Preprint Review Version 1 Preserved in Portico This version is not peer-reviewed

Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies

Simone Papalini
,
Valerio Di Vittori
* ,
Alice Pieri
,
Marina Allegrezza
,
Giulia Frascarelli
,
Laura Nanni
,
Elena Bitocchi
ORCID logo ,
Elisa Bellucci
ORCID logo ,
Tania Gioia
ORCID logo ,
Luis Guasch
,
Karolina Susek
ORCID logo ,
Maud Irène Tenaillon
,
Kerstin Neumann
,
Roberto Papa
* ORCID logo
Version 1 : Received: 5 September 2023 / Approved: 5 September 2023 / Online: 7 September 2023 (09:23:38 CEST)

A peer-reviewed article of this Preprint also exists.

Papalini, S.; Di Vittori, V.; Pieri, A.; Allegrezza, M.; Frascarelli, G.; Nanni, L.; Bitocchi, E.; Bellucci, E.; Gioia, T.; Pereira, L.G.; Susek, K.; Tenaillon, M.; Neumann, K.; Papa, R. Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies. Plants 2023, 12, 3452. Papalini, S.; Di Vittori, V.; Pieri, A.; Allegrezza, M.; Frascarelli, G.; Nanni, L.; Bitocchi, E.; Bellucci, E.; Gioia, T.; Pereira, L.G.; Susek, K.; Tenaillon, M.; Neumann, K.; Papa, R. Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies. Plants 2023, 12, 3452.

Abstract

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. Herbarium collections represent a great source of phenotypic and genotypic information, and their exploitation allowed to infer and to clarify previously unsolved taxonomic and systematic relationships. Moreover, Herbarium specimens offered a new source to study phenological traits in plants and to disentangle biogeography and evolutionary scenarios of species. More recently, advances in the molecular technologies went in parallel with the decreasing costs of the next-generation sequencing (NGS) approaches, that paved the way to the utilization of aDNA for whole-genome studies. Although many studies have been carried out combining modern analytic techniques and Herbarium specimens, this research field is still relatively unexplored, due to the need of improving strategies for aDNA manipulation and exploitation. The higher susceptibility of aDNA to degradation and contamination during the Herbarium conservation and manipulation, and the occurrence of biochemical post-mortem damages, can result in the more challenging reconstruction of the original DNA sequence. Here, we review the methodological approaches that have been developed for the exploitation of historical Herbarium plant materials, such as the best practices for aDNA extraction, amplification and genotyping. We also focus on some strategies to overcome the main problems related to the utilization of Herbarium specimens for their exploitation in plant evolutionary studies.

Keywords

plant genetic resources; population genomics; crop evolution; food legumes

Subject

Biology and Life Sciences, Agricultural Science and Agronomy

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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