Molecular identification of plants: from sequence to species

Hugo de Boer; Marcella Orwick Rydmark; Brecht Verstraete; Barbara Gravendeel

doi:10.3897/ab.e98875

Monograph

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https://doi.org/10.3897/ab.e98875 (23 Dec 2022)

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Book title
Foreword
Introduction
- References
Section 1: Design, sampling, and substrates
- Chapter 1 DNA from plant tissue
  - Plant DNA
  - Storing and preparing plant material for DNA extraction
  - DNA extraction protocols
  - DNA quantification and quality assessment
  - Approaches to challenging DNA extractions
  - Concluding remarks
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 2 DNA from museum collections
  - Introduction
  - Ethical and legal aspects
  - Sampling museum collections
  - Laboratory work with historical samples
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 3 DNA from water
  - Introduction
  - Detection of DNA from aquatic environments
  - Experimental design
  - Conclusion and prospects
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 4 DNA from soil
  - Introduction
  - Soil DNA: degradation, persistence, and decay
  - Soil memory
  - Designing a soil eDNA study
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 5 DNA from pollen
  - Background
  - Pollen DNA extraction
  - Molecular methods for pollen identification
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 6 DNA from food and medicine
  - Why use DNA for the identification of food and medicine?
  - DNA-based methods to identify plants in food and medicine
  - DNA isolation from food and medicines
  - The reality of DNA-based identification
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 7 DNA from faeces
  - Background
  - Experimental design
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 8 aDNA from sediments
  - Background
  - Experimental design
  - Questions
  - Glossary
  - References
  - Answers
Section 2: Methods
- Chapter 9 Sequencing platforms
  - Introduction
  - Sequencing platforms
  - Which sequencing platform?
  - Perspectives
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 10 DNA barcoding
  - DNA barcoding
  - DNA barcoding and species delimitation
  - DNA barcoding for plants
  - Hands-on plant DNA barcoding
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 11 Amplicon metabarcoding
  - Background
  - Setting up a metabarcoding study
  - Future of metabarcoding
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 12 Metagenomics
  - Background
  - The process of metagenomics
  - Future of metagenomics
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 13 DNA Barcoding - High Resolution Melting analysis (Bar-HRM)
  - Introduction
  - High resolution melting analysis
  - HRM assay and reagent optimization
  - Advantages and limitations of HRM
  - HRM applications
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 14 Target capture
  - Introduction
  - What is target capture?
  - Use of target capture for molecular identification
  - Designing a target capture experiment
  - Concluding remarks
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 15 Transcriptomics
  - Background
  - Experimental design
  - Bioinformatics
  - Applications of transcriptomics in species identification
  - Conclusion and future perspectives
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 16 Whole genome sequencing
  - Introduction
  - Sample to sequence: an overview of the workflow for genome sequencing
  - Genome skimming
  - Genome resequencing
  - De novo whole genome sequencing
  - Considerations and example applications
  - Conclusion
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 17 Species delimitation
  - What is a species?
  - Essential considerations to implement a species delimitation study
  - DNA-based species delimitation methods
  - Allopolyploidization and its impact on species delimitation
  - Conclusions
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 18 Sequence to species
  - Introduction
  - Sequencing quality control
  - Database alignment
  - Alignment-free methods
  - Assembly or mapping for multisequence sample alignments
  - Other considerations
  - Questions
  - Glossary
  - References
  - Answers
Section 3: Applications
- Chapter 19 Systematics and evolution
  - Introduction
  - Data sources used in systematics
  - Advances in molecular phylogenetics
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 20 Museomics
  - Museomics in plant research
  - Plant material in museum collections
  - Museum collections: fundamental and applied research
  - Ethical museomics, fair and equitable sharing, and co-design of research
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 21 Palaeobotany
  - Introduction
  - Applications
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 22 Healthcare
  - Plants as medicine
  - Quality control and authentication of herbal medicines
  - DNA-based identification of adulterants in herbal medicines
  - DNA-based identification in ethnopharmacology
  - DNA-based identification in natural product research and bioprospecting
  - Legal framework
  - Future perspectives of DNA-based identification for healthcare
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 23 Food safety
  - Introduction
  - Food hazards and impacts
  - Authentication of plant-based food stuffs
  - From farm to fork - traceability
  - Methodological approaches for the detection of plant food hazards
  - Conclusions and future prospects
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 24 Environmental and biodiversity assessments
  - Introduction
  - Assessing plant DNA from the environment: power, precautions, and limitations
  - Substrates for eDNA in environmental and biodiversity assessments
  - Beyond eDNA samples: assessing biodiversity through eDNA biotic samplers
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 25 Wildlife trade
  - Introduction
  - Methods for identification of plants in trade
  - Recommendations to improve wildlife trade monitoring
  - Questions
  - Glossary
  - References
  - Answers
- Chapter 26 Forensic genetics, botany, and palynology
  - Introduction
  - DNA technology for forensic plant analysis
  - Use of palynology in forensics
  - Forensic case studies
  - Questions
  - Glossary
  - References
  - Answers

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