DNA barcoding and its applications in parasitology
XU Wu-jie1, WANG Yan2, 3, ZOU Jie-xin1, 3, ZHU Chun-chao1, 3, ZHOU Xian-min1, 3
1.Department of Parasitology, Medical College, Nanchang University, Nanchang 330006, China; 2.Medical Genetics and Cell Biology Laboratory, Medical College, Nanchang University, Nanchang 330006, China; 3.Key Laboratory of Poyang Lake Environment and Resource Utilization Supported by the Ministryof Education, Nanchang University, Nanchang 330047, China
Abstract:Parasite is a specific organism group closely related to human health, and its taxonomy and classification are important foundation for parasitological research. "DNA barcoding" is a rapid and accurate method for species identification through a standard DNA fragment. It is a new developed molecular marker technology after RFLP, PCR-RFLP, SSR-PCR, ISSR etc., based on the powerful computers and widely using internet. As it overcomes the negative influence of phenotypic plasticity and genetic variability, and is not restricted by gender and development stage, it has become the current hot spot in taxonomical study. In this paper, we reviewed the evolution of DNA barcode concept and technology, basic methodology, and current controversy, and described it's application in identification of protozoa, helminth and Arthropoda, the development of DNA barcode technology, and its application in parasite research.
徐武杰, 汪雁, 邹节新, 朱春潮, 周宪民. DNA条形码及其在寄生虫学中的应用[J]. 中国人兽共患病学报, 2015, 31(4): 365-370.
XU Wu-jie, WANG Yan, ZOU Jie-xin, ZHU Chun-chao, ZHOU Xian-min. DNA barcoding and its applications in parasitology. Chinese Journal of Zoonoses, 2015, 31(4): 365-370.
[1] Hebert PD, Cywinska A, Ball SL, et al. Biological identifications through DNA barcodes[J]. Proc R Soc Lond B, 2003, 270: 313-321. doi:10.1098/rspb.2002.2218 [2] Frezal L, Leblois R. Four years of DNA barcoding: Current advances and prospects[J]. Infect Genet Evolut 2008, 8: 727-736. doi:10.1016/j.meegid.2008.05.005 [3] Pecnikar ZF, Buzan EV. 20 years since the introduction of DNA barcoding: from theory to application[J]. J Appl Genetics, 2014, 55(1): 43-52. doi:10.1007/s13353-013-0180-y [4] Chen L, Hu JJ, Chen Y, et al. The national natural science fund committee major projects "animal DNA barcode gene and cryptic diversity research" through review[J]. Chin Bullet Life Sci, 2011, 23(3): 231-233. (in Chinese) 陈领, 胡景杰, 陈越, 等. 国家自然科学基金委员会重大项目“动物DNA 条形码基因和隐存多样性的研究”通过评审论证[J]. 生命科学, 2011, 23(3): 231-233. [5] Han YM, Shong JY, Yao H, et al. Comparison of DNA barcoders in identifying medicinal materials[J]. China J Chin Materia Medica, 2012, (8): 1056-1061. (in Chinese) 韩建萍, 宋经元, 姚辉, 等. 中药材DNA 条形码鉴定的基因序列比较[J]. 中国中药杂志, 2012, (8): 1056-1061. [6] Liu MS, Mei H, Lv GX, et al. Construction of medical fungi DNA barcoding and evaluation of its value in applying[J]. Chin J Lepr Skin Dis, 2012, 28(5): 311-313. (in Chinese) 刘沐桑, 梅缳, 吕桂霞, 等. 8种病原真菌DNA条形码的构建和应用评价[J]. 中国麻风皮肤病杂志, 2012, 28(5): 311-313. [7] Ma MY, Yan Y, Wang YW, et al. A study of DNA barcoding on 32 species of bird in China[J]. Sichuan J Zool, 2012, 31(5): 729-733. doi:10.3969 /j.issn.1000-7083.2012.05.008 (in Chinese) 马明义, 闫颖, 王译伟, 等. 我国32 种鸟类DNA 条形码分析[J]. 四川动物, 2012, 31(5): 729-733. [8] Li J, Liu XT, Guo WH, et al. Progress of analytic methods in animal DNA barcoding[J]. Sichuan J Zool, 2013, 32(6): 950-954. doi:10.3969 /j.issn.1000-7083.2013.06.030 (in Chinese) 李晶, 刘雪涛, 郭华威, 等. 