Using DNA Barcoding in Genus Tacca (Dioscoreaceae)

doi:10.3724/SP.J.1143.2011.11060

Abstract

Abstract:

Tacca (Dioscoreaceae) is a small genus which is taxonomically difficult because of a lack of obvious morphologically differences among species. DNA barcoding is a new method of rapid species identification and discovery using short, standardized genes or DNA regions. In this study, four candidate DNA barcoding regions that three (rbcL, matK, trnHpsbA) from chloroplast genome and one (ITS) from the nuclear genome, were evaluated among 36 accessions representing 6 species of Tacca. The capability of those regions were evaluated by intra and interspecific divergence and barcode gap analyses, and the identification efficiency was assessed using Treebased and BBA methods. The results indicated that both ITS and the core barcode rbcL+matK proposed by CBOL exhibited the highest resolution as a single and combined data respectively. Based on overall performance: matK+rbcL can be considered as a potential barcode for identifying the species of Tacca, ITS can be used as a supplementary barcode. DNA barcoding revealed two distinct lineages of T.integrifolia distributed allopatrically in Tibet and Malaysia. And these two lineages with morphological variations may potentially represent new species.

Key words: Tacca, DNA barcoding, ITS, matK, rbcL, trnH-psbA

摘要：

蒟蒻薯属（Tacca）植物种间在形态上差别不大，导致分类上存在一定的困难。DNA条形码是一种利用短的DNA标准片段来鉴别和发现物种的方法。本研究利用核基因ITS片段和叶绿体基因trnHpsbA, rbcL, matK片段对蒟蒻薯属6个种的DNA条形码进行研究,对4个DNA片段可用性，种内种间变异，barcode gap进行了分析，采用Treebased和BBA两种方法比较不同序列的鉴定能力。结果显示：单片段ITS正确鉴定率最高，片段组合rbcL+matK正确鉴定率最高。支持CBOL植物工作组推荐的条码组合rbcL+matK可作为蒟蒻薯属物种鉴定的标准条码，建议ITS片段作为候选条码。丝须蒟蒻薯Tacca integrifolia采自西藏的居群与马来西亚居群形成了2个不同的遗传分支，且两者在形态上也存在一定的差异，很可能是一个新种。

关键词: 蒟蒻薯属, DNA条形码, ITS, matK, rbcL, trnH-psbA

CLC Number:

Q 75，Q 949

DIAO Yue-Mei-, ZHANG Ling. Using DNA Barcoding in Genus Tacca (Dioscoreaceae)[J]. Plant Diversity, 2011, 33(6): 674-682.

赵月梅1、2, 张玲1. 蒟蒻薯属 (薯蓣科) 植物DNA条形码研究[J]. Plant Diversity, 2011, 33(6): 674-682.

