Papalini Simone, Di Vittori Valerio, Pieri Alice, Allegrezza Marina, Frascarelli Giulia, Nanni Laura, Bitocchi Elena, Bellucci Elisa, Gioia Tania, Pereira Luis Guasch, Susek Karolina, Tenaillon Maud, Neumann Kerstin, Papa Roberto
Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy.
School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, 85100 Potenza, Italy.
Plants (Basel). 2023 Sep 30;12(19):3452. doi: 10.3390/plants12193452.
Paleogenomics focuses on the recovery, manipulation, and analysis of ancient DNA (aDNA) from historical or long-dead organisms to reconstruct and analyze their genomes. The aDNA is commonly obtained from remains found in paleontological and archaeological sites, conserved in museums, and in other archival collections. collections represent a great source of phenotypic and genotypic information, and their exploitation has allowed for inference and clarification of previously unsolved taxonomic and systematic relationships. Moreover, specimens offered a new source for studying phenological traits in plants and for disentangling biogeography and evolutionary scenarios of species. More recently, advances in molecular technologies went in parallel with the decreasing costs of next-generation sequencing (NGS) approaches, which paved the way to the utilization of aDNA for whole-genome studies. Although many studies have been carried out combining modern analytic techniques and ancient samples, such as specimens, this research field is still relatively unexplored due to the need for improving strategies for aDNA manipulation and exploitation from ancient samples. The higher susceptibility of aDNA to degradation and contamination during conservation and manipulation and the occurrence of biochemical postmortem damage can result in a more challenging reconstruction of the original DNA sequence. Here, we review the methodological approaches that have been developed for the exploitation of historical plant materials, such as best practices for aDNA extraction, amplification, and genotyping. We also focus on some strategies to overcome the main problems related to the utilization of specimens for their exploitation in plant evolutionary studies.
古基因组学专注于从历史悠久或已灭绝的生物体中恢复、处理和分析古代DNA（aDNA），以重建和分析它们的基因组。aDNA通常从古生物学和考古遗址中发现的遗骸、保存在博物馆以及其他档案收藏中的样本中获取。这些收藏代表了表型和基因型信息的重要来源，对它们的利用有助于推断和厘清以前未解决的分类学和系统发育关系。此外，这些标本为研究植物的物候特征以及解开物种的生物地理学和进化情景提供了新的来源。最近，分子技术的进步与下一代测序（NGS）方法成本的降低同步发展，这为将aDNA用于全基因组研究铺平了道路。尽管已经开展了许多结合现代分析技术和古代样本（如标本）的研究，但由于需要改进从古代样本中处理和利用aDNA的策略，这个研究领域仍相对未被充分探索。aDNA在保存和处理过程中对降解和污染的更高敏感性以及死后生化损伤的发生，可能导致更具挑战性的原始DNA序列重建。在这里，我们回顾了为利用历史悠久的植物材料而开发的方法学途径，例如aDNA提取、扩增和基因分型的最佳实践。我们还关注一些策略，以克服与在植物进化研究中利用标本相关的主要问题。
