Use of DNA Barcoding in Identifying Tropical Trees from Dipterocarpaceae

doi:10.11983/CBB18205

Abstract

Abstract:

Plants from Dipterocarpaceae are vital tropical timber trees in Southeast Asia. They have high potential in forest supervision, forest resource protection and other aspects to evaluate the efficiency of DNA barcodes. We obtained 899 sequences from 244 species for 14 genera combined with sequences from the GenBank. We amplified and sequenced four DNA regions (rbcL, matK, trnL-trnF and ITS2) in samples from the family Dipterocarpaceae. The discrimination ability of DNA barcodes was evaluated by using effective sequence ratios, characteristics of sequences, divergence of intra- and inter-varieties, and identification success rates (Best Match, Best Close Match, BLAST and neighbor-joining methods). The ITS2 fragment showed the highest identification efficiency. High-quality ITS2 sequence can be obtained from the leaves of Dipterocarpaceae plants by using an optimized amplification system. The matK fragment showed obvious genetic variation and 100% amplification and sequencing efficiency, and its identification ability was higher than with other chloroplast markers. Therefore, ITS2 and matK are suitable markers for tropical trees from Dipterocarpaceae.

Key words: Dipterocarpaceae, DNA barcoding, ITS2, matK, tropical region

Jianlin Hu,Zhifang Liu,Xiuqin Ci,Jie Li. Use of DNA Barcoding in Identifying Tropical Trees from Dipterocarpaceae[J]. Chinese Bulletin of Botany, 2019, 54(3): 350-359.

