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通过全基因组牛津纳米孔测序评估多重位移放大效应的好处和局限性

Fiifi Agyabeng-Dadzie¹, Megan S Beaudry², Alex Deyanov³

¹Department of Genetics, University of Georgia, Athens, Georgia, USA.

Molecular ecology resources

|February 28, 2025

概括

多重位移放大 (MDA) 能够从最小的DNA进行高质量的基因组测序. 一个新的工具,CADECT,去除 concatemers 改进基因组组装,对于难以培养的病原体至关重要.

科学领域:

基因组学和分子生物学
生物信息学和计算生物学
传染病研究传染病研究

背景情况:

从有限的DNA进行全基因组放大对于测序具有挑战性的生物是必不可少的.
多重位移放大 (MDA) 是一种强大的放大DNA的技术.
长读测序技术为基因组组装提供了优势.

研究的目的:

评估MDA与牛津纳米孔技术 (ONT) 测序相结合的有效性,以实现低成本的基因组组装.
从微小的DNA数量生成高质量的基因组序列,评估MDA的极限.
开发一种计算方法,用于处理在MDA过程中生成的合体序列.

主要方法:

利用多重位移放大 (MDA) 进行全基因组放大.
采用牛津纳米孔技术 (ONT) 快速图书馆准备和minION测序.
开发并应用CADECT (合体检测工具) 管道来识别和删除合体序列.

主要成果:

实现了对各种 prokaryotic (例如,金黄色葡萄球菌,大肠杆菌) 和真核生物 (Cryptosporidium spp.) 的几乎完整的基因组序列. 病原体. 病原体. 这些病原体.
从0.025 ng的总DNA中生成高质量的数据.
CADECT管道成功地减轻了协同基因组序列的影响,改善了基因组组装连续性,即使有退化的DNA.

结论:

对于从有限的DNA输入中生成高质量的基因组组件,MDA非常有效.
在CADECT管道显著提高基因组组装通过解决MDA诱导的 concatemers.
这种方法对研究不能培养的生物和加快临床诊断具有重大意义.

关键词:

它们是Apicomplexa的复合物.进入细菌体中的细菌.科科科科 (Enterococcaceae) 是一个植物.传染病是一种传染性疾病.低丰富度DNA的DNA是什么罕见的DNA 罕见的DNA

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