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仅使用牛津纳米孔技术 (Oxford Nanopore Technologies) 组装的寄生虫基因组进行 de novo 评估

Kaylee S Herzog¹, Rachel Wu¹, John M Hawdon²

¹Department of Epidemiology, University of Nebraska Medical Center, Omaha, NE 68198, USA.

|August 30, 2024

概括

寄生性线虫的高质量de novo基因组组件仅使用牛津纳米孔技术MINION数据生成. 这些组件的连续性和完整性与现有参考资料相比相当或更好.

科学领域:

基因组学就是基因组学.
寄生虫学的寄生虫学
生物信息学是一种生物信息学.

背景情况:

精确的基因组组合对于理解寄生性线虫生物和开发控制策略至关重要.
以前的基因组组装方法通常依赖于多种测序技术.

研究的目的:

为了评估三种寄生性线虫物种的新基因组组合的质量,仅使用牛津纳米孔技术的MinION数据.
将这些组件与现有的参考基因组和用Illumina数据增强的基因组进行比较.

主要方法:

仅使用MinION数据为Brugia malayi,Trichuris trichiura和Ancylostoma caninum生成了新的基因组组件.
与参考基因组相比较的组装指标 (连续性,完整性,基因含量)
通过比较MinION组合与Illumina抛光或混合组合来评估基因组合的准确性.

主要成果:

与参考基因组相比,只有MinION组件显示出类似或更高的连续性,完整性和基因含量.
基因组合分析显示,MinION-only和Illumina-polished组件之间具有很高的相同性 (88.997.6%).
优化的DNA提取和图书馆准备使得从B. malayi和T. trichiura的单个标本中重新组装成为可能.

结论:

牛津纳米孔技术 (Oxford Nanopore Technologies) 仅凭MiniON数据就足以生成寄生性线虫的高质量的新基因组组.
通过Illumina数据抛光,可以逐步提高基因水平的准确性.
经过修改的协议可以从有限的原始材料中进行基因组组装.

关键词:

生物科学仪器仪器仪器仪表基因组分析基因组分析基因组学就是基因组学.寄生虫学的寄生虫学遗传学的技术在遗传学的技术.

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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.