Tree Genetics & Genomes

, Volume 10, Issue 4, pp 885–893 | Cite as

Primers for 52 polymorphic regions in the Quercus rubra chloroplast, 47 of which amplify across 11 tracheophyte clades

  • Daniel S. Borkowski
  • Tim McCleary
  • Mary McAllister
  • Jeanne Romero-SeversonEmail author
Original Paper


Postglacial migration studies in Quercus rubra L. (northern red oak) are hampered by low levels of population differentiation in the widely used universal chloroplast primers. We sequenced the large single copy (LSC) regions of the Q. rubra and Quercus ellipsoidalis chloroplasts to enable us to query additional regions for future studies on migration and speciation. Using 454 sequencing of long-range PCR amplicons and Sanger sequencing for gap closure, we report 65 coding sequences from Q. rubra and 59 from Q. ellipsoidalis. Comparison of our de novo assembly of the LSC region sequence for Q. rubra to Q. rubra chloroplast sequence (NCBI Reference Sequence: NC_020152.1) from a different tree revealed 106 polymorphisms, all within intergenic regions, that can serve as tools for postglacial migration studies and taxonomic studies within the Lobatae. Sequence alignment for the 59 complete coding regions in common for theQ. rubrachloroplast reference sequence, our Q. rubra sequence and our Q. ellipsoidalis sequence revealed no sequence polymorphisms and no indels. We also report the 52 primer pairs we used for gap closure, including 53 new primer pairs not previously reported. We tested these 52 primer pairs against 11 species representing the Tracheophyta and detected 47 that produced amplicons in all 11 species. The new universal primers we have identified provide additional tools for resolving the taxonomic relationships among the congeneric taxa of forest trees in the temperate and subtropical forests of the Northern Hemisphere.


Quercus rubra Chloroplast genome Universal primers Long-range PCR 



We thank Meg Staton (Clemson University Genomics Institute) for bioinformatics assistance; John Tan, Brent Harker, and Rory Carmichael (Notre Dame Genomics and Bioinformatics Core Facilities) for DNA sequencing and genome assembly; and Amy Fernow for assistance with PCR reactions. Funding for Daniel Borkowski was provided in part by the National Science Foundation (NSF IOS-1025974). The University of Notre Dame Core Genomics Facility provided funding for the 454 sequencing.

Data archiving statement

We have submitted chloroplast genome contigs to GenBank at NCBI, and the accession numbers will be provided as soon as they are available.

Supplementary material

11295_2014_729_MOESM1_ESM.docx (16 kb)
Supplemental Table 1 (DOCX 15 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Daniel S. Borkowski
    • 1
  • Tim McCleary
    • 1
  • Mary McAllister
    • 1
  • Jeanne Romero-Severson
    • 1
    Email author
  1. 1.Department of Biological SciencesUniversity of Notre DameNotre DameUSA

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