Conservation Genetics Resources

, Volume 9, Issue 1, pp 9–12 | Cite as

Design and evaluation of PCR primers for amplification of four chloroplast DNA regions in plants

Technical Note
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Abstract

The high genetic diversity of plants can be a problem when developing molecular methods that require conserved DNA sequences among species. Several chloroplast DNA (cpDNA) regions have been used for the identification of plant DNA from broad taxonomic groups, but many species fail to amplify due to genetic variation at primer-binding sites. Here, we evaluated the conservation degree of four chloroplast DNA (cpDNA) regions commonly used in plant investigations (atpF-atpH, psbA-trnH, trnL CD and trnL GH). We propose new conserved PCR primers for the study of the most common plant families, designed using consensus sequences obtained from 28 multiple sequences alignments with over 11,000 reference sequences. The new primers were able to amplify all target regions in representative samples from the seven families. The conserved genomic regions and PCR primers can be used in diverse areas of plant research, including DNA barcoding, molecular ecology, metagenomics or phylogeny.

Keywords

Plants Conserved genomic regions cpDNA PCR primers 

Supplementary material

12686_2016_605_MOESM1_ESM.pdf (615 kb)
Supplementary material 1 (PDF 614 KB)

References

  1. Doyle JJ (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem bull 19:11–15Google Scholar
  2. Gonçalves J, Marks CA, Obendorf D, Amorim A, Pereira F (2015) A multiplex PCR assay for identification of the red fox (Vulpes vulpes) using the mitochondrial ribosomal RNA genes. Conserv Genet Resour 7:45–48CrossRefGoogle Scholar
  3. Hamilton MB, Braverman JM, Soria-Hernanz DF (2003) Patterns and relative rates of nucleotide and insertion/deletion evolution at six chloroplast intergenic regions in New World species of the Lecythidaceae. Mol Biol Evol 20:1710–1721CrossRefPubMedGoogle Scholar
  4. Hollingsworth PM, Graham SW, Little DP (2011) Choosing and using a plant DNA barcode. PloS One 6:e19254CrossRefPubMedPubMedCentralGoogle Scholar
  5. Li X, Yang Y, Henry RJ, Rossetto M, Wang Y, Chen S (2015) Plant DNA barcoding: from gene to genome. Biol Rev 90:157–166CrossRefPubMedGoogle Scholar
  6. Pereira F, Carneiro J, Matthiesen R, van Asch B, Pinto N, Gusmão L, Amorim A (2010) Identification of species by multiplex analysis of variable-length sequences. Nucleic Acids Res 38:e203–e203CrossRefPubMedPubMedCentralGoogle Scholar
  7. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109CrossRefPubMedGoogle Scholar
  8. Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, Valentini A, Vermat T, Corthier G, Brochmann C, Willerslev E (2007) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res 35:e14–e14CrossRefPubMedGoogle Scholar
  9. Yang F-S, Wang X-Q (2007) Extensive length variation in the cpDNA trnT-trnF region of hemiparasitic Pedicularis and its phylogenetic implications. Plant Syst Evol 264:251–264CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  1. 1.Interdisciplinary Centre of Marine and Environmental Research (CIIMAR)University of PortoMatosinhosPortugal
  2. 2.Faculty of SciencesUniversity of PortoPortoPortugal

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