DNA宏条形码技术在食草动物食性研究中的应用

doi:10.13560/j.cnki.biotech.bull.1985.2020-0988

摘要/Abstract

摘要：

随着测序技术的快速发展,整合DNA条形码和高通量测序的DNA宏条形码技术已经成为当前研究热点之一,在食草动物的食性鉴定中有很大潜力。放牧动物食性研究是动物营养学和草地生态学领域的重要研究内容。而与传统食性研究方法相比,宏条形码技术可通过对植物DNA条形码的高通量测序,获得样本中的物种组成进而分析动物食性。介绍了传统食性分析手段的局限,重点综述了DNA宏条形码技术的产生、操作原理以及在食草类动物食性鉴定领域中的应用,同时还简述了可能存在的挑战,并对该技术今后的发展方向进行了展望。

关键词: 植物条形码, 宏条形码, 高通量测序, 食草动物, 食性鉴定

Abstract:

With the rapid development of sequencing techniques,DNA metabarcoding that derived from the combination of DNA barcoding and high-throughput sequencing technologies,has been a current research hotspot and shows great potential in diet identification of herbivores. Dietary analysis of grazing animal is a key research content in animal nutrition and grassland ecology. In contrast to traditional approach on diet determination,DNA metabarcoding can be used to investigate the species composition of a sample by high-throughput sequencing on plant DNA barcodes,and then to study the food diet of herbivores. This paper briefly reviewed the limitations of traditional diet analysis methods,and then summarized the background and analytical principles of DNA metabarcoding and its applications in the identification of herbivore diet. It also outlined the possible challenges in the research process and prospected the future trends of the DNA metabarcoding technology.

Key words: plant barcode, metabarcoding, high-throughput sequencing, herbivore, diet identification

郭艳萍, 张浩, 赵新钢, 罗海玲, 张英俊. DNA宏条形码技术在食草动物食性研究中的应用[J]. 生物技术通报, 2021, 37(3): 252-260.

GUO Yan-ping, ZHANG Hao, ZHAO Xin-gang, LUO Hai-ling, ZHANG Ying-jun. Applications of DNA Metabarcoding in Diet Identification of Herbivores[J]. Biotechnology Bulletin, 2021, 37(3): 252-260.

