Broad-scale amplification of matK for DNA barcoding plants, a technical note

Botanical Journal of the Linnean Society

Volumn 164, Issue 1, 2010, Pages 1-9

  Dunning, Luke T ^a,b   Savolainen, Vincent ^a,b  

^a ROYAL BOTANIC GARDENS   (United Kingdom)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Biodiversity; Deoxyinosine; Eudicots; Monocots; PCR; Plastid genome; Species identification

Indexed keywords

DICOTYLEDON; DNA; ENZYME ACTIVITY; GENETIC ANALYSIS; GENOME; MONOCOTYLEDON; PLASTID; POLYMERASE CHAIN REACTION;

LILIOPSIDA;

EID: 77956846077     PISSN: 00244074     EISSN: 10958339     Source Type: Journal    
DOI: 10.1111/j.1095-8339.2010.01071.x     Document Type: Article

References (27)

1. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society 2009, 161:105-121. APG III
2. Batzer MA, Carlton JE, Deininger PL. Enhanced evolutionary PCR using oligonucleotides with inosine at the 3'-terminus. Nucleic Acids Research 1991, 19:5081.
3. Candrian U, Furrer B, Hofelein C, Luthy J. Use of inosine containing oligonucleotide primers for enzymatic amplification of different alleles of the gene coding for heat-stable toxin type I of enterotoxigenic Escherichia coli. Applied Environmental Microbiology 1991, 57:955-961.
4. A DNA barcode for land plants. Proceedings of the National Academy of Science 2009, 106:12794-12797. CBOL Plant Working Group
5. Chase MW, Cowan RS, Hollingsworth PM, van den Berg C, Madriñán S, Petersen G, Seberg O, Jørgsensen T, Cameron KM, Carine M, Pedersen N, Hedderson TAJ, Conrad F, Salazar GA, Richardson JE, Hollingsworth ML, Barraclough TG, Kelly L, Wilkinson M. A proposal for a standardised protocol to barcode all land plants. Taxon 2007, 56:295-299.
6. Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, Haidar N, Savolainen V. Land plants and DNA barcodes: short-term and long-term goals. Philosophical Transactions of the Royal Society B, Biological Sciences 2005, 360:1889-1895.
7. Cowan RS, Chase MW, Kress WJ, Savolainen V. 300 000 species to identify: problems, progress, and prospects in DNA barcoding of land plants. Taxon 2006, 55:611-616.
8. Cuénoud P, Savolainen V, Chatrou LW, Powell M, Grayer RJ, Chase MW. Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences. American Journal of Botany 2002, 89:132-114.
9. Drummond AJ, Ashton B, Cheung M, Heled J, Kearse M, Moir R, Stones-Havas S, Thierer T, Wilson A. Geneious v4.7. 2009, http://www.geneious.com/, Available at
10. Edgar RC. MUSCLE: multiple alignment with high accuracy and high throughput. Nucleic Acids Research 2004, 32:1792-1797.
11. Fazekas AJ, Burgess KS, Kesanakurti PR, Graham SW, Newmaster SG, Husband BC, Percy DM, Hajibabaei M, Barrett SCH. Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PLoS ONE 2008, 3:e2802.
12. Ford CS, Ayres KL, Toomey N, Haider N, Stahl JVA, Kelly LJ, Wikström N, Hollingsworth PM, Duff RJ, Hoot SB, Cowan RS, Chase MW, Wilkinson MJ. Selection of candidate coding DNA barcoding regions for use on land plants. Botanical Journal of the Linnean Society 2009, 159:1-11.
13. Gonzalez MA, Baraloto C, Engel J, Mori SA, Pétronelli P, Riéra B, Roger A, Thébaud C, Chave J. Identification of Amazonian trees with DNA barcodes. PLoS ONE 2009, 10:e7483.
14. Hebert PDN, Cywinska A, Ball SL, De Waard JR. Biological identifications through DNA barcodes. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 2003a, 270:313-321.
15. Hebert PDN, Ratnasingham S, De Waard JR. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 2003b, 270:S96-S99.
16. Hollingsworth ML, Clark A, Forrest LL, Richardson J, Pennington RT, Long DG, Cowan R, Chase MW, Gaudeul M, Hollingsworth PM. Selecting barcoding loci for plants: evaluation of seven candidate loci with species level sampling in three divergent groups of land plants. Molecular Ecology Resources 2009, 9:439-457.
17. Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN. Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes 2007, 7:544-548.
18. Kress WJ, Erickson DL. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE 2007, 2:e508.
19. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:8369-8374.
20. Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough TG, Savolainen V. DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences of the United States of America 2008, 105:2923-2928.
21. Maddison DR, Maddison WP. Macclade 4: analysis of phylogeny and character evolution. Version 4.0 2000, Sunderland, Sinauer Associates
22. Newmaster SG, Fazekas AJ, Ragupathy S. DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Canadian Journal of Botany-Revue Canadienne De Botanique 2006, 84:335-341.
23. Pennisi E. Taxonomy. Wanted: a barcode for plants. Science 2007, 318:190-191.
24. Sun H, McLewin W, Fay MF. Molecular phylogeny of Helleborus (Ranunculaceae), with an emphasis on the East Asia-Mediterranean disjunction. Taxon 2001, 50:1001-1018.
25. Swofford DL. PAUP*: phylogenetic analysis using parsimony (* and other methods). Version 4 2000, Sunderland, Sinaeur Associates
26. Valentini A, Pompanon F, Taberlet P. DNA barcoding for ecologists. Trends in Ecology and Evolution 2009, 24:110-117.
27. Wicke S, Quandt D. Universal primers for the amplification of the plastid trnK/matK region in land plants. Anales del Jardín Botánico de Madrid 2009, 66:285-288.