长读测序和自然历史收集样本和具有挑战性的标本的基因组组装
Bernhard Bein1,2,3, Ioannis Chrysostomakis4, Larissa S Arantes5,6
1LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.
bioRxiv : the preprint server for biology
|October 10, 2024
概括
博物馆收藏品为基因组测序提供了尚未开发的潜力. 新的协议使得高质量的基因组组装从保存样本,即使对于微小或困难的生物.
科学领域:
- 基因组学就是基因组学.
- 分子生物学分子生物学
- 生物信息学是一种生物信息学.
背景情况:
- 博物馆收藏包含数以百万计的保存生物样本.
- 这些样本在很大程度上未被用于现代基因组技术,如长读测序.
- 现有的基因组测序协议对古老或小样本有局限性.
研究的目的:
- 为博物馆标本开发和验证新的DNA提取和测序协议.
- 为了从具有挑战性的样本中实现高质量的基因组组装,包括那些具有退化DNA的样本.
- 扩大生物体的范围,可以生成高质量的参考基因组.
主要方法:
- 使用无放大协议进行长读序列的乙醇保存样品.
- 开发了一种基于放大功率的修改协议,使用替代聚合酶来减少PCR偏差.
- 将这些协议应用于各种具有挑战性的样本,包括毫米尺寸的生物.
主要成果:
- 从保存样本中的千基基底大小的DNA中实现了连续的基因组组件.
- 成功组装了3.1Gb载人的基因组,超过了以前的尺寸限制.
- 改善了难以测序的软体动物和关节动物的基因组组合.
结论:
- 以乙醇保存的博物馆藏品是基因组测序的宝贵资源.
- 开发的协议显著提高了从多样化和具有挑战性的样本生成高质量的参考基因组的能力.
- 这项工作促进了更广泛的努力,以创建一个全面的真核生物的基因组数据库.
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