculus domesticus, M. m. musculus, and M. m. castaneus. Both analyses suggested that the Chr 1 sequence of B6-Chr1KM was predominantly derived from M. m. domesticus while 9.7% of the sequence was found to be from M. m. musculus. In conclusion, our analysis provided a detailed description of the genetic variations on Chr 1 of B6-Chr1KM and a new perspective on the subspecies origin of KM mouse which can be used to guide further genetic studies with this mouse strain. |
| format | Article |
| id | doaj-art-3e4725b797404c20b05ebbddeeb70405 |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2017-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-3e4725b797404c20b05ebbddeeb704052025-02-03T06:06:13ZengWileyInternational Journal of Genomics2314-436X2314-43782017-01-01201710.1155/2017/17125301712530Chromosome 1 Sequence Analysis of C57BL/6J-Chr1KM Mouse StrainFuyi Xu0Tianzhu Chao1Yiyin Zhang2Shixian Hu3Yuxun Zhou4Hongyan Xu5Junhua Xiao6Kai Li7College of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, ChinaCollege of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, ChinaCollege of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, ChinaCollege of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, ChinaCollege of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, ChinaDepartment of Biostatistics and Epidemiology, Medical College of Georgia, Augusta University, Augusta, GA, USACollege of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, ChinaCollege of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, ChinaThe Chinese Kunming (KM) mouse is a widely used outbred mouse stock in China. However, its genetic structure remains unclear. In this study, we sequenced the genome of the C57BL/6J-Chr1KM (B6-Chr1KM) strain, the chromosome 1 (Chr 1) of which was derived from one KM mouse. With 36.6× average coverage of the entire genome, 0.48 million single nucleotide polymorphisms (SNPs) and 96,679 indels were detected on Chr 1 through comparison with reference strain C57BL/6J. Moreover, 46,590 of them were classified as novel mutations. Further functional annotation identified 155 genes harboring potentially functional variants, among which 27 genes have been associated with human diseases. We then performed sequence similarity and Bayesian concordance analysis using the SNPs identified on Chr 1 and their counterparts in three subspecies, Mus musculus domesticus, M. m. musculus, and M. m. castaneus. Both analyses suggested that the Chr 1 sequence of B6-Chr1KM was predominantly derived from M. m. domesticus while 9.7% of the sequence was found to be from M. m. musculus. In conclusion, our analysis provided a detailed description of the genetic variations on Chr 1 of B6-Chr1KM and a new perspective on the subspecies origin of KM mouse which can be used to guide further genetic studies with this mouse strain.http://dx.doi.org/10.1155/2017/1712530 |
| spellingShingle | Fuyi Xu Tianzhu Chao Yiyin Zhang Shixian Hu Yuxun Zhou Hongyan Xu Junhua Xiao Kai Li Chromosome 1 Sequence Analysis of C57BL/6J-Chr1KM Mouse Strain International Journal of Genomics |
| title | Chromosome 1 Sequence Analysis of C57BL/6J-Chr1KM Mouse Strain |
| title_full | Chromosome 1 Sequence Analysis of C57BL/6J-Chr1KM Mouse Strain |
| title_fullStr | Chromosome 1 Sequence Analysis of C57BL/6J-Chr1KM Mouse Strain |
| title_full_unstemmed | Chromosome 1 Sequence Analysis of C57BL/6J-Chr1KM Mouse Strain |
| title_short | Chromosome 1 Sequence Analysis of C57BL/6J-Chr1KM Mouse Strain |
| title_sort | chromosome 1 sequence analysis of c57bl 6j chr1km mouse strain |
| url | http://dx.doi.org/10.1155/2017/1712530 |
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