Mouse substrains are an invaluable model for understanding disease. We compared C57BL/6J, which is the most commonly used inbred mouse strain, with 8 C57BL/6 and 5 C57BL/10 closely related inbred substrains. Whole genome sequencing and RNA-sequencing analysis yielded 352,631 SNPs, 109,096 INDELs, 150,344 short tandem repeats (STRs), 3,425 structural variants (SVs) and 2,826 differentially expressed genes (DEGenes) among these 14 strains. 312,981 SNPs (89%) distinguished the B6 and B10 lineages. These SNPs were clustered into 28 short segments that are likely due to introgressed haplotypes rather than new mutations. Outside of these introgressed regions, we identified 53 SVs, protein-truncating SNPs and frameshifting INDELs that were associated with DEGenes. Our results can be used for both forward and reverse genetic approaches, and illustrate how introgression and mutational processes give rise to differences among these widely used inbred substrains.

中文翻译：

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多态性 SNP、短串联重复序列和结构变异是 C57BL/6 和 C57BL/10 亚株之间差异基因表达的原因

小鼠亚系是了解疾病的宝贵模型。我们将最常用的近交小鼠品系 C57BL/6J 与 8 个 C57BL/6 和 5 个 C57BL/10 密切相关的近交亚品系进行了比较。全基因组测序和 RNA 测序分析在这 14 个菌株中产生了 352,631 个 SNP、109,096 个 INDEL、150,344 个短串联重复序列 (STR)、3,425 个结构变异 (SV) 和 2,826 个差异表达基因 (DEGenes)。312,981 个 SNP (89%) 区分了 B6 和 B10 谱系。这些 SNP 被聚集成 28 个短片段，这可能是由于基因渗入的单倍型而不是新突变。在这些基因渗入区域之外，我们鉴定了 53 个与 DEGenes 相关的 SV、蛋白质截断 SNP 和移码 INDEL。我们的结果可用于正向和反向遗传方法，