Plastid Primers for Angiosperm Phylogenetics and Phylogeography

Premise of the study: PCR primers are available for virtually every region of the plastid genome. Selection of which primer pairs to use is second only to selection of the genic region. This is particularly true for research at the species/population interface. Methods: Primer pairs for 130 regions...

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Bibliographic Details
Published in:Applications in plant sciences 2015-06, Vol.3 (6), p.n/a
Main Author: Prince, Linda M
Format: Article
Language:English
Subjects:
Angiosperms
Application
barcoding
chloroplast genome
Chloroplasts
comparative sequencing
complete chloroplast genome
cpDNA
DNA primers
Flowering
Flowers & plants
Genomes
Laboratories
Magnoliophyta
Phylogenetics
Phylogeny
Phylogeography
Plant sciences
polymerase chain reaction
Primers
Species
Taxonomy
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Summary:Premise of the study: PCR primers are available for virtually every region of the plastid genome. Selection of which primer pairs to use is second only to selection of the genic region. This is particularly true for research at the species/population interface. Methods: Primer pairs for 130 regions of the chloroplast genome were evaluated in 12 species distributed across the angiosperms. Likelihood of amplification success was inferred based upon number and location of mismatches to target sequence. Intraspecific sequence variability was evaluated under three different criteria in four species. Results: Many published primer pairs should work across all taxa sampled, with the exception of failure due to genomic reorganization events. Universal barcoding primers were the least likely to work (65% success). The list of most variable regions for use within species has little in common with the lists identified in prior studies. Discussion: Published primer sequences should amplify a diversity of flowering plant DNAs, even those designed for specific taxonomic groups. “Universal” primers may have extremely limited utility. There was little consistency in likelihood of amplification success for any given publication across lineages or within lineage across publications.
ISSN:2168-0450
2168-0450
DOI:10.3732/apps.1400085