Abstract
In this study, we tested the applicability of the core DNA barcode matK for identifying species within the Fabaceae family. Based on an evaluation of genetic
variation, DNA barcoding gaps, and species discrimination power, matK is a useful barcode for Fabaceae species. Of 1355 plant samples collected from 1079
species belonging to 409 diverse genera, matK precisely identified approximately 80 % and 96 % of them at the species and genus
levels, respectively. Therefore, our research indicates that the matK region is a valuable marker for plant species within Fabaceae.
Key words
DNA barcoding - Fabaceae -
matK
- identification
References
- 1 Lewis G, Schrire B, Mackinder B, Lock M. Legumes of the world. Richmond; Royal Botanic
Gardens, Kew 2005
- 2 The State Pharmacopoeia Commission of the PRC .Pharmacopoeia of the People's Republic
of China. Beijing; Chemical Industry Press 2005
- 3
Hebert P D, Cywinska A, Ball S L, de Waard J R.
Biological identifications through DNA barcodes.
Proc Biol Sci.
2003;
270
313-321
- 4
Hebert P D, Ratnasingham S, deWaard J R.
Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species.
Proc Biol Sci.
2003;
270 (Suppl. 1)
S96-S99
- 5
Marshall E.
Taxonomy–will DNA barcodes breathe life into classification?.
Science.
2005;
307
1037
- 6
Kress W J, Wurdack K J, Zimmer E A, Weigt L A, Janzen D H.
Use of DNA barcodes to identify flowering plants.
Proc Natl Acad Sci USA.
2005;
102
8369-8374
- 7
Pennisi E.
Taxonomy. Wanted: a barcode for plants.
Science.
2007;
318
190-191
- 8
Chase M W, Cowan R S, Hollingsworth P M, van den Berg C, Madriñán S, Petersen G, Seberg O,
Jørgsensen T, Cameron K M, Carine M.
A proposal for a standardised protocol to barcode all land plants.
Taxon.
2007;
56
295-299
- 9
Kress W J, Erickson D L.
A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region.
PLoS ONE.
2007;
6
e508
- 10
Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G.
DNA barcoding the floras of biodiversity hotspots.
Proc Natl Acad Sci.
2008;
105
2923-2928
- 11
Newmaster S G, Fazekas A J, Steeves R A D, Janovec J.
Testing candidate plant barcode regions in the Myristicaceae.
Mol Ecol Resour.
2008;
8
480-490
- 12
Selvaraj D, Sarma R K, Sathishkumar R.
Phylogenetic analysis of chloroplast matK gene from Zingiberaceae for plant DNA barcoding.
Bioinformation.
2008;
3
24-27
- 13
Newmaster S G, Ragupathy S.
Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae).
Mol Ecol Resour.
2009;
9 (Suppl. 1)
172-180
- 14
Starr J R, Naczi R F C, Chouinard B N.
Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae).
Mol Ecol Resour.
2009;
9 (Suppl. 1)
151-163
- 15
Ragupathy S, Newmaster S G, Murugesan M, Balasubramaniam V.
DNA barcoding discriminates a new cryptic grass species revealed in an ethnobotany
study by the hill tribes of the Western Ghats in southern India.
Mol Ecol Resour.
2009;
9 (Suppl. 1)
164-171
- 16
CBOL Plant Working Group .
A DNA barcode for land plants.
Proc Natl Acad Sci USA.
2009;
106
12794-12797
- 17
Hu J M, Lavin M, Wojciechowski M F, Sanderson M J.
Phylogenetic systematics of the tribe Millettieae (Leguminosae) based on chloroplast
trnK/matK sequences and its implications for evolutionary patterns in Papilionoideae.
Am J Bot.
2000;
87
418-430
- 18
Wojciechowski M F, Lavin M, Sanderson M J.
A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family.
Am J Bot.
2004;
91
1846-1862
- 19
Lavin M, Herendeen P S, Wojcieehowski M F.
Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages
during the tertiary.
Syst Biol.
2005;
54
575-594
- 20
Hollingsworth M L, Clark A A, Forrest L L, Richardson J, Pennington R T, Long D G,
Cowan R, Chase M W, Gaudeul M, Hollingsworth P M.
Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level
sampling in three divergent groups of land plants.
Mol Ecol Resour.
2009;
9
439-457
- 21
Newmaster S G, Ragupathy S.
Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae).
Mol Ecol Resour.
2009;
9
172-180
- 22
Meyer C P, Paulay G.
DNA barcoding: error rates based on comprehensive sampling.
PLoS Biol.
2005;
3
2229-2238
- 23
Chen S L, Yao H, Han J P, Liu C, Song J Y, Shi L C, Zhu Y J, Ma X Y, Gao T, Pang X H,
Luo K, Li Y, Li X W, Jia X C, Lin Y L, Leon C.
Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant
species.
PLoS ONE.
2010;
5
e8613
- 24
Meier R, Zhang G, Ali F.
The use of mean instead of smallest interspecific distances exaggerates the size of
the “barcoding gap” and leads to misidentification.
Syst Biol.
2008;
57
809
- 25
Slabbinck B, Dawyndt P, Martens M, De Vos P, De Baets B.
TaxonGap: a visualization tool for intra- and inter-species variation among individual
biomarkers.
Bioinformatics.
2008;
24
866-867
- 26
Ross H A, Murugan S, Li W L S.
Testing the reliability of genetic methods of species identification via simulation.
Syst Biol.
2008;
57
216-230
- 27
Fazekas A J, Burgess K S, Kesanakurti P R, Graham S W, Newmaster S G, Husband B C,
Percy D M, Hajibabaei M, Barrett S C H.
Multiple multilocus DNA barcodes from the plastid genome discriminate plant species
equally well.
PLos ONE.
2008;
3
e2802
- 28
Thomas C.
Plant barcode soon to become reality.
Science.
2009;
325
526
- 29
Thompson J D, Higgins D G, Gibson T J.
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through
sequence weighting, position-specific gap penalties and weight matrix choice.
Nucleic Acids Res.
1994;
22
4673
- 30
Tamura K, Dudley J, Nei M, Kumar S.
MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0.
Mol Biol Evol.
2007;
24
1596-1599
Prof. Shilin Chen
Institute of Medicinal Plant Development
Chinese Academy of Medical Sciences
Peking Union Medical College
No. 151 Malianwa North Road, Haidian District
100193 Beijing
People's Republic of China
Phone: + 86 10 62 89 97 00
Fax: + 86 10 62 89 97 76
Email: slchen@implad.ac.cn