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从PacBio HiFi数据估计基因转换通道的长度和速率

Anders Poulsen Charmouh¹, Peter Sørud Porsborg¹, Lasse Thorup Hansen²

¹Bioinformatics Research Centre, Aarhus University, University City 81, DK-8000 Aarhus C, Denmark.

Molecular biology and evolution

|February 21, 2025

概括

估计基因转化率和通道长度是很困难的. 一种使用长期读取的测序数据的新方法可以准确地测量这些因素,即使基因变异很小,也可以应用于人类精子数据.

科学领域:

遗传学是一个遗传学.
分子生物学分子生物学
生物信息学是一种生物信息学.

背景情况:

基因转换是一种关键的遗传重组过程,涉及DNA序列转移.
它在等位基因组合和突变逆转中发挥作用,但准确的速率和通道长度估计仍然具有挑战性.
基因转换是非交叉 (NCO) 事件的一个子集.

研究的目的:

开发和验证一种用于估计基因转换率,通道长度和检测概率的新方法.
为了能够从高保真性 (HiFi) PacBio 长时间读取的测序数据,特别是从子细胞的测序数据中推断.
提供一种无偏见的方法,即使在低单核酸变异 (SNV) 密度下也能有效运行.

主要方法:

开发一种新的计算方法来分析长时间读取的测序数据.
使用模拟的数据集与不同的通道长度,NCO事件数量,SNV密度和SNV密度相关性.
该方法应用于来自人类精子的PacBio测序数据.

主要成果:

这种新方法准确地估计了基因转换通道的长度,速率和检测概率.
该方法在不同的SNV密度中是无偏见的,不需要人口或进化假设.
模拟表明,在较低的SNV密度下 (例如,人类),只有约2%的NCO事件可以被检测为基因转换.

结论:

提出的方法提供了一个强大的方法来量化基因转换事件使用长读序列.
这种工具对于研究包括人类在内的各种生物体中的遗传变异和重组是有价值的.
这些发现凸显了低变异基因组中基因转换事件的低可检测性.

关键词:

基因转换基因转换基因组的演化基因组的演化基因组学方法基因组学方法没有交叉的非交叉.再组合的复合方式.

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