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Plant DNA sequencing for phylogenetic analyses: from plants to sequences
Susana S Neves1, Laura L Forrest
1Plant Cell Biotechnology Laboratory, ITQB Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal. sneves@itqb.unl.pt
Methods in Molecular Biology (Clifton, N.J.)
|August 31, 2011
Summary
This guide details DNA sequencing methods for plant phylogenetics, covering sample collection, DNA extraction, and sequencing protocols. It addresses common issues and prepares data for phylogenetic analysis and public databases.
Area of Science:
- Molecular Biology
- Botany
- Genetics
Background:
- DNA sequences are crucial for phylogenetic analysis.
- DNA sequencing is a standard molecular biology technique.
- Plant phylogenetic projects require specific considerations for researchers new to the field.
Purpose of the Study:
- To provide an overview of methods and protocols for sequencing plant samples for phylogenetic analysis.
- To guide researchers in project design, sample selection, and data preparation.
- To address common challenges in DNA sequencing for plant phylogenetics.
Main Methods:
- Field collection of plant samples.
- Plant sample preparation and DNA extraction.
- Polymerase Chain Reaction (PCR) and cloning.
- Sanger sequencing method.
- Discussion of second-generation sequencing techniques.
Main Results:
- Detailed protocols for critical steps in molecular phylogenetic projects.
- Identification and discussion of common sequencing problems.
- Recommendations for species/taxa and DNA region selection.
- Guidance on preparing sequence data for analysis and database submission.
Conclusions:
- Successful molecular phylogenetic projects depend on meticulous sample preparation, DNA extraction, and sequencing.
- Understanding common sequencing issues and utilizing appropriate techniques enhances phylogenetic accuracy.
- Proper data preparation and submission facilitate broader scientific contribution and accessibility.
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