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使用纳米孔长读技术在三只海 (Teleostei: Kyphosidae) 中组装线粒体基因组
J Antonio Baeza1,2,3, Jeremiah J Minish4, Todd P Michael4
1Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA.
Molecular ecology resources
|October 15, 2024
概括
牛津纳米孔技术 (ONT) 长时间阅读可以在高低测序深度准确地组装完整的线粒体基因组. 这种方法为植物遗传学研究和生物监测提供了具有成本效益的替代方案,特别是在资源有限的环境中.
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:
- 完整的线粒体基因组对于跨越各种分类层次的遗传学分析至关重要.
- 短读测序是组装线粒体基因组的传统方法.
- 长时间读取的测序技术为基因组组装提供了潜在的优势.
研究的目的:
- 为了评估使用牛津纳米孔技术 (ONT) 的线粒体基因组组合的准确性,长读.
- 通过不同测序深度,将ONT长读组合与已建立的短读组合进行比较.
- 评估基于ONT的线粒体基因组在遗传学和生物监测应用中的实用性.
主要方法:
- 通过使用ONT Kit 14 R10.4.1在不同测序深度 (高,低,非常低) 进行长读取,组装了三种海物种的线粒体基因组.
- 组件与由Illumina NovaSeq生成的参考线粒体基因组进行了比较.
- 用翻译的蛋白质编码基因进行了族群基因组分析,以推断家族关系并识别潜在的GenBank错误识别.
主要成果:
- 在两种物种中,高深度ONT长读数组 (> 25×) 与短读数组相同,没有发现错误.
- 第三个物种的长度差异很小,原因是ONT组件中的重复动机.
- 低深度 (3-5×) 的ONT组件几乎是完美的,而非常低深度 (1×) 的组件包含了许多错误.
- 遗传学分析表明,Kyphosidae家族不是单类,并突出显示了公共数据库中潜在的误认的线粒体基因组.
结论:
- 完美或准完美的线粒体基因组可以使用ONT长读在高 (>25×) 和低 (3-5×) 测序深度可靠地组装.
- ONT技术,特别是与Kit 14和R10.4.1一起,为线粒体基因组组装提供了一个准确和可访问的方法.
- 组装的基因组对于环境DNA研究,生物勘探,生物监测和改善低资源环境中的测序可访问性非常有价值.
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