Add to citation manager EndNote|Ris|BibTeX

URL: https://www.chinbullbotany.com/EN/10.11983/CBB18205

https://www.chinbullbotany.com/EN/Y2019/V54/I3/350

Figures/Tables 8

References 55

[1]	成俊卿 (1980). 中国热带及亚热带木材——识别、材性和利用. 北京: 科学出版社. pp. 413-418.
[2]	戴文君, 周磊, 杨梅 ( 2017). 中国龙脑香科植物研究及利用现状. 世界林业研究 30(6), 46-51.
[3]	李德铢, 曾春霞 ( 2015). 植物DNA条形码研究展望. 生物多样性 23, 297-298.
[4]	李锡文, 李捷 , Ashton P ( 2002). 中国龙脑香料植物纪要. 云南植物研究 24, 409-420.
[5]	卢孟孟, 慈秀芹, 杨国平, 李捷 ( 2013). 亚热带森林乔木树种DNA条形码研究——以哀牢山自然保护区为例. 植物分类与资源学报 35, 733-741.
[6]	罗良才 ( 1988). 云南龙脑香科树种木材识别与利用的研究. 云南林业科技 ( 1), 1-13.
[7]	罗良才 ( 2008). 云南进口龙脑香科树种的木材识别与利用. 西部林业科学 37, 99-107.
[8]	乔梦吉, 陈柏旭, 符韵林 ( 2018). 基于DNA条形码技术的楠属和润楠属5种木材的识别. 基因组学与应用生物学 37, 4013-4021.
[9]	任保青, 陈之端 ( 2010). 植物DNA条形码技术. 植物学报 45, 1-12.
[10]	宋慧芳, 刘海双, 杨义明, 范书田, 李昌禹, 艾军 ( 2017). 山葡萄种质资源DNA条形码通用序列的筛选. 植物学报 52, 723-732.
[11]	童绍全, 陶国达 ( 1990). 龙脑香科. 见: 钱崇澍, 陈焕镛, 主编. 中国植物志, 第50卷2分册. 北京: 科学出版社. pp. 113-131.
[12]	王锦亮, 丁靖垲, 程治英, 杨崇仁 ( 1992). 两种云南龙脑香属植物树脂精油的倍半萜成分及其季节性变化. 云南植物研究 14, 337-342.
[13]	杨家驹, 刘鹏, 卢鸿俊 ( 1989). 龙脑香亚科木材. 木材工业 3(3), 43-49.
[14]	杨家驹, 刘鹏, 卢鸿俊 ( 1991). 娑罗双属商品材. 木材工业 5, 45-50, 55.
[15]	于永福 ( 1999). 中国野生植物保护工作的里程碑——《国家重点保护野生植物名录(第一批)》出台. 植物杂志 ( 5), 3.
[16]	周亮, 黄建平, 黄自云 ( 2013). 热带植物云南娑罗双. 园林 ( 6), 62-63.
[17]	朱华, 王洪 ( 1992). 西双版纳龙脑香科植物纪要. 云南植物研究 14, 21-26.
[18]	Ashton PS ( 1982). Flora Malesiana. Series I—Spermatophyta. Flowering Plants, Vol. 9, Part 2. Dipterocarpaceae. The Netherlands: Martinun Nijhoff Pub.
[19]	CBOL Plant Working Group, Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, van der Bank M, Chase MW, Cowan RS, Erickson DL, Fazekas AJ, Graham SW, James KE, Kim KJ, Kress WJ, Schneider H, van AlphenStahl J, Barrett SCH, van den Berg C, Bogarin D, Burgess KS, Cameron KM, Carine M, Chacón J, Clark A, Clarkson JJ, Conrad F, Devey DS, Ford CS, Hedderson TAJ, Hollingsworth ML, Husband BC, Kelly LJ, Kesanakurti PR, Kim JS, Kim YD, Lahaye R, Lee HL, Long DG, Madriñán S, Maurin O, Meusnier I, Newmaster SG, Park CW, Percy DM, Petersen G, Richardson JE, Salazar GA, Savolainen V, Seberg O, Wilkinson MJ, Yi DK, Little DP ( 2009). A DNA barcode for land plants. Proc Natl Acad Sci USA 106, 12794-12797.
[20]	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 ( 2007). A proposal for a standardised protocol to barcode all land plants. Taxon 56, 295-299.
[21]	Chen SL, Yao H, Han JP, Liu C, Song JY, Shi LC, Zhu YJ, Ma XY, Gao T, Pang XH, Luo K, Li Y, Li XW, Jia XC, Lin YL, Leon C ( 2010). Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One 5, e8613.
[22]	China Plant BOL Group, Li DZ, Gao LM, Li HT, Wang H, Ge XJ, Liu JQ, Chen ZD, Zhou SL, Chen SL, Yang JB, Fu CX, Zeng CX, Yan HF, Zhu YJ, Sun YS, Chen SY, Zhao L, Wang K, Yang T, Duan GW ( 2011). Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proc Natl Acad Sci USA 108, 19641-19646.
[23]	Cuénoud P, Savolainen V, Chatrou LW, Powell M, Grayer RJ, Chase MW ( 2002). Molecular phylogenetics of Caryo- phyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences. Am J Bot 89, 132-144.
[24]	de Boer HJ, Ghorbani A, Manzanilla V, Raclariu AC, Kreziou A, Ounjai S, Osathanunkul M, Gravendeel B ( 2017). DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade. Proc Roy Soc B 284, 20171182.
[25]	Dormontt EE, Boner M, Braun B, Breulmann G, Degen B, Espinoza E, Gardner S, Guillery P, Hermanson JC, Koch G, Lee SL, Kanashiro M, Rimbawanto A, Thomas D, Wiedenhoeft AC, Yin YF, Zahnen J, Lowe AJ ( 2015). Forensic timber identification: it's time to integrate disciplines to combat illegal logging. Biol Conserv 191, 790-798.
[26]	Doyle JJ, Doyle JL ( 1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19, 11-15.
[27]	Fay MF, Cameron KM, Prance GT, Lledó MD, Chase MW ( 1997). Familial relationships of Rhabdodendron( Rhabdodendraceae): plastid rbcL sequences indicate a caryo- phyllid placement. Kew Bull 52, 923-932.
[28]	Gasson P, Miller R, Stekel DJ, Whinder F, Ziemińska K ( 2010). Wood identification of Dalbergia nigra( CITES Appendix I) using quantitative wood anatomy, principal components analysis and naïve Bayes classification. Ann Bot 105, 45-56.
[29]	Gonzalez MA, Baraloto C, Engel J, Mori SA, Pétronelli P, Riéra B, Roger A, Thébaud C, Chave J ( 2009). Iden- tification of Amazonian trees with DNA barcodes. PLoS One 4, e7483.
[30]	Hassold S, Lowry II PP, Bauert MR, Razafintsalama A, Ramamonjisoa L, Widmer A ( 2016). DNA barcoding of Malagasy rosewoods: towards a molecular identification of CITES-listed Dalbergia species. PLoS One 11, e0157881.
[31]	Hebert PDN, Cywinska A, Ball SL, deWaard JR ( 2003). Biological identifications through DNA barcodes. Proc Roy Sci B 270, 313-321.
[32]	Heckenhauer J, Samuel R, Ashton PS, Turner B, Barfuss MHJ, Jang TS, Temsch EM, Mccann J, Salim KA, Attanayake AMAS, Chase MW ( 2017). Phylogenetic analyses of plastid DNA suggest a different interpretation of morphological evolution than those used as the basis for previous classifications of Dipterocarpaceae (Malvales). Bot J Linn Soc 185, 1-26.
[33]	Hollingsworth PM, Li DZ, van der Bank M, Twyford AD ( 2016). Telling plant species apart with DNA: from barcodes to genomes. Philos Trans Roy Soc B 371, 2015-0338.
[34]	Huang XC, Ci XQ, Conran JG, Li J ( 2015). Application of DNA barcodes in Asian tropical trees—a case study from Xishuangbanna Nature Reserve, Southwest China. PLoS One 10, e0129295.
[35]	Jiao LC, Yu M, Wiedenhoeft AC, He T, Li JN, Liu B, Jiang XM, Yin YF ( 2018). DNA barcode authentication and library development for the wood of six commercial Pterocarpus species: the critical role of xylarium specimens. Sci Rep 8, 1945.
[36]	Kamiya K, Harada K, Tachida H, Ashton PS ( 2005). Phylogeny of PgiC gene in Shorea and its closely related genera (Dipterocarpaceae), the dominant trees in southeast Asian tropical rain forests. Am J Bot 92, 775-788.
[37]	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, e508.
[38]	Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH ( 2005). Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA 102, 8369-8374.
[39]	Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough TG, Savolainen V ( 2008). DNA barcoding the floras of biodiversity hotspots. Proc Natl Acad Sci USA 105, 2923-2928.
[40]	Meier R, Shiyang K, Vaidya G, Ng PKL ( 2006). DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst Biol 55, 715-728.
[41]	Newmaster SG, Fazekas AJ, Ragupathy S ( 2006). DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Can J Bot 84, 335-341.
[42]	Ng CH, Lee SL, Tnah LH, Ng KKS, Lee CT, Maria M ( 2016). Genome size variation and evolution in Dipterocarpaceae. Plant Ecol Divers 9, 437-446.
[43]	Olmstead RG, Michaels HJ, Scott KM, Palmer JD ( 1992). Monophyly of the Asteridae and identification of their major lineages inferred from DNA sequences of rbcL. Ann Mo Bot Gard 79, 249-265.
[44]	Schultz J, Wolf M ( 2009). ITS2 sequence-structure analysis in phylogenetics: a how-to manual for molecular syste- matics. Mol Phylogenet Evol 52, 520-523.
[45]	Sun Y, Skinner DZ, Liang GH, Hulbert SH ( 1994). Phylogenetic analysis of Sorghum and related taxa using internal transcribed spacers of nuclear ribosomal DNA. Theor Appl Genet 89, 26-32.
[46]	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.
[47]	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, 1105-1109.
[48]	Tamura K, Stecher G, Peterson D, Filipski A, Kumar S ( 2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30, 2725-2729.
[49]	Trang NTP, Duc NM, Sinh NV, Triest L ( 2015). Application of DNA barcoding markers to the identification of Hopea species. Genet Mol Res 14, 9181-9190.
[50]	Tsumura Y, Kado T, Yoshida K, Abe H, Ohtani M, Taguchi Y, Fukue Y, Tani N, Ueno S, Yoshimura K, Kamiya K, Harada K, Takeuchi Y, Diway B, Finkeldey R, Na’iem M, Indrioko S, Ng KKS, Muhammad N, Lee SL ( 2011). Molecular database for classifying Shorea species (Dipterocarpaceae) and techniques for checking the legitimacy of timber and wood products. J Plant Res 124, 35-48.
[51]	White TJ, Bruns TD, Lee S, Taylor J ( 1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds. PCR Protocols: a Guide to Methods and Applications. San Diego: Academic Press. pp. 315-322.
[52]	Wilson EO ( 2016). Half-Earth: Our Planet’s Fight for Life. New York: Liveright Publishing Corporation.
[53]	Yu M, Jiao LC, Guo J, Wiedenhoeft AC, He T, Jiang XM, Yin YF ( 2017). DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species. Planta 246, 1165-1176.
[54]	Zeng CX, Hollingsworth PM, Yang J, He ZS, Zhang ZR, Li DZ, Yang JB ( 2018). Genome skimming herbarium spe- cimens for DNA barcoding and phylogenomics. Plant Methods 14, 43.
[55]	Zhu RW, Li YC, Zhong DL, Zhang JQ ( 2017). Establishment of the most comprehensive ITS2 barcode database to date of the traditional medicinal plant Rhodiola ( Crassulaceae). Sci Rep 7, 10051.

