Newly developed primers for complete YCF1 amplification in Pinus (Pinaceae) chloroplasts with possible family-wide utility

Abstract

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. 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. 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.

Citation

Parks, Matthew; Liston, Aaron; Cronn, Rich. 2011. Newly developed primers for complete YCF1 amplification in Pinus (Pinaceae) chloroplasts with possible family-wide utility. American Journal of Botany. 10.3732/ajb.1100088:e1-e4.