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Mandrioli M. From Dormant Collections to Repositories for the Study of Habitat Changes: The Importance of Herbaria in Modern Life Sciences. Life (Basel) 2023; 13:2310. [PMID: 38137911 PMCID: PMC10744909 DOI: 10.3390/life13122310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/25/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
In recent decades, the advent of new technologies for massive and automatized digitization, together with the availability of new methods for DNA sequencing, strongly increased the interest and relevance of herbarium collections for the study of plant biodiversity and evolution. These new approaches prompted new projects aimed at the creation of a large dataset of molecular and phenological data. This review discusses new challenges and opportunities for herbaria in the context of the numerous national projects that are currently ongoing, prompting the study of herbarium specimens for the understanding of biodiversity loss and habitat shifts as a consequence of climate changes and habitat destruction due to human activities. With regard to this, the National Biodiversity Future Center (active in Italy since 2022) started a large-scale digitization project of the Herbarium Centrale Italicum in Florence (Italy), which is the most important Italian botanical collection, consisting of more than 4 million samples at present.
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Affiliation(s)
- Mauro Mandrioli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 213/D, 41125 Modena, Italy
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Quatela AS, Cangren P, Jafari F, Michel T, de Boer HJ, Oxelman B. Retrieval of long DNA reads from herbarium specimens. AoB Plants 2023; 15:plad074. [PMID: 38130422 PMCID: PMC10735254 DOI: 10.1093/aobpla/plad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 11/06/2023] [Indexed: 12/23/2023]
Abstract
High-throughput sequencing of herbarium specimens' DNA with short-read platforms has helped explore many biological questions. Here, for the first time, we investigate the potential of using herbarium specimens as a resource for long-read DNA sequencing technologies. We use target capture of 48 low-copy nuclear loci in 12 herbarium specimens of Silene as a basis for long-read sequencing using SMRT PacBio Sequel. The samples were collected between 1932 and 2019. A simple optimization of size selection protocol enabled the retrieval of both long DNA fragments (>1 kb) and long on-target reads for nine of them. The limited sampling size does not enable statistical evaluation of the influence of specimen age to the DNA fragmentation, but our results confirm that younger samples, that is, collected after 1990, are less fragmented and have better sequencing success than specimens collected before this date. Specimens collected between 1990 and 2019 yield between 167 and 3403 on-target reads > 1 kb. They enabled recovering between 34 loci and 48 (i.e. all loci recovered). Three samples from specimens collected before 1990 did not yield on-target reads > 1 kb. The four other samples collected before this date yielded up to 144 reads and recovered up to 25 loci. Young herbarium specimens seem promising for long-read sequencing. However, older ones have partly failed. Further exploration would be necessary to statistically test and understand the potential of older material in the quest for long reads. We would encourage greatly expanding the sampling size and comparing different taxonomic groups.
