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Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies

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 ar...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10575153/
https://www.ncbi.nlm.nih.gov/pubmed/37836192
http://dx.doi.org/10.3390/plants12193452
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author 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
author_facet 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
author_sort Papalini, Simone
collection PubMed
description 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 has allowed for inference and clarification of previously unsolved taxonomic and systematic relationships. Moreover, herbarium 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 herbarium 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 herbarium 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 herbarium 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 herbarium specimens for their exploitation in plant evolutionary studies.
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spelling pubmed-105751532023-10-14 Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies 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 Plants (Basel) Review 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 has allowed for inference and clarification of previously unsolved taxonomic and systematic relationships. Moreover, herbarium 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 herbarium 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 herbarium 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 herbarium 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 herbarium specimens for their exploitation in plant evolutionary studies. MDPI 2023-09-30 /pmc/articles/PMC10575153/ /pubmed/37836192 http://dx.doi.org/10.3390/plants12193452 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
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
Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies
title Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies
title_full Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies
title_fullStr Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies
title_full_unstemmed Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies
title_short Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies
title_sort challenges and opportunities behind the use of herbaria in paleogenomics studies
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10575153/
https://www.ncbi.nlm.nih.gov/pubmed/37836192
http://dx.doi.org/10.3390/plants12193452
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