跨技术观察到的海洋病毒多样性的有限共识
Marina Vila-Nistal1,2, Francisco Martinez-Hernandez1,2, Monica Lluesma-Gomez1,2
1Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, 03690, Alicante, Spain.
Environmental microbiome
|December 30, 2025
概括
通过比较病毒学方法,PacBio HiFi和Illumina测序最能恢复海洋病毒多样性和微型多样性. 结合方法对于完全了解病毒基因组至关重要.
科学领域:
- 海洋生物学 海洋生物学
- 病毒学 病毒学
- 基因组学就是基因组学.
背景情况:
- 病毒对生态系统功能至关重要,但目前的方法限制了探索病毒多样性的方法.
- 了解病毒多样性和微型多样性需要评估不同的病毒学方法和测序技术.
- 方法上的限制影响了病毒多样性和功能的估计,阻碍了对病毒组合和宿主相互作用的理解.
研究的目的:
- 为了比较短读和长读病毒基因组学和单个病毒基因组学,以恢复病毒多样性和微型多样性.
- 评估不同测序方法 (Illumina,PacBio-HiFi,MinION) 和单病毒基因组学 (SVG) 的共识和局限性.
- 评估各种方法在不同分类层捕获病毒多样性的能力,并解决基因组微多样性的能力.
主要方法:
- 针对病毒学,Illumina,PacBio-HiFi和MinION测序的比较.
- 700个未培养的病毒的高通量单病毒基因组学 (SVG).
- 对病毒结合体,在属和物种层面的操作分类单元 (OTU) 和病毒家族的分析.
- 使用丰富的类动物 (Pelagimarinivirus ubique) 来评估微生物多样性恢复的案例研究.
主要成果:
- 获得了大约42,000个病毒结合体 (>10 kb),分别在属和物种层面产生了约12,500个和23,400个病毒OTU.
- 单个病毒基因组学 (SVG) 在病毒家族层面显示出一个独特的分类特征.
- 通过所有方法捕获的物种和属不到1%;PacBio-HiFi和Illumina显示了最高的对对多样性共识 (~11%的物种级重叠).
- 微型多样性病毒的完整基因组组合需要将所有数据集结合起来;通过任何单一方法都无法恢复菌株级集群.
结论:
- 方法上的偏见仍然是恢复海洋病毒多样性和微生物多样性的挑战.
- 与Illumina测序相结合的PacBio HiFi在标准病毒学技术中提供了病毒物种和属的最佳恢复.
- 综合性病毒基因组恢复需要整合来自多种测序和基因组方法的数据.
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