通过掩盖参考基因组中的微生物类区域来改进古代环境元基因组的分类学推断
Nikolay Oskolkov1, Chenyu Jin2,3,4, Samantha López Clinton2,3,4
1Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, SE-223 62 Lund, Sweden.
GigaScience
|October 3, 2025
概括
通过识别真核基因组中的微生物样序列,改善了古代DNA (eDNA) 分析. 这种方法通过防止在元基因组学数据中错误分类细菌和考古DNA来增强古代生态系统的重建.
科学领域:
- 环境DNA (eDNA) 是一种环境DNA.
- 转基因组学是指转基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 古代环境DNA (eDNA) 对于重建过去的生态系统至关重要,特别是当化石记录稀缺时.
- 在环境样本中检测古老的植物和动物DNA通常使用真核生物参考基因组进行元基因组学数据分析.
- 一个重大的挑战是,在真核基因组内存在微生物样DNA序列,导致细菌和考古读数的错误分类,在稀少的古代eDNA中尤其存在问题.
研究的目的:
- 开发和应用一种方法来识别真核生物基因组内的细菌和古生物学类序列.
- 创建一个全面的微生物类序列位置和分类注释在各种真核生物基因组的综合资源.
- 提高古代环境元基因组数据集的准确性和可靠性.
主要方法:
- 应用了一种新的方法来识别来自NCBI RefSeq和GenBank (脊椎动物,无脊椎动物,植物) 的近3000个参考基因组中的细菌和考古类序列.
- 分析了1323个来自北方高度草本馆样本的PhyloNorway植物基因组组合.
- 为已识别的微生物类区域生成基因组坐标和分类学注释.
主要成果:
- 微生物样DNA序列广泛分布在广泛的真核生物基因组中.
- 已经编制了这些微生物类区域的综合数据库,包括它们的基因组坐标和分类学分类.
- 开发的方法成功地识别了真核基因组中的这些有问题的序列.
结论:
- 在元基因组学分析过程中,可以掩盖已识别的微生物类区域.
- 这种掩盖显著提高了古代环境DNA数据集的可靠性,用于下游生态和进化分析.
- 这些发现为研究古代eDNA和元基因组学的研究人员提供了宝贵的资源.
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