Application of DNA Barcoding in Chinese Acacia s.l. (Leguminosae)

doi:10.7677/ynzwyj201312148

Abstract

Abstract:

It is difficult to identify Chinese species of Acacia accurately based on morphological assessment unless an intact specimen is at hand. In contrast, DNA barcoding through the analysis of short DNA sequences from a small sample of tissue can provide an accurate method for identifying species. In this study, we used four DNA fragments (rbcL, matK, psbAtrnH, and ITS) to develop a potential barcoding method for Chinese Acacia. Our analysis involved calculating inter and intraspecific genetic distances, conducting Wilcoxon signed rank tests to analyze the sequence variation, and constructing phylogenetic trees from distance data. The results showed that barcoding gaps exist between Acacia species for each of the four sequences, with ITS showing highest interspecific divergence. Both the use of ITS on its own and in combination with rbcL sequence variation gave the highest level of species identification. We therefore propose the use of ITS sequence variation on its own or combined with rbcL as a DNA barcode for identifying Acacia species in China.

Key words: Acacia, ITS, rbcL, matK, psbA-trnH, DNA barcoding, Species identification

CLC Number:

OU Yang-Cheng-Ren-, SUN Hang-, LI Zhi-Min-**, ZHANG Jian-Wen. Application of DNA Barcoding in Chinese Acacia s.l. (Leguminosae)[J]. Plant Diversity, 2013, 35(5): 547-554.

References

Chen SL, Yao H, Han JP et al., 2010. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species［J］. PloS One, 5: e8613
China Plant BOL Group, 2011. Comparative analysis of a large dataset indicates that internal transcribed spacer(ITS) should be incorporated into the core barcode for seed plants［J］. Proceedings of the National Academy of Sciences of USA, 108: 19641—19646
CBOL Plant Working Group, 2009. A DNA barcode for land plants［J］. Proceedings of the National Academy of Sciences of USA, 106: 12794—12797
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
Du ZY, Yang CF, Chen JM et al., 2011. Testing four barcoding markers for species identification of Potamogetonaceae［J］. Journal of Systematics and Evolution, 49 (3): 246—251
Fay MF, Swensen SM, Chase MW, 1997. Taxonomic affinities of Medusagyne oppositifolia (Medusagynaceae)［J］. Kew Bulletin, 52 (1): 111—120
Fu YM, Jiang WW, Fu CX, 2011. Identification of species within Tetrastigma (Miq.) Planch. (Vitaceae) based on DNA barcoding techniques［J］. Journal of Systematics and Evolution, 49 (3): 237—245
Gao T, Yao H, Song JY et al., 2010. Identification of medicinal plants in the family Fabaceae using a potential DNA barcode ITS2［J］. Journal of Ethnopharmacology, 130: 116—121
Hall TA, 1999. BioEdit: a user friendly biological sequences alignment editor and analysis program for Windows 95/98/NT［J］. Nucleic Acids Symposium Series, 41: 95—98
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: 313—321
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: 439—457
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 of USA, 102: 8369—8374
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: e508
Li M, Cao H, Shaw PC et al., 2011. Identification of herbal medicinal materials using DNA barcodes［J］. Journal of Systematics and Evolution, 49 (3): 271—283
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
Logacheva MD, ValiejoRoman CM, Pimenov MG, 2008. ITS phylogeny of West Asian Heracleum species and related taxa of UmbelliferaeTordylieae W.D.J.Koch, with notes on evolution of their psbAtrnH sequences［J］. Plant Systematics and Evolution, 270: 139—157
Maslin BR, Miller JT, Seigler DS, 2003. Overview of the generic status of Acacia (Leguminosae: Mimosoideae) ［J］. Australian Systematic Botany, 16: 1—18
Meyer CP, Paulay G, 2005. DNA barcoding: Error rates based on comprehensive sampling［J］. PLoS Biology, 3: e422
Miller JT, Grimes JW, Murphy, DJ et al., 2003. A phylogenetic analysis of the Acacieae and Ingeae (Mimosoideae: Fabaceae) based on trnK, matK, psbAtrnH, and trnL/trnF sequence data［J］. Systematic Botany, 28 (3): 558—566
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
Nielsen IC, 1985. LeguminosaeMimosoideae［A］. In: Smitinand T, Larsen K (eds.), Flora of Thailand［M］. Bangkok, Thailand: The Forest Herbarium, Royal Forest Department, Vol.4 (2): 131—222
Ning SP (宁淑萍), Yan HF (颜海飞), Hao G (郝刚) et al., 2008. Current advances of DNA barcoding study in plants［J］. Biodiversity Science (生物多样性), 16 (5): 417—425
Ren BQ (任保青), Chen ZD (陈之端), 2010. DNA barcoding plant life［J］. Chinese Bulletin of Botany (植物学报), 45 (1): 1—12
Sun H (孙航), 2006. Acacieae［A］. In: Kunming Institute of Botany, Chinese Academy of Sciences (中国科学院昆明植物研究所) (ed.), Flora Yunnanica (云南植物志) ［M］. Beijing: Science Press, 10: 293—307
Sun H (孙航), Chen J (陈介), 1990. Taxonomy, distribution and possible floristic origin of the genus Acacia from China［J］. Acta Botanica Yunnanica (云南植物研究), 12 (3): 255—268
Thompson JD, Higgins DG, Gibson TJ, 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice［J］. Nucleic Acids Research, 22: 4673—4680
Tamura K, Peterson D, Peterson N et al., 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods［J］. Molecular Biology and Evolution, 28 (10): 2731—2739
Wang Q, Yu SQ, Liu JQ, 2011. Are nuclear loci ideal for barcoding plants? A case study of genetic delimitation of two sister species using multiple loci and multiple intraspecific individuals［J］. Journal of Systematics and Evolution, 49 (3): 182—188
White TJ, Bruns TD, Lee SB et al., 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics［A］. In: Innis M, Gelfand D, Sninsky J et al. (eds.), PCR Protocols: A Guide to Methods and Applications［M］. San Diego: Academic Press, 315—322
Wu DL (吴德邻), 1988. Mimosoideae［A］. In: Chen DS (陈德绍) (ed.), Flora Reipublicae Popularis Sinicae (中国植物志) ［M］. Beijing: Science Press, 39: 22—37
Wu DL, 2010. Tribe Acacieae［A］. In: Chen DS (ed.), Flora of China［M］. Beijing: Science Press and St.Louis.: Missouri Botanical Garden Press, 10: 55—59
Yan HX (闫化学), Yu J (于杰), 2010. Current status of the study of DNA barcoding in plants［J］. Chinese Bulletin of Botany (植物学报), 45 (1): 102—108
Yu J, Xue JH, Zhou SL, 2011. New universal matK primers for DNA barcoding angiosperms［J］. Journal of Systematics and Evolution, 49 (3): 176—181
Zhao YM (赵月梅), Zhang L (张玲), 2011. Using DNA barcoding in genus Tacca (Dioscoreaceae) ［J］. Plant Diversity and Resources (植物分类与资源学报), 33 (6): 674—682

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