References

傅立国, 金鉴明, 1992. 中国植物红皮书-稀有濒危植物(第1册)［M］. 北京: 科学出版社
贾敏如, 李星炜, 2005. 中国民族药志要［M］. 北京: 中国医药科技出版社
凌萍萍, 1985. 中国植物志［A］. 中科院中国植物志编辑委员会［M］. 北京: 科学出版社, 16: 42—54
张玲, 2006. 蒟蒻薯科植物的系统学、物种生物学与进化生态学研究［D］. 昆明: 中国科学院昆明植物研究所（博士学位论文）
CBOL Plant Working Group, 2009. A DNA barcode for land plants［J］. Proceedings National Academy of Sciences of the United States of America, 106: 12794—12797
Chase MW, Cowan RS, Hollingsworth PM et al., 2007. A proposal for a standardised protocol to barcode all land plants［J］. Taxon, 56 (2): 295—299
Chase MW, Salamin N, Wilkinson M et al., 2005. Land plants and DNA barcodes: shortterm and longterm goals［J］. Philosophical Transactions of the Royal Society B: Biological Sciences, 360 (1462): 1889—1895
Cowan RS, Chase MW, Kress WJ et al., 2006. 300000 species to identify: problems, progress, and prospects in DNA barcoding of land plants［J］. Taxon, 55 (3): 611—616
Doyle J, Doyle J, 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue［J］. Phytochemistry,19: 11—15
Drenth E, 1972. A revision of the family Taccaceae［J］. Blumea, 20 (2): 367—406
Grierson M, Green PS, 1996. A Hawaiian Florilegium: Botanical Portraits from Paradise［M］. Hawai‘i: University of Hawai‘i Press, 70
Hebert PDN, Cywinska A, Ball SL et al., 2003. Biological identifications through DNA barcodes［J］. Proceedings of the Royal Society of London Series B: Biological Sciences, 270 (1512): 313—321
Hewitt G, 2000. The genetic legacy of the Quaternary iceages［J］. Nature, 405: 907—913
Hollingsworth ML, Clark AA, Forrest LL et al., 2009. Selecting barcoding loci for plants: evaluation of seven candidate loci with specieslevel sampling in three divergent groups of land plants［J］. Molecular Ecology Resources,9 (2): 439—457
Jarman SN, Elliott NG, 2000. DNA evidence for morphological and cryptic Cenozoic speciations in the Anaspididae,‘living fossils’ from the Triassic［J］. Journal of Evolutionary Biology,13 (4): 624—633
Knowlton N, 1993. Sibling species in the sea［J］. Annual Review of Ecology and Systematics, 24: 189—216
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［J］. PLoS One, 2 (6): e508
Kress WJ, Wurdack KJ, Zimmer EA et al., 2005. Use of DNA barcodes to identify flowering plants［J］. Proceedings of the National Academy of Sciences, 102 (23): 8369—8374
Lahaye R, Van der Bank M, Bogarin D et al., 2008. DNA barcoding the floras of biodiversity hotspots［J］. Proceedings of the National Academy of Sciences, 105 (8): 2923—2928
Larkin MA, Blackshields G, Brown NP et al., 2007. Clustal W and clustal X version 2.0［J］. Bioinformatics, 23 (21): 2947—2948
Liu J, Mller M, Gao LM et al., 2011. DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species［J］. Molecular Ecology Resources, 11: 89—100
Meier R, Kwong S, Vaidya G et al., 2006. DNA barcoding and taxonomy in Diptera:a tale of high intraspecific variability and low identification success transactions［J］. Systematic Biology, 55: 715—728
Meyer CP, Paulay G, 2005. DNA barcoding: Error rates based on comprehensive sampling［J］. PLoS Biology, 3 (12): 2229—2238
Newmaster SG, Ragupathy S, 2009. Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae) ［J］. Molecular Ecology Resources, 9 (s1): 172—180
Tamura K, Dudley J, Nei M et al., 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0［J］. Molecular Biology and Evolution, 24: 1596—1599
Tautz D, Arctander P, Minelli A et al., 2002. DNA points the way ahead of taxonomy-In assessing new approaches, it’s time for DNA’s unique contribution to take a central role［J］. Nature, 418: 479—479
The Angiosperm Phylogeny Group, 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II［J］. Botanical Journal of the Linnean Society, 141: 399—436
Valentini A,Pompanon F,Taberlet P,2009.DNA barcoding for
ecologist［J］. Trends in Ecology & Evolution, 24 (2): 110—117
Zhang L (张玲), Li QJ (李庆军), Li DZ (李德铢), 2006. Genetic diversity of Tacca integrifolia (Taccaceae) in the Brahmaputra valley, Tibet［J］. Biodiversity Science (生物多样性),14 (1): 65—72

