DNA条形码分析方法研究进展

doi:10.13287/j.1001-9332.201803.032

摘要/Abstract

摘要： DNA条形码是一段短的、标准化的DNA序列,DNA条形码技术通过对DNA条形码序列分析实现物种的有效鉴定.随着生物DNA条形码序列的大量测定,DNA条形码分析方法得到迅速发展,推动了其在生物分子鉴定中的应用.2003年以来,DNA条形码技术已广泛应用于动物、植物和真菌等物种的鉴定,并有力地推动了生物分类学、生物多样性和生态学等学科的发展.本文在综述DNA条形码技术的基础上,总结了5类主要的DNA条形码分析方法,即基于遗传距离的分析、基于遗传相似度的分析、基于系统发育树的分析、基于序列特征的分析和基于统计分类法的分析,并进一步展望了DNA条形码技术的发展与应用.

关键词: 遗传距离, 系统发育树, 遗传相似度, 序列特征, 分子鉴定, DNA条形码, 统计分类

Abstract: DNA barcode is a fragment of short DNA sequence from a standard part of the genome. DNA barcoding is an effective taxonomic method for species identification through analyzing the DNA barcodes. With the dramatic increasing of DNA barcode sequences, the analysis methods have developed rapidly, which promoted their applications in molecular identification for organisms. Since 2003, DNA barcoding has been widely used in species identification for animals, plants, fungi, etc. It has also robustly promoted the development of scientific disciplines, such as taxonomy, biodiversity science, and ecology. Based on review of DNA barcoding techniques, we summarized five main analysis methods on DNA barcodes, i.e. the genetic distance-, genetic similarity-, phylogenetic tree-, sequence characters-, and statistical classification-based methods. Moreover, we proposed a prospect for research and applications of DNA barcoding in the future.

Key words: phylogenetic tree, molecular identification, statistical classification, sequence character, DNA barcode, genetic similarity, genetic distance

杨倩倩, 刘苏汶, 俞晓平. DNA条形码分析方法研究进展[J]. 应用生态学报, 2018, 29(3): 1006-1014.

YANG Qian-qian, LIU Su-wen, YU Xiao-ping. Research progress on DNA barcoding analysis methods.[J]. Chinese Journal of Applied Ecology, 2018, 29(3): 1006-1014.

