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Newly developed primers for complete ycf 1 amplification in Pinus (Pinaceae) chloroplasts with possible family‐wide utility
Author(s) -
Parks Matthew,
Liston Aaron,
Cronn Rich
Publication year - 2011
Publication title -
american journal of botany
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.218
H-Index - 151
eISSN - 1537-2197
pISSN - 0002-9122
DOI - 10.3732/ajb.1100088
Subject(s) - pinaceae , biology , chloroplast dna , sanger sequencing , pinus <genus> , locus (genetics) , primer (cosmetics) , genetics , phylogenetic tree , evolutionary biology , dna sequencing , botany , gene , chemistry , organic chemistry
• Premise of the study: Primers were designed to amplify the highly variable locus ycf 1 from all 11 subsections of Pinus to facilitate plastome assemblies based on short sequence reads as well as future phylogenetic and population genetic analyses. • Methods and Results: Primer design was based on alignment of 33 Pinus and four Pinaceae plastomes with mostly incomplete ycf 1 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 ycf 1 in Pinus represents the development of a valuable tool in pine genetic studies, and should facilitate studies throughout Pinaceae.