[1]	Zhi-Chao Li, Chao-Qun Xu, Wei Zhao, Shuai Nie, Yu-Tao Bao, Hui Liu, Zhen Xing, Jian-Feng Mao, Xiao-Ru Wang. Ecophysiological transition mediated by hybridization in a hybrid pine species complex [J]. Plant Diversity, 2025, 47(04): 604-619.
[2]	Yu-Mei Yan, Ze-Xin Fan, Pei-Li Fu, Zhi-Yong Zhang. Drought tolerance traits explain differential stem growth rates of evergreen and deciduous trees in a tropical karst forest [J]. Plant Diversity, 2025, 47(03): 454-465.
[3]	Xue Wang, Xinrui Liu, Shuang Chen, Jiang Zhu, Yanqi Yuan, Rong Zhu, Kaixi Chen, Xue Yang, Xiaochun Wang, Weiyi Mo, Ruili Wang, Shuoxin Zhang. Elevational variation in anatomical traits of the first-order roots and their adaptation mechanisms [J]. Plant Diversity, 2025, 47(02): 291-299.
[4]	Wenjie Guo, Lu Gong, Yan Luo, Qian Guo. Does season regulate heterochronous leaf growth? Mechanisms of petiole-lamina trade-offs in broad-leaved woody plants of the Tianshan Mountains [J]. Plant Diversity, 2024, 46(06): 755-765.
[5]	Tana Wuyun, Lu Zhang, Tiina Tosens, Bin Liu, Kristiina Mark, José ángel Morales-Sánchez, Jesamine Jöneva Rikisahedew, Vivian Kuusk, ülo Niinemets. Extremely thin but very robust: Surprising cryptogam trait combinations at the end of the leaf economics spectrum [J]. Plant Diversity, 2024, 46(05): 621-629.
[6]	Jingya Zhang, Cui Xiao, Xiaoyu Duan, Xin Gao, Hao Zeng, Rong'an Dong, Gang Feng, Keping Ma. Species' geographical range, environmental range and traits lead to specimen collection preference of dominant plant species of grasslands in Northern China [J]. Plant Diversity, 2024, 46(03): 353-361.
[7]	Rong Ma, Qi Xu, Yongqian Gao, Deli Peng, Hang Sun, Bo Song. Patterns and drivers of plant sexual systems in the dry-hot valley region of southwestern China [J]. Plant Diversity, 2024, 46(02): 158-168.
[8]	Ju Li, Shu-Bin Zhang, Yang-Ping Li. Photosynthetic response dynamics in the invasive species Tithonia diversifolia and two co-occurring native shrub species under fluctuating light conditions [J]. Plant Diversity, 2024, 46(02): 265-273.
[9]	Ming-Yue Jin, Daniel J. Johnson, Guang-Ze Jin, Qing-Xi Guo, Zhi-Li Liu. Soil water content and nitrogen differentially correlate with multidimensional leaf traits of two temperate broadleaf species [J]. Plant Diversity, 2023, 45(06): 694-701.
[10]	Hai-Su Hu, Jiu-Yang Mao, Xue Wang, Yu-Ze Liang, Bei Jiang, De-Quan Zhang. Plastid phylogenomics and species discrimination in the “Chinese” clade of Roscoea (Zingiberaceae) [J]. Plant Diversity, 2023, 45(05): 523-534.
[11]	Yan Ke, Feng-Ping Zhang, Yun-Bing Zhang, Wei Li, Qin Wang, Da Yang, Jiao-Lin Zhang, Kun-Fang Cao. Convergent relationships between flower economics and hydraulic traits across aquatic and terrestrial herbaceous plants [J]. Plant Diversity, 2023, 45(05): 601-610.
[12]	Amarpreet Kaur, Shalinder Kaur, Harminder Pal Singh, Daizy R. Batish. Is intraspecific trait differentiation in Parthenium hysterophorus a consequence of hereditary factors and/or phenotypic plasticity? [J]. Plant Diversity, 2023, 45(05): 611-620.
[13]	Korina Ocampo-Zuleta, Ángela Parrado-Rosselli. Functional diversity in an Andean subpáramo affected by wildfire in Colombia [J]. Plant Diversity, 2023, 45(04): 385-396.
[14]	Shi-Yu Lv, Xia-Ying Ye, Zhong-Hu Li, Peng-Fei Ma, De-Zhu Li. Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia [J]. Plant Diversity, 2023, 45(02): 147-155.
[15]	Harshita Bhatia, Gaurav Srivastava, R. C. Mehrotra. Legumes from the Paleocene sediments of India and their ecological significance [J]. Plant Diversity, 2023, 45(02): 199-210.