参考文献 67

[1]	单继红, 吴建平. 食草动物食性研究的主要方法及其评价[J]. 野生动物, 2005,26(3):47-49.
	Shan JH, Wu JP. The review and evaluation on the study methods for herbivore food habit[J]. Chinese Wildlift, 2005,26(3):47-49.
[2]	任继周. 草业科学研究方法[M]. 北京: 中国农业出版社, 1998.
	Ren JZ. Research method of pratacultural science[M]. Beijing: China Agriculture Press, 1998.
[3]	Ali H, Mayes RW, Hector BL, et al. The possible use of n-alkanes, long-chain fatty alcohols and long-chain fatty acids as markers in studies of the botanical composition of the diet of free-ranging herbivores[J]. Journal of Agricultural Science, 2005,143(2):85-95.
[4]	Chen XJ, Hou FJ, Matthew C, et al. Stocking rate effects on metabolizable energy intake and grazing behaviour of Tan sheep in steppe grassland on the Loess Plateau of Northwest China[J]. The Journal of Agricultural Science, 2010,148(6):709-721. doi: 10.1017/S0021859610000511 URL
[5]	Lin L, Dickhoefer U, Müller K, et al. Grazing behavior of sheep at different stocking rates in the Inner Mongolian steppe, China[J]. Applied Animal Behaviour Science, 2011,129(1):36-42. doi: 10.1016/j.applanim.2010.11.002 URL
[6]	Arceo G, Mandujano S, Gallina S, et al. Diet diversity of white-tailed deer(Odocoileus virginianus)in a tropical dry forest in Mexico[J]. Mamm, 2005,69(2):159-168.
[7]	徐学良. 驼鹿[J]. 动物学杂志, 1980(3):48-52.
	Xu XL. Moose[J]. Chinese Journal of Zoology, 1980(3):48-52.
[8]	李继承, 颜廷峰, 林仲凡. 林区野生马鹿食性与危害幼林的分析[J]. 动物学杂志, 1989,24(3):34-36.
	Li JC, Yan TF, Lin ZF. Analysis on feeding habits of wild red deer in forest area and its damage to young forest[J]. Chinese Journal of Zoology, 1989,24(3):34-36.
[9]	Stewart D. Analysis of plant epidermis in faeces:a technique for studying the food preferences of grazing herbivores[J]. The Journal of Applied Ecology, 1967,4:83. doi: 10.2307/2401411 URL
[10]	Holechek J, Gross B, Dabo S, et al. Effects of sample preparation, growth stage, and observer on microhistological analysis of herbivore diets[J]. The Journal of Wildlife Management, 1982,46:502.
[11]	Norbury GL. Microscopic analysis of herbivore diets - a problem and a solution[J]. Australian Wildlife Research, 1988,15(1):51-57. doi: 10.1071/WR9880051 URL
[12]	Fox A, Francis IS, Bergersen E. Diet and habitat use of Svalbard pink-footed geese anser brachyrhynchus during arrival and pre-breeding periods in Adventdalen[J]. Ardea, 2006,94:691-699.
[13]	Marti C. Accuracy of fecal analysis for identifying foods of black grouse[J]. The Journal of Wildlife Management, 1982,46:773.
[14]	Gill R, Carpenter L, Bartmann R, et al. Fecal analysis to estimate mule deer diets[J]. Journal of Wildlife Management, 1983,487:902-915.
[15]	Barker RD. An investigation into the accuracy of herbivore diet analysis[J]. Wildlife Research, 1986,13:559-568. doi: 10.1071/WR9860559 URL
[16]	Dove H, Mayes R. Plant wax components:a new approach to estimating intake and diet composition in herbivores[J]. The Journal of Nutrition, 1996,126(1):13. doi: 10.1093/jn/126.1.13 URL pmid: 8558293
[17]	Dove H, Mayes R. Using n-alkanes and other plant wax components to estimate intake, digestibility and diet composition of grazing/browsing sheep and goats[J]. Small Ruminant Research, 2005,59(2):123-139. doi: 10.1016/j.smallrumres.2005.05.016 URL
[18]	Höss M, Kohn M, Pääbo S, et al. Excrement analysis by PCR[J]. Nature, 1992,359(6392):199. doi: 10.1038/359199a0 URL pmid: 1528260
