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Ferrari G, Esselens L, Hart ML, Janssens S, Kidner C, Mascarello M, Peñalba JV, Pezzini F, von Rintelen T, Sonet G, Vangestel C, Virgilio M, Hollingsworth PM. Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections. Biodivers Data J 2023; 11:e102317. [PMID: 38327316 PMCID: PMC10848826 DOI: 10.3897/bdj.11.e102317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/04/2023] [Indexed: 02/09/2024] Open
Abstract
Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples.
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Affiliation(s)
- Giada Ferrari
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Lore Esselens
- Royal Museum for Central Africa, Tervuren, BelgiumRoyal Museum for Central AfricaTervurenBelgium
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Michelle L Hart
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Steven Janssens
- Meise Botanic Garden, Meise, BelgiumMeise Botanic GardenMeiseBelgium
- Leuven Plant Institute, Department of Biology, Leuven, BelgiumLeuven Plant Institute, Department of BiologyLeuvenBelgium
| | - Catherine Kidner
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | | | - Joshua V Peñalba
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Flávia Pezzini
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Gontran Sonet
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Carl Vangestel
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, Department of African Zoology, Tervuren, BelgiumRoyal Museum for Central Africa, Department of African ZoologyTervurenBelgium
| | - Peter M Hollingsworth
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
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Luo T, Li L, Wang S, Cheng N. Research Progress of Nucleic Acid Detection Technology for Genetically Modified Maize. Int J Mol Sci 2023; 24:12247. [PMID: 37569623 PMCID: PMC10418336 DOI: 10.3390/ijms241512247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Genetically modified (GM) maize is one of the earliest GM crops to have achieved large-scale commercial cultivation globally, and it is of great significance to excel in the development and implementation of safety policy regarding GM, and in its technical oversight. This article describes the general situation regarding genetically modified maize, including its varieties, applications, relevant laws and regulations, and so on. From a technical point of view, we summarize and critically analyze the existing methods for detecting nucleic acid levels in genetically modified maize. The nucleic acid extraction technology used for maize is explained, and the introduction of traditional detection techniques, which cover variable-temperature and isothermal amplification detection technology and gene chip technology, applications in maize are described. Moreover, new technologies are proposed, with special attention paid to nucleic acid detection methods using sensors. Finally, we review the current limitations and challenges of GM maize nucleic acid testing and share our vision for the future direction of this field.
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Affiliation(s)
- Tongyun Luo
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (T.L.); (L.L.); (S.W.)
| | - Lujing Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (T.L.); (L.L.); (S.W.)
| | - Shirui Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (T.L.); (L.L.); (S.W.)
| | - Nan Cheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (T.L.); (L.L.); (S.W.)
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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