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Plastid primers for angiosperm phylogenetics and phylogeography
1Department of Botany, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605 USA.
Applications in Plant Sciences
|June 18, 2015
Summary
Selecting chloroplast genome primers is crucial for plant research. Many published primer pairs work broadly, but "universal" primers are unreliable for species-level studies.
Area of Science:
- Plant genomics
- Molecular biology
- Evolutionary biology
Background:
- Numerous primer pairs exist for the plastid genome.
- Primer selection is critical, especially for species/population interface research.
Purpose of the Study:
- Evaluate the amplification success of published chloroplast genome primer pairs across diverse angiosperms.
- Assess primer utility for intraspecific variability studies.
Main Methods:
- Tested 130 primer pairs in 12 angiosperm species.
- Inferred amplification success based on sequence mismatches.
- Evaluated intraspecific sequence variability.
Main Results:
- Most primer pairs amplified DNA across taxa, barring genomic rearrangements.
- "Universal" barcoding primers showed low success rates (65%).
- Regions identified as highly variable within species differed from previous studies.
Conclusions:
- Published primer sequences generally amplify diverse flowering plant DNA.
- "Universal" primers have limited utility.
- Primer amplification success varied inconsistently across lineages and publications.
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