[19]	Sidransky D, Tokino T, Hamilton, et al. Identification of ras oncogene mutations in the stool of patients with curable colorectal tumors[J]. Science, 1992,256(5053):102-105. doi: 10.1126/science.1566048 URL pmid: 1566048
[20]	Waraniak JM, Marsh TL, Scribner KT. 18S rRNA metabarcoding diet analysis of a predatory fish community across seasonal changes in prey availability[J]. Ecology and Evolution, 2019,9(3):1410-1430. doi: 10.1002/ece3.4857 URL pmid: 30805170
[21]	Tautz D, Arctander P, Minelli A, et al. DNA points the way ahead in taxonomy[J]. Nature, 2002,418(6897):479-479. doi: 10.1038/418479a URL pmid: 12152050
[22]	Hebert PD, Cywinska A, Ball SL, et al. Biological identifications through DNA barcodes[J]. Proceedings of the Royal Society of London. Series B:Biological Sciences, 2003,270(1512):313-321. URL pmid: 12614582
[23]	Iffat P, Singh HK, Saurabh R, et al. DNA barcoding of endangered Indian Paphiopedilum species[J]. Molecular Ecology Resources, 2011,12(1):82-90. doi: 10.1111/j.1755-0998.2011.03071.x URL pmid: 21951639
[24]	Pečnikar ŽF, Buzan EV, 20 years since the introduction of DNA barcoding:from theory to application[J]. Journal of Applied Genetics, 2014,55(1):43-52. doi: 10.1007/s13353-013-0180-y pmid: 24203863
[25]	裴男才. DNA条形码在进化生态学研究中的应用[J]. 生物多样性, 2015,23(3):291-292. doi: 10.17520/biods.2015063 URL
	Pei NC. Applications of DNA barcoding in evolutionary ecology[J]. Biodiversity Science, 2015,23(3):291-292.
[26]	吕冬梅, 黄原, 文慧, 等. DNA条形码技术在食品鉴定中的应用[J]. 食品科学, 2015(9):248-253. doi: 10.7506/spkx1002-6630-201509046 URL
	Lǚ DM, Huang Y, Wen H, et al. Application of DNA barcoding in authentication of food product[J]. Food Science, 2015(9):248-253.
[27]	刘杰昌, 王莹, 黎建至, 等. 利用rbcL-a序列模拟检测小鼠食性[J]. 生物学杂志, 2013,30(4):86-89.
	Liu JC, Wang Y, Li JZ, et al. Use of rbcL-a to simulate detecting guinca pig's diet[J]. Journal of Biology, 2013,30(4):86-89.
[28]	Robeson MS, Khanipov K, Golovko G, et al. Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig(Sus scrofa)[J]. Ecology and Evolution, 2018,8(1):185-196. doi: 10.1002/ece3.3638 URL pmid: 29321862
[29]	Coissac É, Riaz T, Puillandre N. Bioinformatic challenges for DNA metabarcoding of plants and animals[J]. Molecular Ecology, 2012,21(8):1834-1847. doi: 10.1111/j.1365-294X.2012.05550.x pmid: 22486822
[30]	Taberlet P, Coissac É, Pompanon F, et al. Towards next-generation biodiversity assessment using DNA metabarcoding[J]. Molecular Ecology, 2012,21(8):2045-2050. doi: 10.1111/j.1365-294X.2012.05470.x pmid: 22486824
[31]	Tillmar AO, Dell’Amico B, Welander J, et al. A universal method for species identification of mammals utilizing next generation sequencing for the analysis of DNA mixtures[J]. PLoS One, 2013,8(12):e83761. doi: 10.1371/journal.pone.0083761 URL pmid: 24358309
[32]	Nock CJ, Waters DLE, Edwards MA, et al. Chloroplast genome sequences from total DNA for plant identification[J]. Plant Biotechnology Journal, 2011,9(3):328. URL pmid: 20796245
[33]	Hajibabaei M, Smith MA, Janzen DH, et al. A minimalist barcode can identify a specimen whose DNA is degraded[J]. Molecular Ecology Notes, 2006,6(4):959-964. doi: 10.1111/men.2006.6.issue-4 URL
[34]	Meusnier I, Singer G, Landry JF, et al. A universal DNA mini-barcode for biodiversity analysis[J]. BMC Genomics, 2008,9(1):214. doi: 10.1186/1471-2164-9-214 URL
[35]	付涛, 王志龙, 钱萍仙, 等. 高等植物DNA条形码最新研究进展及其应用[J]. 核农学报, 2016,30(5):887-896.
	Fu T, Wang ZL, Qian PX, et al. The latest research progress and application of the DNA barcode in higher plants[J]. Journal of Nuclear Agricultural Science, 2016,30(5):887-896.