No.	Species	Voucher numbers	GenBank accession number
No.	Species	Voucher numbers	rbcL	matK	trnL-trnF	ITS2
1	Dipterocarpus turbinatus C. F. Gaertner	JL5901	MK030561	MK051080	MK051054	MK051069
2	D. turbinatus C. F. Gaertner	JL5902	MK030562	MK051081	MK051055	MK051070
3	D. retusus Blume	JL9601	MK030559	MK051078	MK051052	MK193032
4	D. retusus Blume	JL9602	MK030560	MK051079	MK051053	MK193031
5	Hopea chinensis (Merr.) Hand.-Mazz.	JL110A	MK030563	MK051082	MK193024	MK193026
6	H. chinensis (Merr.) Hand.-Mazz.	JL110B	MK030564	MK051083	MK051059	MK193025
7	H. hainanensis Merrill & Chun	JL2201	MK030565	MK051084	MK051060	MK193029
8	H. hainanensis Merrill & Chun	JL2202	MK030566	MK051085	MK051061	MK193028
9	H. hainanensis Merrill & Chun	JL2203	MK030567	MK051086	MK051062	MK193030
10	Parashorea chinensis H. Wang	JL6101	MK030568	MK051087	MK051056	MK051071
11	P. chinensis H. Wang	JL6102	MK030569	MK051088	MK051057	MK051072
12	Shorea assamica Dyer	JL3901	MK030571	MK051090	MK051063	-
13	S. assamica Dyer	JL3902	MK030570	MK051089	MK051058	MK051073
14	Vatica diospyroides Symington	JL7601	MK030572	MK051091	MK051064	MK051074
15	V. diospyroides Symington	JL7602	MK030573	MK051092	MK193023	MK051075
16	V. guangxiensis X. L. Mo	JL4801	MK030574	MK051093	MK051065	MK051076
17	V. guangxiensis X. L. Mo	JL4802	MK030575	MK051094	MK051066	MK051077
18	V. mangachapoi Blanco	JL111A	MK030576	MK051095	MK051067	-
19	V. mangachapoi Blanco	JL111B	MK030577	MK051096	MK051068	MK193027