参考文献

[1] Hebert PDN, Cywinska A, Ball SL, et al. Biological identifications through DNA barcodes. Proceeding of the Royal Society of London Series B Biological Sciences, 2003, 270: 313-321
[2] Hebert PDN, Ratnasingham S, de Waard JR. Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London Series B Biological Sciences, 2003, 270: 596-599
[3] Ratnasingham S, Hebert PDN. BOLD: The Barcode of Life Data System. Molecular Ecology Notes, 2007, 7: 355-364
[4] Stoeckle M. Taxonomy, DNA and the barcode of life. Bioscience, 2003, 53: 2-3
[5] Chase MW, Fay MF. Barcoding of plants and fungi. Science, 2009, 325: 682-683
[6] Pei N-C (裴男才). Identification of plant species based on DNA barcode technology. Chinese Journal of Applied Ecology (应用生态学报), 2012, 23(5): 1240-1246 (in Chinese)
[7] Chen S, Yao H, Han J, et al. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One, 2010, 5(1): e8613, doi:10.1371/journal.pone.0008613
[8] Zhang Y (张宇), Guo L-D (郭良栋). Progress of fungal DNA barcode. Mycosystema (菌物学报), 2012, 31(6): 809-820 (in Chinese)
[9] Xue Y-Y (薛应钰), Fan W-Z (范万泽), Zhang S-W (张树武), et al. Screening, identification and biocontrol effect of antagonistic actinomycetes against the pathogen of Cytospora sp. for apple tree. Chinese Journal of Applied Ecology (应用生态学报), 2016, 27(10): 3379-3386 (in Chinese)
[10] Zhao G-Y (赵广宇), Li H (李虎), Yang H-L (杨海林), et al. Application of DNA barcoding in entomo-logy: A review. Acta Phytophylacica Sinica (植物保护学报), 2014, 41(2): 129-141 (in Chinese)
[11] Sullivan J, Joyce P. Model selection in phylogenetics. Annual Review of Ecology, Evolution, and Systematics, 2005, 36: 445-466
[12] Nei M, Kumar S. Molecular Evolution and Phylogene-tics. New York: Oxford University Press, 2000
[13] Candek K, Kuntner M. DNA barcoding gap: Reliable species identification over morphological and geographical scales. Molecular Ecology Resources, 2015, 15: 268-277
[14] Srivathsan A, Meier R. On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature. Cladistics, 2012, 28: 190-194
[15] Schoch CL, Seifert KA, Huhndorf S, et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109: 6241-6246
[16] Puillandre N, Lambert A, Brouillet S, et al. ABGD, automatic barcode gap discovery for primary species delimitation. Molecular Ecology, 2012, 21: 1864-1877
[17] Brown SDJ, Collins RA, Boyer S, et al. Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding. Mole-cular Ecology Resources, 2012, 12: 562-565
[18] Kent WJ. Blata: The blast-like alignment tool. Genome Research, 2002, 12: 656-664
[19] Meier R, Shiyang K, Vaidya G, et al. DNA barcoding and taxonomy in Diptera: A tale of high intraspecific variability and low identification success. Systematic Biology, 2006, 55: 715-728
[20] Zhang AB, Muster C, Liang HB, et al. A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding. Molecular Ecology, 2012, 21: 1848-1863
[21] Chesters D, Zheng WM, Zhu CD. A DNA barcoding system integrating multigene sequence data. Methods in Ecology and Evolution, 2015, 6: 930-937
[22] Sarkar IN, Planet PJ, Bael TE, et al. Characteristic attributes in cancer microarrays. Journal of Biomedical Informatics, 2002, 35: 111-122
[23] Bertolazzi P, Felici G, Weitschek E. Learning to classify species with barcodes. BMC Bioinformatics, 2009, 10: S7, doi:10.1186/1471-2105-10-S14-S7
[24] DasGupta B, Konwar KM, Mandoiu II, et al. DNA-bar: Distinguisher selection for DNA barcoding. Bioinforma-tics, 2005, 21: 3424-3426
[25] Little DP. DNA barcode sequence identification incorporating taxonomic hierarchy and within taxon variability. PLoS One, 2011, 6(8): e20552, doi:10.1371/journal.pone.0020552
[26] Tyagi A, Bag SK, Shukla V, et al. Oligonucleotide frequencies of barcoding loci can discriminate species across kingdoms. PLoS One, 2010, 5(8): e12330, doi:10.1371/journal.pone.0012330
