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一种向丰富方法,用于增强Synchytrium endobioticum核基因组序列的恢复
Hai D T Nguyen1, Ekaterina Ponomareva1, Kasia Dadej1
1Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada.
PloS one
|February 12, 2024
概括
一个新的杂交协议显著改善了Synchytrium endobioticum的DNA恢复,这是导致土豆病的真菌. 这种方法提高了基因组测序和检测在具有挑战性的样本.
科学领域:
- 植物病理学 植物病理学
- 菌类学 菌类学是指菌类学.
- 基因组学就是基因组学.
- 分子生物学分子生物学
背景情况:
- 马病是由有义务的真菌病原体Synchytrium endobioticum引起的.
- 低DNA度和来自宿主和微生物DNA的高污染阻碍了S. endobioticum基因组测序.
- 现有的方法导致S. endobioticum核基因组序列的低于最佳的恢复.
研究的目的:
- 开发一种基于杂交的目标丰富协议,以增强S. endobioticum的DNA恢复.
- 提高基因组测序和S. endobioticum在复杂样本中的分子检测的效率.
主要方法:
- 设计了18万个分子诱,针对S. endobioticum的基因和非基因区域.
- 将诱应用于堆肥中各种S. endobioticum病变型的全基因组放大DNA,纯化的子和组织.
- 利用Illumina测序和生物信息分析对富化和非富化样本.
主要成果:
- 目标缩显著增加了对S. endobioticum基因组映射的序列基因的比例,特别是在原始组织中.
- 丰富样本产生了更高和更好的核基因组覆盖率,并偏向S. endobioticum序列的组装.
- 从丰富样本中检测到基因组组合中增加了S. endobioticum基因的数量.
结论:
- 开发的基于杂交的目标丰富协议是增强S. endobioticum基因组测序的宝贵工具.
- 这种方法改善了基于NGS的S. endobioticum分子检测,特别是从具有挑战性的环境和宿主衍生样本.
- 该协议有效地丰富了目标DNA,同时最大限度地减少了非目标生物体的DNA捕获.
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