title: Newly developed primers for complete ycf1 amplification in Pinus (Pinaceae) chloroplasts with possible family-wide utility.
abstract: OBJECTIVE
  Primers were designed to amplify the highly variable locus ycf1 from all 11 subsections of Pinus to facilitate plastome assemblies based on short sequence reads as well as future phylogenetic and population genetic analyses.
  
  
  RESULTS
  Primer design was based on alignment of 33 Pinus and four Pinaceae plastomes with mostly incomplete ycf1 sequences. Sanger sequencing of 12 Pinus accessions resulted in open reading frames ranging in size from 5.2 to 6.1 kbp. Highest sequence diversity was identified in two regions totaling 5.5 kbp aligned length, which can be targeted in all pine subsections with three primer combinations. Preliminary results suggest the primers described also amplify homologous targets in the broader Pinaceae.
  
  
  CONCLUSIONS
  The successful design and implementation of PCR primers spanning the large, variable locus ycf1 in Pinus represents the development of a valuable tool in pine genetic studies, and should facilitate studies throughout Pinaceae.
authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331-2902, USA. parksma@science.oregonstate.edu
authors: Matthew
authors: M
authors: Parks
authors: Aaron
authors: A
authors: Liston
authors: Rich
authors: R
authors: Cronn
mesh_terms: D002736:Chloroplasts / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics*; D060146:Ecotype; D056426:Genetic Loci / Q000235:genetics*; D008969:Molecular Sequence Data; D028223:Pinus / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods*; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers