메뉴 건너뛰기




Volumn 15, Issue 2, 2015, Pages 250-261

Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus)

Author keywords

Colobines; Environmental DNA; Faeces; Shotgun sequencing

Indexed keywords

MAGNOLIOPHYTA; PYGATHRIX NEMAEUS;

EID: 84922598627     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12302     Document Type: Article
Times cited : (112)

References (47)
  • 1
    • 84878850219 scopus 로고    scopus 로고
    • Diversity and distribution of Blastocystis sp. subtypes in non-human primates
    • Alfellani MA, Jacob AS, Perea NO et al. (2013) Diversity and distribution of Blastocystis sp. subtypes in non-human primates. Parasitology, 140, 966-971.
    • (2013) Parasitology , vol.140 , pp. 966-971
    • Alfellani, M.A.1    Jacob, A.S.2    Perea, N.O.3
  • 2
    • 79961109150 scopus 로고    scopus 로고
    • BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons
    • Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics, 12, 402.
    • (2011) BMC Genomics , vol.12 , pp. 402
    • Alikhan, N.F.1    Petty, N.K.2    Ben Zakour, N.L.3    Beatson, S.A.4
  • 4
    • 77956644833 scopus 로고    scopus 로고
    • Reproduction and infant pelage colouration of the banded leaf monkey (Mammalia: Primates: Cercopithecidae) in Singapore
    • Ang A, Ismail MRB, Meier R (2010) Reproduction and infant pelage colouration of the banded leaf monkey (Mammalia: Primates: Cercopithecidae) in Singapore. The Raffles Bulletin of Zoology, 58, 411-415.
    • (2010) The Raffles Bulletin of Zoology , vol.58 , pp. 411-415
    • Ang, A.1    Ismail, M.R.B.2    Meier, R.3
  • 7
    • 34249986709 scopus 로고    scopus 로고
    • Plant DNA sequences from feces: potential means for assessing diets of wild primates
    • Bradley BJ, Stiller M, Doran-Sheehy DM et al. (2007) Plant DNA sequences from feces: potential means for assessing diets of wild primates. American Journal of Primatology, 69, 699-705.
    • (2007) American Journal of Primatology , vol.69 , pp. 699-705
    • Bradley, B.J.1    Stiller, M.2    Doran-Sheehy, D.M.3
  • 8
    • 84866760894 scopus 로고    scopus 로고
    • OligoTag: a program for designing sets of tags for Next-Generation Sequencing of multiplexed samples
    • In (eds Pompanon F & Bonin A). Humana Press, New York.
    • Coissac E (2012) OligoTag: a program for designing sets of tags for Next-Generation Sequencing of multiplexed samples. In: Data Production and Analyses in Population Genomics (eds Pompanon F & Bonin A), pp. 13-31. Humana Press, New York.
    • (2012) Data Production and Analyses in Population Genomics , pp. 13-31
    • Coissac, E.1
  • 9
    • 84859574767 scopus 로고    scopus 로고
    • Bioinformatic challenges for DNA metabarcoding of plants and animals (2012)
    • Coissac E, Riaz T, Puillandre N (2012) Bioinformatic challenges for DNA metabarcoding of plants and animals (2012). Molecular Ecology, 21, 1834-1847.
    • (2012) Molecular Ecology , vol.21 , pp. 1834-1847
    • Coissac, E.1    Riaz, T.2    Puillandre, N.3
  • 10
    • 84894242220 scopus 로고    scopus 로고
    • DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet
    • De Barba M, Miquel C, Boyer F et al. (2014) DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet. Molecular Ecology Resources, 14, 306-323.
    • (2014) Molecular Ecology Resources , vol.14 , pp. 306-323
    • De Barba, M.1    Miquel, C.2    Boyer, F.3
  • 11
    • 38849163396 scopus 로고    scopus 로고
    • Studying seabird diet through genetic analysis of faeces: a case study on macaroni penguins (Eudyptes chrysolophus)
    • Deagle BE, Gales NJ, Evans K et al. (2007) Studying seabird diet through genetic analysis of faeces: a case study on macaroni penguins (Eudyptes chrysolophus). PLoS ONE, 2, e831.
    • (2007) PLoS ONE , vol.2 , pp. e831
    • Deagle, B.E.1    Gales, N.J.2    Evans, K.3
  • 12
    • 77956879874 scopus 로고    scopus 로고
    • Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out?
    • Deagle BE, Chiaradia A, McInnes J, Jarman SN (2010) Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out? Conservation Genetics, 11, 2039-2048.
    • (2010) Conservation Genetics , vol.11 , pp. 2039-2048
    • Deagle, B.E.1    Chiaradia, A.2    McInnes, J.3    Jarman, S.N.4
  • 13
    • 0030054023 scopus 로고    scopus 로고
    • Plant wax components: a new approach to estimating intake and diet composition in herbivores