[27] Breiman L, Friedman JH, Olshen RA, et al. Classifi-cation and Regression Trees. Pacific Grove, CA: Wads-worth, 1984
[28] Austerlitz F, David O, Schaeffer B, et al. DNA barcode analysis: A comparison of phylogenetic and statistical classification methods. BMC Bioinformatics, 2009, 10: S10, doi:10.1186/1471-2105-10-S14-S10
[29] Breiman L. Random forests. Machine Learning, 2001, 45: 5-32
[30] Collins RA, Cruickshank RH. The seven deadly sins of DNA barcoding. Molecular Ecology Resources, 2013, 13: 969-975
[31] Barr NB, Islam MS, De Meyer M, et al. Molecular identification of Ceratitis capitata (Diptera: Tephriti-dae) using DNA sequences of the COI barcode region. Annals of the Entomological Society of America, 2012, 105: 339-350
[32] Robinson EA, Blagoev GA, Hebert PDN, et al. Prospects for using DNA barcoding to identify spiders in species-rich genera. Zookeys, 2009, 46: 27-46
[33] Chen L (陈璐), Huang B-Y (黄伯炎), Xue D (薛丹), et al. DNA barcoding of Terapontidae and taxonomic status of a new record of Terapon puta in costal waters of China. Marine Fisheries (海洋渔业), 2017, 39(2): 121-130 (in Chinese)
[34] Hebert PDN, Stoeckle MY, Zemlak TS, et al. Identification of birds through DNA barcodes. PLoS Biology, 2004, 2(10): 1657-1663
[35] Gontran S, Kurt J, Nagy ZT, et al. Adhoc: An R package to calculate ad hoc distance thresholds for DNA barcoding identification. Zookeys, 2013, 365: 329-336
[36] Jorge D, Diaz-Real J, Mironov S. DNA barcoding and minibarcoding as a powerful tool for feather mite studies. Molecular Ecology Resources, 2015, 15: 1216-1225
[37] Rolo E, Oliveira AR, Dourado CG, et al. Identification of sarcosaprophagous Diptera species through DNA barcoding in wildlife forensics. Forensic Science International, 2013, 228: 160-164
[38] Ashfaq M, Asif M, Anjum ZI, et al. Evaluating the capacity of plant DNA barcodes to discriminate species of cotton (Gossypium: Malvaceae). Molecular Ecology Resources, 2013, 13: 573-582
[39] Saddhe AA, Jamdade RA, Kumar K. Evaluation of multilocus marker efficacy for delineating mangrove species of West Coast India. PLoS One, 2017, 12(8): e0183245, doi:10.1371/journal.pone.0183245
[40] Jiang F, Jin Q, Liang L, et al. Existence of species complex largely reduced barcoding success for invasive species of Tephritidae: A case study in Bactrocera spp. Molecular Ecology Resources, 2014, 14: 1114-1128
[41] Mehta RS, Bryant D, Rosenberg NA. The probability of monophyly of a sample of gene lineages on a species tree. Proceedings of the National Academy of Sciences of the United States of America, 2016, 113: 8002-8009
[42] Evans J, Sheneman L, Foster J. Relaxed neighbor joining: A fast distance-based phylogenetic tree construction method. Journal of Molecular Evolution, 2006, 62: 785-792
[43] Duarte S, Batista D, Barlocher F, et al. Some new DNA barcodes of aquatic hyphomycete species. Mycoscience, 2015, 56: 102-108
[44] Lu Y, Ju BL, Gao L, et al. Identification of Campsis Flos and its common adulterants using ITS2 sequence of DNA molecular barcoding. Journal of Medicinal Plant Research, 2017, 11: 373-379
[45] Brandão JHSG, Bitencourt JDA, Santos FB, et al. DNA barcoding of coastal ichthyofauna from Bahia, northeas-tern Brazil, South Atlantic: High efficiency for systema-tics and identification of cryptic diversity. Genome, 2015, 65: 214-224
[46] Liu Z, Song N, Yanagimoto T, et al. Identification of Odontamblyopus iacepedii, via morphology and DNA barcoding. Biochemical Systematics & Ecology, 2016, 66: 281-285
[47] Li X, Su Y, Li X, et al. Identification of Fritillariae bulbus from adulterants using ITS2 regions. Plant Gene, 2016, 7: 42-49
[48] Jordaens K, Goergen G, Virgilio M, et al. DNA Barcoding to improve the taxonomy of the Afrotropical hoverflies (Insecta: Diptera: Syrphidae). PLoS One, 2015, 10(10): e0140264, doi:10.1371/journal.pone.0140264