[36]	CBOL Plant Working Group. A DNA barcode for land plants[J]. PNAS, 2009,106(31):12794-12797. doi: 10.1073/pnas.0905845106 URL pmid: 19666622
[37]	Pennisi E. Wanted:A barcode for plants[J]. Science, 2007,318:190-191. doi: 10.1126/science.318.5848.190 URL pmid: 17932267
[38]	Fazekas AJ, Kesanakurti PR, Burgess KS, et al. Are plant species inherently harder to discriminate than animal species using DNA barcoding markers?[J]. Molecular Ecology Resources, 2009,9(s1):130-139. doi: 10.1111/men.2009.9.issue-s1 URL
[39]	Liu J, Yan HF, Newmaster SG, et al. The use of DNA barcoding as a tool for the conservation biogeography of subtropical forests in China[J]. Diversity and Distributions, 2015,21(2):188-199. doi: 10.1111/ddi.2014.21.issue-2 URL
[40]	Chen S, Yao H, Han J, et al. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species[J]. PLoS One, 2010,5(1):e8613. doi: 10.1371/journal.pone.0008613 URL pmid: 20062805
[41]	Hou D, Song J, Shi L, et al. Stability and accuracy assessment of identification of traditional Chinese materia medica using DNA barcoding:a case study on Flos Lonicerae Japonicae[J]. BioMed Research International, 2013(1):549037.
[42]	Li DZ, Gao LM, Li HT, et al. Comparative analysis of a large dataset indicates that internal transcribed spacer(ITS)should be incorporated into the core barcode for seed plants[J]. PNAS, 2011,108(49):19641. doi: 10.1073/pnas.1104551108 URL pmid: 22100737
[43]	Hollingsworth PM. Refining the DNA barcode for land plants[J]. PNAS, 2011,108(49):19451-19452. doi: 10.1073/pnas.1116812108 URL pmid: 22109553
[44]	Guo YP, Zhang H, Chen WQ, et al. Herbivore-diet analysis based on Illumina MiSeq sequencing:the potential use of an ITS2-barcoding approach to establish qualitative and quantitative predictions of diet composition of Mongolian sheep[J]. Journal of Agricultural and Food Chemistry, 2018,66(37):9858-9867. doi: 10.1021/acs.jafc.8b02814 URL pmid: 30198261
[45]	Li X, Yang Y, Henry RJ, et al. Plant DNA barcoding:from gene to genome[J]. Biological Reviews, 2015,90(1):157-166. doi: 10.1111/brv.12104 URL pmid: 24666563
[46]	Zhang W, Xie Y, Yang J, et al. Applications and prospects of metabarcoding in environmental monitoring of phytoplankton community[J]. Asian Journal of Ecotoxicology, 2017,12(1):15-24.
[47]	高连明, 刘杰, 蔡杰, 等. 关于植物DNA条形码研究技术规范[J]. 植物分类与资源学报, 2012,34(6):592-606. doi: 10.3724/SP.J.1143.2012.12138 URL
	Gao LM, Liu J, Cai J, et al. A synopsis of technical notes on the standards for plant DNA barcoding[J]. Plant Diversity and Resources, 2012,34(6):592-606.
[48]	李德铢, 曾春霞. 植物DNA条形码研究展望[J]. 生物多样性, 2015,23(3):297-298. doi: 10.17520/biods.2015135 URL
	Li DZ, Zeng CX. Prospects for plant DNA barcoding[J]. Biodiversity Science, 2015,23(3):297-298.
[49]	Banchi E, Ametrano CG, Greco S, et al. PLANiTS:a curated sequence reference dataset for plant ITS DNA metabarcoding[J]. Database, 2020,baz155.
[50]	Pompanon F, Coissac É, Taberlet P. Metabarcoding, a new way of analysing biodiversity[J]. Biofutur, 2011,319:30-32.
[51]	Willerslev E, Davison J, Moora M, et al. Fifty thousand years of arctic vegetation and megafaunal diet[J]. Nature, 2014,506(7486):47-51. doi: 10.1038/nature12921 URL pmid: 24499916
[52]	Pompanon F, Deagle BE, Symondson WO, et al. Who is eating what:diet assessment using next generation sequencing[J]. Molecular Ecology, 2012,21(8):1931-1950. doi: 10.1111/j.1365-294X.2011.05403.x URL
