The publication is finally out! See http://www.bioone.org/doi/pdf/10.3732/apps.1400085 to obtain a copy.
· 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 twelve species distributed across the angiosperms tree. 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 publication.
[Old intro: The quest for variable molecular markers continues because, despite the publication of PCR primers for numerous plastid introns or intergenic spacer regions (IGSs), many botanists are still unable to resolve relationships within their study group. This is particularly true for research at the species/population interface. Primers were designed for 36 non-coding portions of the large and small single copy region of the chloroplast genome based on the complete chloroplast genome of sixteen flowering plant species. The utility of the primers was assessed for a variety of flowering and non-flowering land plants. Amplification of most primer pairs was successful for several non-model plants including the basal angiosperm Magnolia (Magnoliaceae), the monocots Agave (Agavaceae), Canna (Cannaceae), and Guzmania (Bromeliaceae), and the eudicots Acer (Aceraceae), Agryoxiphium (Asteraceae), Monardella (Lamiaceae) and Sidalcea (Malvaceae). There was little consistency in the relative sequence divergence across Angiosperm taxonomy, suggesting the need for a thorough exploration of markers prior to undertaking a large comparative sequencing project. A combination of data mining and genomic approaches is worth the investment of time and money.]
UPDATES
12 June 2015:
Revised comparison tables, appendices.
25 Jan 2015:
Infraspecific comparisons have been added for Fragaria versa, Gossypium herbaceum, Olea europaea, and Oryza sativa.
Published primers for 130 regions of the chloroplast genome have been evaluated for Fragaria versa, Gossypium herbaceum, Olea europaea, and Oryza sativa.