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T2T Colletotrichum lini 基因组与Hifiasm:ONT R9和R10 阅读处理和组装指南的真菌.

Elizaveta A Ivankina1, Ekaterina M Dvorianinova1, Alexander A Arkhipov1,2

  • 1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.

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概括

优化的牛津纳米孔技术 (ONT) 测序和Hifiasm组合参数使得像Collettotrichum lini.等真菌病原体的完整的端粒到端粒 (T2T) 基因组组合成为可能. 这有助于基因组研究和对亚麻麻病的理解.

关键词:
科莱托特里 (Colletotrichum lini) 是一种植物.这是一个纳米孔.R9.4.1 和 R10.4.1 流量细胞在T2T基因组组装中.人类鼻 (英语:anthracnose) 是一种人类鼻.基础调用工具 基础调用工具亚麻病原体是亚麻中的病原体.阅读处理 阅读处理

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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.
  • 菌类学 菌类学是指菌类学.

背景情况:

  • 端粒对端粒 (T2T) 基因组组装对于理解复杂的真菌病原体基因组至关重要.
  • 科莱托里奇 (Colletotrichum lini) 引起了显著的亚麻人科病,需要进行详细的基因组分析.

研究的目的:

  • 使用牛津纳米孔技术 (ONT) 测序数据优化T2T基因组组合的指导方针.
  • 为了评估不同的基调工具,阅读过策略和基因组覆盖水平,以提高组装质量.

主要方法:

  • 分析了来自四个C. lini菌株的ONT R9.4.1和R10.4.1测序数据.
  • 与Guppy和Dorado基调器进行比较,质量/长度读取过率 (Q10/Q15,5kb/10kb) 和覆盖率 (5x-160x).
  • 使用了 Hifiasm 0.25.0 组装器与 --ont 模块进行基因组组装.

主要成果:

  • 多拉多基础调用提高了读数质量和端粒分辨率,特别是R10.4.1数据.
  • 通过中等覆盖率 (40-65x) 和特定过 (R10.4.1的Q15/5kb,R9.4.1的Q10/5kb) 实现了最佳组装.
  • 实现了T2T/近T2T组合 (53.7-56.1 Mb),12-13个染色体,完整的线粒体基因组和>98.5%的BUSCO完整性.

结论:

  • 优化了ONT数据预处理和Hifiasm组装,为C. lini. lini提供了高质量的T2T基因组.
  • 使用ONT技术为真菌基因组组装建立了一个强大的框架.
  • 这些发现支持未来的研究基因组变异和致病性在Colletotrichum物种.