No.	Species	Voucher numbers	GenBank accession number
No.	Species	Voucher numbers	rbcL	matK	trnL-trnF	ITS2
1	Dipterocarpus turbinatus C. F. Gaertner	JL5901	MK030561	MK051080	MK051054	MK051069
2	D. turbinatus C. F. Gaertner	JL5902	MK030562	MK051081	MK051055	MK051070
3	D. retusus Blume	JL9601	MK030559	MK051078	MK051052	MK193032
4	D. retusus Blume	JL9602	MK030560	MK051079	MK051053	MK193031
5	Hopea chinensis (Merr.) Hand.-Mazz.	JL110A	MK030563	MK051082	MK193024	MK193026
6	H. chinensis (Merr.) Hand.-Mazz.	JL110B	MK030564	MK051083	MK051059	MK193025
7	H. hainanensis Merrill & Chun	JL2201	MK030565	MK051084	MK051060	MK193029
8	H. hainanensis Merrill & Chun	JL2202	MK030566	MK051085	MK051061	MK193028
9	H. hainanensis Merrill & Chun	JL2203	MK030567	MK051086	MK051062	MK193030
10	Parashorea chinensis H. Wang	JL6101	MK030568	MK051087	MK051056	MK051071
11	P. chinensis H. Wang	JL6102	MK030569	MK051088	MK051057	MK051072
12	Shorea assamica Dyer	JL3901	MK030571	MK051090	MK051063	-
13	S. assamica Dyer	JL3902	MK030570	MK051089	MK051058	MK051073
14	Vatica diospyroides Symington	JL7601	MK030572	MK051091	MK051064	MK051074
15	V. diospyroides Symington	JL7602	MK030573	MK051092	MK193023	MK051075
16	V. guangxiensis X. L. Mo	JL4801	MK030574	MK051093	MK051065	MK051076
17	V. guangxiensis X. L. Mo	JL4802	MK030575	MK051094	MK051066	MK051077
18	V. mangachapoi Blanco	JL111A	MK030576	MK051095	MK051067	-
19	V. mangachapoi Blanco	JL111B	MK030577	MK051096	MK051068	MK193027