动物DNA条形码之分析方法研究进展[J]. 四川动物, 2013, (32)6: 950-954. [9] Zemlak TS, Ward RD, Connell AD, et al. DNA barcoding reveals overlooked marine fishes[J]. Mol Ecol Resour, 2009, 9(s1): 237-242. doi:10.1111/j.1755-0998.2009.02649.x [10] Hebert PD, Stoeckle MY, Zemlak TS, et al. Identification of birds through DNA Barcodes[J]. PLoS Biol, 2004, 2(10): 1657-1663. doi:10.1371/journal.pbio.0020312.g003 [11] Ma H, Ma C, Ma L. Molecular identification of genus Scylla (Decapoda: Portunidae) based on DNA barcoding and polymerase chain reaction[J]. Biochem Syst Ecol, 2012, 41: 41-47. doi:10.1016/j.bse. 2011. 12.016 [12] Velzen RV, Weitschek E, Felici G, et al. DNA barcoding of recently diverged Species: relative performance of matching methods[J]. PLoS ONE, 2012, 7(1): 1-12. doi:10.1371/journal.pone.0030490.t001 [13] Bertolazzi P, Felici G, Weitschek E. Learning to classify species with barcodes[J]. BMC Bioinformatics, 2009, 10(s14): S7. doi:10.1186/1471-2105-10-S14-S7 [14] Weitschek E, Velzen RV, Felici G, et al. BLOG 2. 0: a software system for character-based species classification with DNA barcode sequences. What it does, how to use it[J]. Mol Ecol Resour, 2013, 13(6): 1043-1046.doi:10.1111/1755-0998.12073. [15] Piganeau G, Walker AE, Grimsley N, et al. How and why DNA barcodes underestimate the diversity of microbial eukaryotes[J]. PLoS ONE, 2011, 6(2): 1-6. doi:10.1371/journal.pone.0016342.t001 [16] Maia VH, Mata CS, Franco LO, et al. DNA barcoding bromeliaceae: achievements and pitfalls[J]. PLoS ONE, 2012, 7(1): 1-6. doi:10.1371/journal.pone.0029877.g001 [17] Meyer CP, Paulay G. DNA Barcoding: Error rates based on comprehensive sampling[J]. PLoS Biol, 2005, 3(12): 1-10. doi:10.1371/journal.pbio.0030422 [18] Wiemers M, Fiedler K. Does the DNA barcoding gap exist? - a case study in blue butterflies (Lepidoptera: Lycaenidae)[J]. Front Zool, 2007, 4(8): 1-16. doi:10.1186/1742-9994-4-8 [19] Meier R, Zhang G, Ali F. The use of mean instead of smallest interspecific distances exaggerates the size of the "Barcoding Gap" and leads to misidentification[J]. Syst Biol, 2008, 57(5): 809-813. doi:10.1080/10635150802406343 [20] Hurst GD, Jiggins FM. Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts[J]. Proc R Soc B, 2005, 272: 1525-1534. doi:10.1098/rspb.2005.3056 [21] Nabholz B, Mauffrey JF, Bazin E, et al. Determination of mitochondrial genetic diversity in mammals[J]. Genetics, 2008, 178: 351-361. doi:10.1534/genetics.107.073346 [22] Chase MW, Fay MF. Barcoding of plants and fungi[J]. Science, 2009, 325: 682-683. doi:10.1126/science.1176906 [23] Liu SY, Chan CL, Lin O, et al. DNA barcoding of shark meats identify species composition and CITES-listed species from the markets in Taiwan[J]. PLoS ONE, 2013, 8(11): 1-8. doi:10.1371/journal.pone.0079373.t001 [24] Kosakyan A, Gomaa F, Mitchell EA, et al. Using DNA-barcoding for sorting out protist species complexes: A case study of the Nebela tincta-collaris-bohemica group (Amoebozoa; Arcellinida, Hyalospheniidae)[J]. Europ J Protistol, 2013, 49: 222-237. doi:10.1016/j.ejop.2012.08.006 [25] Hamilton PB, Stevens JR. Resolving relationships between Australian trypanosomes using DNA barcoding data[J]. Trends Parasitol, 2011, 27(3): 99. doi:10.1016/j.pt.2010.11.009 [26] Ogedengbe JD, Hanner RH, Barta JR. DNA barcoding identifies Eimeria species and contributes to the phylogenetics