Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
Department of Biology, Stanford University, Stanford, CA, USA.
Mol Ecol Resour. 2020 Sep;20(5):1228-1247. doi: 10.1111/1755-0998.13168. Epub 2020 May 12.
Species' responses at the genetic level are key to understanding the long-term consequences of anthropogenic global change. Herbaria document such responses, and, with contemporary sampling, provide high-resolution time-series of plant evolutionary change. Characterizing genetic diversity is straightforward for model species with small genomes and a reference sequence. For nonmodel species-with small or large genomes-diversity is traditionally assessed using restriction-enzyme-based sequencing. However, age-related DNA damage and fragmentation preclude the use of this approach for ancient herbarium DNA. Here, we combine reduced-representation sequencing and hybridization-capture to overcome this challenge and efficiently compare contemporary and historical specimens. Specifically, we describe how homemade DNA baits can be produced from reduced-representation libraries of fresh samples, and used to efficiently enrich historical libraries for the same fraction of the genome to produce compatible sets of sequence data from both types of material. Applying this approach to both Arabidopsis thaliana and the nonmodel plant Cardamine bulbifera, we discovered polymorphisms de novo in an unbiased, reference-free manner. We show that the recovered genetic variation recapitulates known genetic diversity in A. thaliana, and recovers geographical origin in both species and over time, independent of bait diversity. Hence, our method enables fast, cost-efficient, large-scale integration of contemporary and historical specimens for assessment of genome-wide genetic trends over time, independent of genome size and presence of a reference genome.
物种在遗传水平上的反应是理解人为全球变化对长期影响的关键。标本馆记录了这些反应，并结合当代采样，提供了植物进化变化的高分辨率时间序列。对于具有小基因组和参考序列的模式物种，特征遗传多样性是很简单的。对于非模式物种-具有小或大基因组-多样性传统上是使用基于限制酶的测序来评估的。然而，与年龄相关的 DNA 损伤和碎片化排除了这种方法在古老标本馆 DNA 中的应用。在这里，我们结合了简化代表性测序和杂交捕获来克服这一挑战，并有效地比较当代和历史标本。具体来说，我们描述了如何从新鲜样本的简化代表性文库中产生自制 DNA 诱饵，并将其用于有效地富集历史文库，以获得相同基因组部分的兼容数据集，从而从两种类型的材料中产生序列数据。将这种方法应用于拟南芥和非模式植物菘蓝，我们以无偏、无参考的方式发现了新的多态性。我们表明，所恢复的遗传变异再现了拟南芥中已知的遗传多样性，并在两个物种中随着时间的推移恢复了地理起源，而与诱饵多样性无关。因此，我们的方法能够快速、经济高效地整合当代和历史标本，以评估随时间变化的全基因组遗传趋势，而不受基因组大小和参考基因组的影响。