[49] Witt JD, Threloff DL, Hebert PDN. DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: Implications for desert spring conservation. Molecular Ecology, 2006, 15: 3073-3082
[50] Rach J, DeSalle R, Sarkar IN, et al. Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata. Proceedings of the Royal Society London B Biological Sciences, 2008, 275: 237-247
[51] Little DP, Stevenson DW. A comparison of algorithms for the identification of specimens using DNA barcodes: Examples from gymnosperms. Cladistics, 2007, 23: 1-21
[52] Nielsen R, Matz MV. Statistical approaches for DNA barcoding. System Biology, 2006, 55: 162-169
[53] Dejaegher B, Dhooghe L, Goodarzi M, et al. Classification models for neocryptolepine derivatives as inhibitors of the β-haemat information. Analytica Chimica Acta, 2011, 705: 98-110
[54] Nicolas V, Schaeffer B, Missoup AD, et al. Assessment of three mitochondrial genes (16S, Cytb, COI) for identifying species in the Praomyini tribe (Rodentia: Muridae). PLoS One, 2012, 7(5): e36586, doi:10.1371/journal.pone.0036586
[55] Kuksa P, Pavlovic V. Fast kernel methods for SVM sequence classifiers//Giancarlo R, Hannenhalli S, eds. Algorithms in Bioinformatics. Lecture Notes in Computer Science. Berlin: Springer, 2007: 228-239
[56] Meyer CP, Paulay G. DNA barcoding: Error rates based on comprehensive sampling. PLoS Biology, 2005, 3(12): 2229-2238
[57] Knowles LL, Carstens BC. Delimiting species without monophyletic gene trees. Systematic Biology, 2007, 56: 887-895
[58] Zou S, Li Q, Kong LF, et al. Comparing the usefulness of distance, monophyly and character-based DNA barcoding methods in species identification: A case study of Neogastropoda. PLoS One, 2011, 6(10): e26619
[59] Velzen RV, Weitschek E, Felici G, et al. DNA barcoding of recently diverged species: Relative performance of matching methods. PLoS One, 2012, 7(1): 1-12
[60] Stefan S, Christian SE, Jérôme M, et al. DNA barcoding largely supports 250 years of classical taxonomy: Identifications for Central European bees (Hymenoptera, Apoideapartim). Molecular Ecology Resources, 2015, 154: 985-1000
[61] Zhou X, Li YY, Liu SL, et al. Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. GigaScience, 2013, 2: 4-16
[62] Cao Y (曹云), Shen W-J (沈文静), Chen L (陈炼), et al. Application of metabarcoding technology in studies of fungal diversity. Biodiversity Science (生物多样性), 2016, 24(8): 932-939 (in Chinese)
[63] Ji Y, Ashton L, Pedley SM, et al. Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecology Letters, 2013, 16: 1245-1257
[64] Geml J, Gravendeel B, van der Gaag KJ, et al. The contribution of DNA metabarcoding to fungal conservation: Diversity assessment, habitat partitioning and mapping red-listed fungi in protected coastal Salix repens communities in the Netherlands. PLoS One, 2014, 9(6): e99852, doi:10.1371/journal.pone.0099852
[65] Yoccoz NG, Brathen KA, Gielly L, et al. DNA from soil mirrors plant taxonomic and growth form diversity. Molecular Ecology, 2012, 21: 3647-3655
[66] Yang C-X (杨晨雪), Ji Y-Q (季吟秋), Wang X-Y (王晓阳), et al. Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity. Science China Life Science (中国科学:生命科学), 2012, 42(12): 993-1001 (in Chinese)
[67] Epp LS, Boessenkool S, Bellemain EP, et al. New environmental metabarcodes for analyzing soil DNA: Potential for studying past and present ecosystems. Molecular Ecology, 2012, 21: 1821-1833
[68] Murray DC, Pearson SG, Fulagar R, et al. High-throughput sequencing of ancient plant and mammal DNA preserved in herbivore middens. Quaternary Science Reviews, 2012, 58: 135-145
[69] Coissac E, Riaz T, Puillandre N. Bioinformatic challenges for DNA metabarcoding of plants and animals. Molecular Ecology, 2012, 21: 1834-1847