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在长时间读取的基因组组合中,使用MiSeq amplicons改进了高度重复的MHC基因的简单型分辨率

Samantha Mellinger¹, Martin Stervander^1,2,3, Max Lundberg¹

¹Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden.

|July 17, 2023

概括

安普利康测序验证了鸟类基因组中的主要基因相容性复合体 (MHC) 基因多样性. 这种方法补充了长读测序,改善了复杂多基因家族的对应数准确性和哈普洛型推断.

科学领域:

基因组学就是基因组学.
生物信息学是一种生物信息学.
进化生物学进化生物学

背景情况:

长读测序推进了复杂的基因组区域组合,包括主要基因相容性综合体 (MHC).
流鸟的MHC基因扩张产生了众多,高度相似的类似物,即使使用先进的技术也具有挑战性的组装.
MHC等位基因之间的高序列分歧可能会导致双体意识组装器错误地分类类型,导致对等位基因数的高估/低估.

研究的目的:

通过使用长读和安普利康测序来验证大 (Acrocephalus arundinaceus) 的MHC多样性.
在长读组合中评估MHC基因注释的准确性.
评估安普利康序列化作为验证MHC对应数和推断单元类型的补充方法.

主要方法:

产生了原始和经过哈普洛型清理的长读基因组组件.
执行了MHC I类 (MHC-I) 和IIB类 (MHC-IIB) 等位基因单个前基因的Illumina MiSeq扩增序列.
将安普利康序列映射到MHC-IIB等位基因的长读组合和确定父系起源.

主要成果:

安普利康测序检测到84%的注释MHC-I和78%的MHC-IIB等位基因,表明长读组合中的注释不完整.
某些MHC-IIB支架的高核酸相似性和母/父起源表明错误分配是作为单独的基点而不是单元型.
由于错误分类的平分类型,在平分类基因组组合中高估了MHC-IIB平分类型的数量.

结论:

安普利康测序是验证MHC基因注释和从长读测序中获得的对应数值的宝贵工具.
这种方法提高了在具有高序列相似性的多基因家族中哈普洛型推断的准确性.
整合长时间读取数据的安普利康测序可以提高像MHC这样复杂的基因组区域的分辨率.

关键词:

安普利康测序的测序方法副本数量变化的变化家庭家庭家庭家庭哈普洛伊德基因组组装组链接分析链接分析 MHC多样性的多样性主要的组织相容性复杂.

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