Using DNA Barcodes to Identify and Classify Living Things:
III. Amplify DNA by PCR: Primer Sequences and References

Primers

Primer Sequence

Organism

Reference

PLANT COCKTAIL

rbcLaF

5’- TGTAAAACGACGGCCAGTATGTCACCACAAACAGAGACTAAAGC-3’ Plants

Kress WJ, Erickson DL (2007) A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region. PLoS ONE 2(6)

rbcLa rev

 5’- CAGGAAACAGCTATGACGTAAAATCAAGTCCACCRCG-3’

FISH COCKTAIL

VF2_t1

 5’-TGTAAAACGACGGCCAGTCAACCAACCACAAAGACATTGGCAC-3’ Fish and mammals

Ivanova et. al. (2007). Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes 7, 544-548

FishF2_t1

 5’- TGTAAAACGACGGCCAGTCGACTAATCATAAAGATATCGGCAC-3’

FishR2_t1

 5’- CAGGAAACAGCTATGACACTTCAGGGTGACCGAAGAATCAGAA-3’

FR1d_t1

 5’- CAGGAAACAGCTATGACACCTCAGGGTGTCCGAARAAYCARAA-3’

MAMMAL COCKTAIL

LepF1_t1

 5’- TGTAAAACGACGGCCAGTATTCAACCAATCATAAAGATATTGG-3’ Mammals, reptiles, fish, amphibians, and some insects

Ivanova et. al. (2007). Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes 7, 544-548

VF1_t1

 5’- TGTAAAACGACGGCCAGTTCTCAACCAACCACAAAGACATTGG-3’
VF1d_t1 5’- TGTAAAACGACGGCCAGTTCTCAACCAACCACAARGAYATYGG-3’
VF1i_t1 5’- TGTAAAACGACGGCCAGTTCTCAACCAACCAIAAIGAIATIGG-3’
LepR1_t1 5’- CAGGAAACAGCTATGACTAAACTTCTGGATGTCCAAAAAATCA-3’
VR1d_t1 5’- CAGGAAACAGCTATGACTAGACTTCTGGGTGGCCRAARAAYCA-3’
VR1_t1 5’- CAGGAAACAGCTATGACTAGACTTCTGGGTGGCCAAAGAATCA-3’
VR1i_t1 5’- CAGGAAACAGCTATGACTAGACTTCTGGGTGICCIAAIAAICA-3’

DMI

LCO1490 5'-TGTAAAACGACGGCCAGTCAACAAATCATAAAGATATTGG-3' Various phyla from the animal kingdom

Folmer et al. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology (1994)3(5), 294-299.
HC02198 5'-CAGGAAACAGCTATGACTAAACTTCAGGGTGACCAAAAAATCA-3'

FUNGI COCKTAIL

ITS1F

 5'-TGTAAAACGACGGCCAGTCCGTAGGTGAACCTGCGG-3' Fungi

Gardes M, Bruns T (1993) ITS primers with enhanced specificity for Basidiomycetes-application to the identification ofmycorrhizae and rusts. Molecular Ecology, 2,113-118.

ITS4

 5'-CAGGAAACAGCTATGACTCCTCCGCTTATTGATATGC-3'

Jackson CJ; Barton RC; Evans EGV (1999). Species identification and strain differentiation of dermatophyte fungi by analysis of ribosomal-DNA intergenic spacer regions. J. Clinical Microbiology,  37, 4: 931-936

Primers for Sequencing
5´ TGTAAAACGACGGCCAGT 3´ M13F (-21)
5´ CAGGAAACAGCTATGAC 3´ M13R (-27)
Messing J., (1983). New M13 vectors for cloning. Methods in Enzymology, 101, 20–78.

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