of coccidian parasites (Eimeriorina, Apicomplexa, Alveolata)[J]. Int J Parasitol, 2011, 41: 843-850. doi:10.1016/j.ijpara.2011.03.007 [27] Thompson RC, Lymbery AJ, Smith A. Parasites, emerging disease and wildlife conservation[J]. Int J Parasitol, 2010, 40: 1163-1170. doi:10.1016/j.ijpara.2010.04.009 [28] Lawton SP, Majoros G. A foreign invader or a reclusive native? DNA barcoding reveals a distinct European lineage of the zoonotic parasite Schistosoma turkestanicum (syn. Orientobilharzia turkestanicum (Dutt and Srivastava, 1955))[J]. Infect Genet Evolut, 2013, 14: 186-193. doi:10.1016/j.meegid.2012.11.013 [29] Zhang GT. Feasible analysis of DNA barcoding on the Echinococcus species and a primary research on the Echinococcus infection rate of plateau pika[D]. Shanghai: East China Normal University, 2012. (in Chinese) 张高天. 棘球绦虫的DNA条形码可行性分析及高原鼠兔棘球绦虫感染率初步研究[D]. 上海: 华东师范大学, 2012. [30] Ferri E, Barbuto M, Bain O, et al. Integrated taxonomy: traditional approach and DNA barcoding for the identification of filarioid worms and related parasites (Nematoda)[J]. Front Zool, 2009, 6(1): 1-12. doi:10.1186/1742-9994-6-1 [31] Guardone L, Deplazes P, Macchioni F, et al. Ribosomal and mitochondrial DNA analysis of Trichuridae nematodes of carnivores and small mammals[J]. Vet Parasitol, 2013, 197: 364-369. doi:10.1016/j.vetpar.2013.06.022 [32] Wang G, Li CX, Guo XX, et al. Identifying the main mosquito species in China based on DNA barcoding[J]. PLoS ONE, 2012, 7(10): 1-11. doi:10.1371/journal.pone.0047051.g001 [33] Li GQ. DNA barcoding and molecular phylogeny of the spider mites in China (Acari: tetranychidae)[D]. Nanjing: Nanjing Agricultural University, 2010. (in Chinese) 李国庆. 中国叶螨DNA条形码的研究及其系统发育分析[D]. 南京: 南京农业大学, 2010. [34] Costa FO, deWaard JR, Boutillier J, et al. Biological identifications through DNA barcodes: the case of the Crustacea[J]. Can J Fish Aquat Sci, 2007, 64: 272-295. doi:10.1139/F07-008 [35] Betson M, Halstead FD, Nejsum P, et al. A molecular epidemiological investigation of Ascaris on Unguja, Zanzibar using isoenyzme analysis, DNA barcoding and microsatellite DNA profiling[J]. Transact Royal Soc Trop Med Hyg, 2011, 105: 370-379. doi:10.1016/j.trstmh.2011.04.009 [36] Azpurua J, Cruz DD, Valderama A, et al. Lutzomyia sand fly diversity and rates of infection by Wolbachia and an Exotic Leishmania species on Barro Colorado Island, Panama[J]. PLoS Negl Trop Dis, 2010, 4(3): 1-9. doi:10.1371/journal.pntd.0000627.g001 [37] Ji Y, Ashton L, Pedley SM, et al. Reliable verifiable and efficient monitoring of biodiversity via metabarcoding[J]. Ecol Lett, 2013, 16: 1245-1257.doi:10.1111/ele.12162. [38] Zhou X, Li YY, Liu SL, et al. Ultra-deep sequencing enables highfidelity recovery of biodiversity for bulk arthropod samples without PCR amplification[J]. GigaScience, 2013, 2(4): 1-12.doi:10.1186/2047-217X-2-4. [39] Lees DC, Rougerier R, Lukashortc CZ, et al. DNA mini-barcodesin taxonomic assignment: a morphologically unique new homoneurousmoth clade from the Indian Himalayas described in Micropterix (Lepidoptera, Micropterigidae)[J]. Zoologica Scripta, 2010, 39: 642-661. doi:10.1111/j.1463-6409.2010.00447.x [40] Cheng P, Zhang AB, Wang ZS. Mini DNA barcode utilizes in fish classification[J]. J Capital Normal Univ:Nat Sci Ed, 2012, 33(2): 48-52. (in Chinese) 程鹏, 张爱兵, 王忠锁. 微型DNA条形码在鱼类识别上的应用[J]. 首都师范大学学报: 自然科学版, 2012, 33(2): 48-52.