[53]	Valentini A, Miquel C, Nawaz MA, et al. New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing:the trnL approach[J]. Molecular Ecology Resources, 2009,9(1):51-60. doi: 10.1111/j.1755-0998.2008.02352.x pmid: 21564566
[54]	Soininen EM, Valentini A, Coissac E, et al. Analysing diet of small herbivores:the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures[J]. Frontiers in Zoology, 2009,6(1):16. doi: 10.1186/1742-9994-6-16 URL
[55]	Nichols RV, Åkesson M, Kjellander P. Diet assessment based on rumen contents:a comparison between DNA metabarcoding and macroscopy[J]. PLoS One, 2016,11(6):e0157977. doi: 10.1371/journal.pone.0157977 URL pmid: 27322387
[56]	杨预展. 长江中下流域草食性雁食性及肠道微生物研究[D]. 合肥:中国科学技术大学, 2016.
	Yang YZ. Diet analysis and gut microbiota of herbivorous Anseriformes in the middle and lower Yangtze river floodplain[D]. Hefei:University of Science and Technology of China, 2016.
[57]	Quéméré E, Hibert F, Miquel C, et al. A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range[J]. PLoS One, 2013,8(3):e58971. doi: 10.1371/journal.pone.0058971 URL pmid: 23527060
[58]	Kowalczyk R, Wójcik JM, Taberlet P, et al. Foraging plasticity allows a large herbivore to persist in a sheltering forest habitat:DNA metabarcoding diet analysis of the European bison[J]. Forest Ecology and Management, 2019,449:117474. doi: 10.1016/j.foreco.2019.117474 URL
[59]	Erickson DL, Reed E, Ramachandran P, et al. Reconstructing a herbivore’s diet using a novel rbcL DNA mini-barcode for plants[J]. AOB Plants, 2017,9(3):plx015. doi: 10.1093/aobpla/plx014 URL pmid: 28533897
[60]	Kim BJ, Lee NS, Lee SD. Feeding diets of the Korean water deer(Hydropotes inermis argyropus)based on a 202 bp rbcL sequence analysis[J]. Conservation Genetics, 2011,12(3):851-856. doi: 10.1007/s10592-011-0192-2 URL
[61]	Mallott EK, Garber PA, Malhi RS. trnL outperforms rbcL as a DNA metabarcoding marker when compared with the observed plant component of the diet of wild white-faced capuchins(Cebus capucinus, Primates)[J]. PLoS One, 2018,13(6):e0199556. doi: 10.1371/journal.pone.0199556 URL pmid: 29944686
[62]	Bhattacharyya S, Dawson DA, Hipperson H, et al. A diet rich in C3 plants reveals the sensitivity of an alpine mammal to climate change[J]. Molecular Ecology, 2019,28(2):250-265. doi: 10.1111/mec.14842 URL pmid: 30136323
[63]	Pinol J, Senar MA, Symondson WOC. The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative[J]. Molecular Ecology, 2019,28(2):407-419. doi: 10.1111/mec.14776 URL pmid: 29939447
[64]	Parducci L, Väliranta M, Salonen JS, et al. Proxy comparison in ancient peat sediments:pollen, macrofossil and plant DNA[J]. Philosophical Transactions of the Royal Society B Biological Sciences, 2015,370:20130382. doi: 10.1098/rstb.2013.0382 URL
[65]	Corse E, Meglécz E, Archambaud G, et al. A from-benchtop-to-desktop workflow for validating HTS data and for taxonomic identification in diet metabarcoding studies[J]. Molecular Ecology Resources, 2017,17(6):e146-e159. doi: 10.1111/1755-0998.12703 URL pmid: 28776936
[66]	Zhou X, Li Y, Liu S, et al. Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification[J]. GigaScience, 2013,2(1):4. doi: 10.1186/2047-217X-2-4 pmid: 23587339
[67]	张彩云, 黄珊珊, 颜海飞. DNA条形码技术在中药鉴定中的应用进展[J]. 中草药, 2017,48(11):2306-2312.
	Zhang CY, Huang SS, Yan HF. Applications of DNA barcoding in Chinese materia medica identification[J]. Chinese Traditional and Herbal Drugs, 2017,48(11):2306-2312.