Abstract
Comparative studies of next-generation sequencing (NGS) and clone sequencing in diet analysis have not been conducted. This study compares the performance of NGS and clone sequencing to analyze the diet of Asian great bustard (Otis tarda dybowskii). Identification of known taxa using NGS method was significantly greater than by clone method (t = 8.12, df = 14, p < 0.01), which has highlighted the higher sensitivity of the NGS approach. The proportion of occurrence for NGS method and clone method was significantly correlated (r = 0.63, p = 0.01), suggesting the prey taxa present at low frequency could not be identified by clone method. The cost and time of NGS method was also low compared with the clone method. We recommend the NGS opens up for new possibilities in the diet study, and has wide applicability to other species whose faeces can be collected easily and non-invasively in the field.
This is a preview of subscription content, log in via an institution to check access.
References
Alonso JC (2010) The world status and population trends of the Great Bustard (Otis tarda): 2010 update. Chin Bird (Engl Vers) 1:141–147
Barba MD, Miquel C, Boyer F, Mercier C, Rioux D, Coissac E, Taberlet P (2014) DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet. Mol Ecol Resour 14:306–323
Boyer S, Wratten SD, Holyoake A, Abdelkrim J, Cruickshank RH (2013) Using next-generation sequencing to analyse the diet of a highly endangered land snail (Powelliphanta augusta) feeding on endemic earthworms. PLoS ONE 8:e75962
Boyer F, Mercier C, Bonin A, Le BY, Taberlet P, Coissac E (2016) OBITools: a Unix-inspired software package for DNA metabarcoding. Mol Ecol Resour 16:176–182
Braley M, Goldsworthy SD, Page B, Steer M, Austin JJ (2010) Assessing morphological and DNA-based diet analysis techniques in a generalist predator, the arrow squid Nototodarus gouldi. Mol Ecol Resour 10:466–474
Coissac E (2012) OligoTag: a program for designing sets of tags for next-generation sequencing of multiplexed samples. Methods Mol Biol 888:13–31
Deagle B, Tollit D, Hindell Sn M, Trites A, Gales N (2005) Molecular scatology as a tool to study diet: analysis of prey DNA in scats from captive Steller sea lions. Mol Ecol 14:1831–1842
Deagle BE, Gales NJ, Evans K, Jarman SN, Robinson S, Trebilco R, Hindell MA (2007) Studying seabird diet through genetic analysis of faeces: a case study on macaroni penguins (Eudyptes chrysolophus). PLoS ONE 2:e831
Deagle BE, Thomas AC, Shaffer AK, Trites AW, Jarman SN (2013) Quantifying sequence proportions in a DNA-based diet study using ion torrent amplicon sequencing: which counts count? Mol Ecol Resour 13:620–633
Emami-Khoyi A et al (2016) Identifying prey items from New Zealand fur seal (Arctocephalus forsteri) faeces using massive parallel sequencing. Conserv Genet Resour 8:1–10
Jiang JS (2004) The status of resources and conservation of Great Bustard in China. Dissertation, Northeast Forestry University
Kessler A (2015) Asian Great Bustards: from conservation biology to sustainable grassland development. Dissertations and Theses, Arizona State University
Lobo (2008) Basic local alignment search tool (BLAST). J Mol Biol 215:403–410
Lopes CM et al (2015) DNA metabarcoding diet analysis for species with parapatric vs sympatric distribution: a case study on subterranean rodents. Heredity 114:525–534
Marucco F, Pletscher DH, Boitani L (2008) Accuracy of scat sampling for carnivore diet analysis: wolves in the Alps as a case study. J Mammal 89:665–673
Oehm J, Juen A, Nagiller K, Neuhauser S, Traugott M (2011) Molecular scatology: how to improve prey DNA detection success in avian faeces? Mol Ecol Resour 11:620–628
Pompanon F, Deagle BE, Symondson WO, Brown DS, Jarman SN, Taberlet P (2012) Who is eating what: diet assessment using next generation sequencing. Mol Ecol 21:1931–1950
Shores C, Mondol S, Wasser SK (2015) Comparison of DNA and hair-based approaches to dietary analysis of free-ranging wolves (Canis lupus). Conserv Genet Resour 7:1–8
Taberlet P et al (2007) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucl Acids Res 35:e14
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
Valentini A et al (2009) New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach. Mol Ecol Resour 9:51–60
Zeale MRK, Butlin RK, Barker GLA, Lees DC, Jones G (2011) Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces. Mol Ecol Resour 11:236–244
Zhao J, Wan DM, Wang HT, Gao W (2007) The study on the population ecology of Great bustard(Otis tarda dybowskii) during its breeding season in Tumuji area of Inner Mongolia. J Northeast Norm Univ 39:103–105
Acknowledgements
This work was financed by the Fundamental Research Funds of CAF (Grant No. CAFINT2015K05), and the National Natural Science Foundation (No. 31500303).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Gong, M., Ning, Y., Han, M. et al. A comparison of next-generation sequencing with clone sequencing in the diet analysis of Asian great bustard. Conservation Genet Resour 11, 15–17 (2019). https://doi.org/10.1007/s12686-017-0952-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12686-017-0952-5