摘要
目的利用全基因组测序方法比较BALB/c突变卷毛鼠与正常BALB/c小鼠基因组之间的差异。方法采用Illumina PE 150测序平台对BALB/c突变卷毛鼠与正常BALB/c小鼠进行全基因组测序并对遗传变异信息(SNP、INDEL、SV和CNV)进行对比分析。结果正常小鼠与卷毛小鼠产生的Raw Data分别为122.85 Gb和118.04 Gb,过滤后的Clean Data分别为119.82 Gb和112.18 Gb,表明测序质量合格。正常小鼠与卷毛小鼠的GC含量分别为40.63%和40.48%,说明GC分布正常。卷毛小鼠的杂合分型SNPs总数显著高于正常小鼠,同时正常小鼠与卷毛小鼠之间的累计SNPs深度分布也存在显著的差异。卷毛小鼠与正常小鼠插入缺失(Indels)以及累计Indels深度分布均存在差异。卷毛小鼠与正常小鼠的SV类型中大片段的插入卷毛小鼠大于正常小鼠,而其他类型则小于正常小鼠。而拷贝数变异(CNVs)结果显示正常小鼠和卷毛小鼠的拷贝数增加的个数分别为1270和967个;而拷贝数减少的个数分别为5027和3505个。结论本研究发现正常小鼠与突变卷毛鼠的基因组存在一定的差异。
Objective Whole genome sequencing was used to compare the genomic differences between BALB/c mutant curly mice and normal BALB/c mice.Method The whole genome of BALB/c mutant curly mice and normal BALB/c mice were sequenced by Illumina PE 150 sequencing platform,and the genetic variation information(SNP,INDEL,SV and CNV)were compared and analyzed.Result The raw data produced by normal mice and curly mice were 122.85 Gb and 118.04 Gb respectively,the filtered clean data were 119.82 Gb and 112.18 Gb respectively,and the GC contents were 40.63%and 40.48%respectively.The sequencing quality was qualified,the GC distribution was normal,and the library was established and sequenced successfully.The total number of heterozygous SNPs in curly mice was significantly higher than that in normal mice,and there were significant differences in the depth distribution of cumulative SNPs between normal mice and curly mice.There were differences in indels and cumulative indels depth distribution between curly mice and normal mice.The insertion of large fragments in SV types of curly mice and normal mice was larger than that of normal mice,while other types were smaller than that of normal mice.The copy number variation(CNVs)result showed that the number of copies increased in abnormal mice and curly mice were 1270 and 967,respectively;the number of copies decreased by 5027 and 3505 respectively.Conclusion This study found that there were some differences between the genomes of normal mice and mutant curly haired mice.
作者
汤紫荣
李晓娟
姜棋予
李兴杰
孙慧伟
李瑞生
TANG Zirong;LI Xiaojuan;JIANG Qiyu;LI Xingjie;SUN Huiwei;LI Ruisheng(Department of Inpatient and Medical Record Management,the Fifth Medical Center of the PLA General Hospital,Beijing 100039,China;Department of Infectious Disease Medicine,the Fifth Medical Center of the PLA General Hospital,Beijing 100039,China)
出处
《实验动物科学》
2023年第5期33-37,共5页
Laboratory Animal Science
基金
军队实验动物专项基金面上项目(SYDW[2016]005,SYDW[2020]05)。
关键词
卷毛鼠
全基因组测序
遗传变异信息
curly hair mice
whole genome sequencing
genetic variation information