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Affiliation(s)
- Anne-Sophie Quatela
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
- Gothenburg Global Biodiversity Center, Gothenburg, Box 463, 405 30, Sweden
| | - Patrik Cangren
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
| | - Farzaneh Jafari
- Department of Biology, Faculty of Basic Sciences, Lorestan University, P.O. BOX 6815144316, Khorramabad, Iran
- Department of Plant Science, Center of Excellence in Phylogeny of Living Organisms, School of Biology, College of Science, University of Tehran, P.O. Box 14155-6455, Tehran, Iran
| | - Thibauld Michel
- Tropical Diversity Research Department, Royal Botanic Garden of Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LRUK
| | - Hugo J de Boer
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318 Oslo, Norway
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
- Gothenburg Global Biodiversity Center, Gothenburg, Box 463, 405 30, Sweden
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Papalini S, Di Vittori V, Pieri A, Allegrezza M, Frascarelli G, Nanni L, Bitocchi E, Bellucci E, Gioia T, Pereira LG, Susek K, Tenaillon M, Neumann K, Papa R. Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies. Plants (Basel) 2023; 12:3452. [PMID: 37836192 PMCID: PMC10575153 DOI: 10.3390/plants12193452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023]
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 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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Affiliation(s)
- Simone Papalini
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
| | - Valerio Di Vittori
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
| | - Alice Pieri
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
| | - Marina Allegrezza
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
| | - Giulia Frascarelli
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, 85100 Potenza, Italy;
| | - Luis Guasch Pereira
- Spanish Plant Genetic Resources National Center, National Institute for Agricultural and Food Research and Technology (CRF-INIA-CSIC), 28805 Alcalá de Henares, Madrid, Spain;
| | - Karolina Susek
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznan, Poland;
| | - Maud Tenaillon
- Génétique Quantitative et Evolution–Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, 91190 Gif-sur-Yvette, France;
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany;
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
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McAssey EV, Downs C, Yorkston M, Morden C, Heyduk K. A comparison of freezer-stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming. Appl Plant Sci 2023; 11:e11527. [PMID: 37342160 PMCID: PMC10278930 DOI: 10.1002/aps3.11527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/30/2023] [Accepted: 05/04/2023] [Indexed: 06/22/2023]
Abstract
Premise The use of DNA from herbarium specimens is an increasingly important source for evolutionary studies in plant biology, particularly in cases where species are rare or difficult to obtain. Here we compare the utility of DNA from herbarium tissues to their freezer-stored DNA counterparts via the Hawaiian Plant DNA Library. Methods Plants collected for the Hawaiian Plant DNA Library were simultaneously accessioned as herbarium specimens at the time of collection, from 1994-2019. Paired samples were sequenced using short-read sequencing and assessed for chloroplast assembly and nuclear gene recovery. Results Herbarium specimen-derived DNA was statistically more fragmented than freezer-stored DNA derived from fresh tissue, leading to poorer chloroplast assembly and overall lower coverage. The number of nuclear targets recovered varied mostly by total sequencing reads per library and age of specimen, but not by storage method (herbarium or long-term freezer). Although there was evidence of DNA damage in the samples, there was no evidence that it was related to the length of time in storage, whether frozen or as herbarium specimens. Discussion DNA extracted from herbarium tissues will continue to be invaluable, despite being highly fragmented and degraded. Rare floras would benefit from both traditional herbarium storage methods and extracted DNA freezer banks.
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Affiliation(s)
- Edward V. McAssey
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - Cassidy Downs
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
| | - Mitsuko Yorkston
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
| | - Clifford Morden
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
| | - Karolina Heyduk
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
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González-Toral C, Cires E. Relevance of DNA preservation for future botany and ecology. Mol Ecol 2022; 31:5125-5131. [PMID: 36214196 DOI: 10.1111/mec.16652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/20/2022] [Accepted: 08/03/2022] [Indexed: 12/15/2022]
Abstract
The use of molecular methods in plant systematics and taxonomy has increased during the last decades; however, the accessibility of curated genetic samples and their metadata is a bottleneck for DNA-based genetic studies in botany. Plant biodiversity DNA banks and DNA-friendly collections could be critical suppliers of curated genetic material for researchers in the current context of plant biodiversity loss. Here, we aimed to understand the potential of plant DNA banks and DNA-friendly collections to enhance the growth and openness of scientific knowledge. The preservation of genetic material should become part of a natural collection's process for the generation of extended specimens enabling the preservation of both the phenotype and genotype and contributing to the generation of data networks which cross-fertilize other fields. These curated collections are advantageous in endangered species research, detecting processes related to extinction, giving a genetic dimension to IUCN assessments or completing the Leipzig Catalogue of Vascular Plants. Therefore, DNA collections are fundamental in producing FAIR data, responsible research and innovation (RRI) and meeting the goals of international conservation programmes. The completion of natural collections is important for current research efforts and furthermore vital to support future research in an era of ongoing plant biodiversity loss.
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Affiliation(s)
| | - Eduardo Cires
- Department of Organisms and Systems Biology, University of Oviedo, Oviedo, Spain.,Institute of Natural Resources and Territorial Planning (INDUROT), Mieres, Spain
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