DNA条形码在热带龙脑香科树种鉴定中的应用
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摘要
龙脑香科植物是东南亚地区重要的热带木材来源树种,对其开展DNA条形码评估在林业监管及森林资源保护等方面具有非常重要的实际应用价值。通过对龙脑香科植物样品进行rbcL、matK、trnL-trnF和ITS2四个片段的扩增和测序,结合GenBank下载的数据,共获得龙脑香科树种14属244种共计899条序列。通过比较4个片段的通用性、序列特征、种内和种间的遗传变异,基于Best Match (BM)、Best Close Match (BCM)、相似性搜索算法(BLAST)和邻接树(NJ) 4种方法评估DNA条形码对于龙脑香科树种的鉴定能力。结果表明,ITS2在龙脑香科树种中鉴定效率最高,通过优化的扩增体系能够从该科植物叶片中获得较高质量的ITS2片段;叶绿体matK片段扩增和测序效率为100%,且种内及种间遗传变异明显,鉴定成功率高于其它叶绿体片段,并据此提出ITS2和matK适合作为龙脑香科树种的DNA条形码。
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 Gen Bank. We amplified and sequenced four DNA regions(rbc L, matK, trn L-trn F 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.
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 Gen Bank. We amplified and sequenced four DNA regions(rbc L, matK, trn L-trn F 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.
引文
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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.
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.
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.
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.
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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.
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.
任保青,陈之端(2010).植物DNA条形码技术.植物学报45,1-12.
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.
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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 B284,20171182.
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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.PLo SOne 10,e0129295.
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.
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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.
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.
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.
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.
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.
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.
任保青,陈之端(2010).植物DNA条形码技术.植物学报45,1-12.
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.
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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.
周亮,黄建平,黄自云(2013).热带植物云南娑罗双.园林(6),62-63.
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.
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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.PLo S One 5,e8613.
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 USA108,19641-19646.
Cuénoud P,Savolainen V,Chatrou LW,Powell M,Grayer RJ,Chase MW(2002).Molecular phylogenetics of Caryophyllales based on nuclear 18S r DNA and plastid rbc L,atp B,and mat K DNA sequences.Am J Bot 89,132-144.
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 B284,20171182.
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.
Doyle JJ,Doyle JL(1987).A rapid DNA isolation procedure for small quantities of fresh leaf tissue.Phytochem Bull19,11-15.
Fay MF,Cameron KM,Prance GT,LledóMD,Chase MW(1997).Familial relationships of Rhabdodendron(Rhabdodendraceae):plastid rbc L sequences indicate a caryophyllid placement.Kew Bull 52,923-932.
Gasson P,Miller R,Stekel DJ,Whinder F,Ziemińska K(2010).Wood identification of Dalbergia nigra(CITESAppendix I)using quantitative wood anatomy,principal components analysis and na?ve Bayes classification.Ann Bot 105,45-56.
Gonzalez MA,Baraloto C,Engel J,Mori SA,Pétronelli P,Riéra B,Roger A,Thébaud C,Chave J(2009).Identification of Amazonian trees with DNA barcodes.PLo SOne 4,e7483.
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.PLo S One 11,e0157881.
Hebert PDN,Cywinska A,Ball SL,de Waard JR(2003).Biological identifications through DNA barcodes.Proc Roy Sci B 270,313-321.
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.
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.
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.PLo SOne 10,e0129295.
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.
Kamiya K,Harada K,Tachida H,Ashton PS(2005).Phylogeny of Pgi C gene in Shorea and its closely related genera(Dipterocarpaceae),the dominant trees in southeast Asian tropical rain forests.Am J Bot 92,775-788.
Kress WJ,Erickson DL(2007).A two-locus global DNAbarcode for land plants:the coding rbc L gene complements the non-coding trn H-psb A spacer region.PLo SOne 2,e508.
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.
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.
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.
Newmaster SG,Fazekas AJ,Ragupathy S(2006).DNAbarcoding in land plants:evaluation of rbc L in a multigene tiered approach.Can J Bot 84,335-341.
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.
Olmstead RG,Michaels HJ,Scott KM,Palmer JD(1992).Monophyly of the Asteridae and identification of their major lineages inferred from DNA sequences of rbc L.Ann Mo Bot Gard 79,249-265.
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