Barcodes	Primers sequence (5'-3')	Amplification protocol	References
rbcL	1F: ATGTCACCACAAACAGAGACTAAAGC 724R: TCGCATGTACCTGCAGTAGC	94°C 4 min; 94°C 30 s, 55°C 45 s, 72°C 1 min, 5 cycles; 94°C 30 s, 54°C 45 s, 72°C 10 min, 30 cycles; 72°C 10 min	Fay et al., 1997 Olmstead et al., 1992
matK	3F: CGTACAGTACTTTTGTGTTTACGA 1R: ACCCAGTCCATCTGGAAATCTTGG	94°C 4 min; 94°C 30 s, 51°C 50 s, 72°C 50 s, 35 cycles; 72°C 10 min	Unpublished
	390F: CGATCTATTCATTCAATATTTC 1326R: TCTAGCACACGAAAGAAGT	94°C 4 min; 94°C 30 s, 50°C 50 s, 72°C 50 s, 35 cycles; 72°C 10 min	Cuénoud et al., 2002
trnL-trnF	F: GGTTCAAGTCCCTCTATCCC R: ATTTGAACTGGTGACACGAG	94°C 4 min; 94°C 30 s, 55°C 1 min, 72°C 1 min, 35 cycles; 72°C 5 min	Taberlet et al.,1991
ITS2	ITS2 2F: ATGCGATACTTGGTGTGAAT ITS2 3R: GACGCTTCTCCAGACTACAAT	94°C 4 min; 94°C 30 s, 55°C 45 s, 72°C 45 s, 35 cycles; 72°C 10 min	Chen et al., 2010 Chen et al., 2010
	ITS3: GCATCGATGAAGAACGCAGC 26SE: TAGAATTCCCCGGTTCGCTCGCCGTTAC	94°C 4 min; 94°C 30 s, 57°C 45 s, 72°C 45 s, 35 cycles; 72°C 10 min	White et al., 1990; Sun et al., 1994

Barcodes	Primers sequence (5'-3')	Amplification protocol	References
rbcL	1F: ATGTCACCACAAACAGAGACTAAAGC 724R: TCGCATGTACCTGCAGTAGC	94°C 4 min; 94°C 30 s, 55°C 45 s, 72°C 1 min, 5 cycles; 94°C 30 s, 54°C 45 s, 72°C 10 min, 30 cycles; 72°C 10 min	Fay et al., 1997 Olmstead et al., 1992
matK	3F: CGTACAGTACTTTTGTGTTTACGA 1R: ACCCAGTCCATCTGGAAATCTTGG	94°C 4 min; 94°C 30 s, 51°C 50 s, 72°C 50 s, 35 cycles; 72°C 10 min	Unpublished
	390F: CGATCTATTCATTCAATATTTC 1326R: TCTAGCACACGAAAGAAGT	94°C 4 min; 94°C 30 s, 50°C 50 s, 72°C 50 s, 35 cycles; 72°C 10 min	Cuénoud et al., 2002
trnL-trnF	F: GGTTCAAGTCCCTCTATCCC R: ATTTGAACTGGTGACACGAG	94°C 4 min; 94°C 30 s, 55°C 1 min, 72°C 1 min, 35 cycles; 72°C 5 min	Taberlet et al.,1991
ITS2	ITS2 2F: ATGCGATACTTGGTGTGAAT ITS2 3R: GACGCTTCTCCAGACTACAAT	94°C 4 min; 94°C 30 s, 55°C 45 s, 72°C 45 s, 35 cycles; 72°C 10 min	Chen et al., 2010 Chen et al., 2010
	ITS3: GCATCGATGAAGAACGCAGC 26SE: TAGAATTCCCCGGTTCGCTCGCCGTTAC	94°C 4 min; 94°C 30 s, 57°C 45 s, 72°C 45 s, 35 cycles; 72°C 10 min	White et al., 1990; Sun et al., 1994

Barcodes	Amplification efficiency (%)	Success rate of sequencing (%)	Effective sequence ratio (%)
rbcL	100.0	100.0	100.0
matK	100.0	100.0	100.0
trnL-trnF	100.0	100.0	100.0
ITS2	100.0	89.5	89.5