Table S2 The primer sequences for five barcoding regions used to amplify 531 tree
species of the DNNR
Marker
Primer
Sequence(5′-3′)
rbcL
rbcLa_For
ATGTCACCACAAACAGAGACTAAAGC
rbcLa_Rev GTAAAATCAAGTCCACCRCG
matK
KIM_3F
CGTACAGTACTTTTGTGTTTACGAG
KIM 1R
ACCCAGTCCATCTGGAAATCTTGGTTC
1326R
TCTAGCACACGAAAGTCGAAGT
390F
CGATCTATTCATTCAATATTTC
Kew 5R
GTTCTAGCACAAGAAAGTCG
Kew xF
TAATTTACGATCAATTCATTC
GYM-R1A TCAYCCGGA RATTTTGGTTCG
GYM-F1A ATYGYRCTTTTATGTTTACARGC
trnH-psbA psbA3
GTTATGCATGAACGTAATGCTC
trnH05
CGCGCATGGTGGATTCACAATCC
ITS
ITS-leu1
GTCCACTGAACCTTATCATTTAG
ITS4
TCCTCCGCTTATTGATATGC
ITS5
CCTTATCATTTAGAGGAAGGAG
ITS_17SE
ACGAATTCATGGTCCGGTGAAGTGTTC
ITS_26SE
TAGAATTCCCCGGTTCGCTCGCCGTTAC
*LAUR1
ACCACCACCGGCGAACCA
*ITSB
CTTTTCCTCCGCTTATTGATATG
ITS2
ITS2_S2F
ATGCGATACTTGGTGTGAAT
ITS2_S3R
GACGCTTCTCCAGACTACAAT
*: the specific pair of primer for species of the Lauraceae.
References
(Kress et al. 2009)
Kim, unpublished
(Cuénoud et al. 2002)
(Ford et al. 2009)
(Li et al. 2011)
(Sang et al. 1997)
(Tate& Simpson 2003)
Urbatsh et al.(2000)
(White et al. 1990)
(Stanford et al.2000)
(Sun et al. 1994)
(Chanderbali et al. 2001)
(Blattner 1999)
(Chen et al. 2010)
REFERENCES
Blattner FR (1999) Direct amplification of the entire ITS region from poorly preserved plant material
using recombinant PCR. Biotechniques 27, 1180.
Chanderbali AS, van der Werff H, Renner SS (2001) Phylogeny and historical biogeography of
Lauraceae: Evidence from the chloroplast and nuclear genomes. Annals of the Missouri Botanical
Garden 88, 104-134.
Chen S, Yao H, Han J, et al. (2010) Validation of the ITS2 region as a novel DNA barcode for
identifying medicinal plant species. PLoS ONE 5, e8613.
Cuénoud P, Savolainen V, Chatrou LW, et al. (2002) Molecular phylogenetics of Caryophyllales based
on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences. American Journal of
Botany 89, 132-144.
Ford CS, Ayres KL, Toomey N, Liu C (2009) Selection of candidate coding DNA barcoding regions for
use on land plants. Botanical Journal of the Linnean Society, 159, 1–11.
Kress WJ, Erickson DL, Jones FA, et al. (2009) Plant DNA barcodes and a community phylogeny of a
tropical forest dynamics plot in Panama. Proceedings of the National Academy of Sciences of the
United States of America 106, 18621-18626.
Li Y, Gao L-M, Poudel RC, Li D-Z, Forrest A (2011) High universality of matK primers for barcoding
gymnosperms. Journal of Systematics and Evolution 49, 169-175.
Sang T, Crawford D, Stuessy T (1997) Chloroplast DNA phylogeny, reticulate evolution, and
biogeography of Paeonia (Paeoniaceae). American Journal of Botany 84, 1120-1120.
Sun Y, Skinner D, Liang G, Hulbert S (1994) Phylogenetic analysis of Sorghum and related taxa using
internal transcribed spacers of nuclear ribosomal DNA. Theoretical and Applied Genetics 89, 26-32.
Tate JA, Simpson BB (2003) Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploid
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Table S3 Species composition of seven Asian forest dynamics plots
(Data from: Center for Tropical Forest Science, www.ctfs.si.edu; elevation less than 1000 m and
plot size between 10 ha and 50 ha)
CTFS Plot
Location
Latitude
(N)
Elevation
(m)
Plot
Size
Number
of
Species
Number
of genus
Number
of large
genera*
Number of
species
(large genera*)
(species ratio)
Pasoh,
(Malaysia)
Lambir,
(Malaysia)
2°58′
70-90
50 ha
814
299
79
550 (67.57%)
4°11′
104-244
52 ha
1182
290
110
943 (79.78%)
Palanan,
(Philippines)
17°2′
85-140
16 ha
335
159
30
163(48.66%)
Xishuangbana,
(China)
Dinghushan,
(China)
21°36′
709-869
20 ha
470
210
50
264 (56.17%)
23°10′
230-470
20 ha
190
115
18
82 (41.41%)
Gutianshan,
(China)
29°15′
446-714
24 ha
159
103
9
42 (26.42 %)
Changbaishan,
(China)
42°16′
791-809
25 ha
52
35
1
8 (5.4%)
*: Large genera indicate the genera containing more than two species per genus.
Figure S1 Comparision of the performance of DNA barcode regions and their
combinations for distinguinshing species, genera and families, accounting for
sequence recoverability, using BLASTn at the DNNR.
Figure S2. Species resolution (NJ analysis) of DNA barcode regions and their
combinations at species, genus and family levels in the DNNR (Bootstrap support
value exceeded 70% and based on 1000 bootstrap replicates).