    • Dove H, Mayes RW (1996) Plant wax components: a new approach to estimating intake and diet composition in herbivores. Journal of Nutrition, 126, 13-26.
    • (1996) Journal of Nutrition , vol.126 , pp. 13-26
    • Dove, H.1    Mayes, R.W.2
  • 15
    • 77954554269 scopus 로고    scopus 로고
    • An in silico approach for the evaluation of DNA barcodes
    • Ficetola GF, Coissac E, Zundel S et al. (2010) An in silico approach for the evaluation of DNA barcodes. BMC Genomics, 11, 434.
    • (2010) BMC Genomics , vol.11 , pp. 434
    • Ficetola, G.F.1    Coissac, E.2    Zundel, S.3
  • 17
    • 84875797249 scopus 로고    scopus 로고
    • Unveiling the diet of elusive rainforest herbivores in Next Generation Sequencing era? The Tapir as a case study
    • Hilbert F, Taberlet P, Chave J, Scotti-Saintagne C, Sabatier D, Richard-Hansen C (2013) Unveiling the diet of elusive rainforest herbivores in Next Generation Sequencing era? The Tapir as a case study. PLoS ONE, 8, e60799.
    • (2013) PLoS ONE , vol.8 , pp. e60799
    • Hilbert, F.1    Taberlet, P.2    Chave, J.3    Scotti-Saintagne, C.4    Sabatier, D.5    Richard-Hansen, C.6
  • 19
    • 37549050969 scopus 로고    scopus 로고
    • A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation
    • Hunt T, Bergsten J, Levkanicova Z et al. (2007) A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science, 318, 1913-1916.
    • (2007) Science , vol.318 , pp. 1913-1916
    • Hunt, T.1    Bergsten, J.2    Levkanicova, Z.3
  • 20
    • 1942517869 scopus 로고    scopus 로고
    • Group-specific polymerase chain reaction for DNA-based analysis of species diversity and identity in dietary samples
    • Jarman SN, Deagle BE, Gales NJ (2004) Group-specific polymerase chain reaction for DNA-based analysis of species diversity and identity in dietary samples. Molecular Ecology, 13, 1313-1322.
    • (2004) Molecular Ecology , vol.13 , pp. 1313-1322
    • Jarman, S.N.1    Deagle, B.E.2    Gales, N.J.3
  • 21
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Research, 12, 656-664.
    • (2002) Genome Research , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 23
    • 84869196690 scopus 로고    scopus 로고
    • An update on DNA barcoding: low species coverage and numerous unidentified sequences
    • Kwong S, Srivathsan A, Meier R (2012) An update on DNA barcoding: low species coverage and numerous unidentified sequences. Cladistics, 28, 639-644.
    • (2012) Cladistics , vol.28 , pp. 639-644
    • Kwong, S.1    Srivathsan, A.2    Meier, R.3
  • 24
    • 80053052840 scopus 로고    scopus 로고
    • Genetic characterization of Strongyloides spp. from captive, semi-captive and wild Bornean orangutans (Pongo pygmaeus) in Central and East Kalimantan, Borneo, Indonesia
    • Labes EM, Nurcahyo W, Deplazes P, Mathis A (2011) Genetic characterization of Strongyloides spp. from captive, semi-captive and wild Bornean orangutans (Pongo pygmaeus) in Central and East Kalimantan, Borneo, Indonesia. Parasitology, 138, 1417-1422.
    • (2011) Parasitology , vol.138 , pp. 1417-1422
    • Labes, E.M.1    Nurcahyo, W.2    Deplazes, P.3    Mathis, A.4
  • 25
    • 0032221248 scopus 로고    scopus 로고
    • Primate digestion: interactions among anatomy, physiology, and feeding ecology
    • Lambert JE (1998) Primate digestion: interactions among anatomy, physiology, and feeding ecology. Evolutionary Anthropology, 7, 8-20.
    • (1998) Evolutionary Anthropology , vol.7 , pp. 8-20
    • Lambert, J.E.1
  • 27
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler Transform
    • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25, 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 29
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
    • Luo R, Liu B, Xie Y et al. (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience, 1, 18.
    • (2012) Gigascience , vol.1 , pp. 18
    • Luo, R.1    Liu, B.2    Xie, Y.3
  • 30
    • 33749535839 scopus 로고    scopus 로고
    • DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success
    • Meier R, Shiyang K, Vaidya G, Ng PKL (2006) DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology, 55, 715-728.
    • (2006) Systematic Biology , vol.55 , pp. 715-728
    • Meier, R.1    Shiyang, K.2    Vaidya, G.3    Ng, P.K.L.4
  • 31
    • 80053605834 scopus 로고    scopus 로고
    • DNA-Based faecal dietary analysis: a comparison of qPCR and High Throughput Sequencing approaches
    • Murray DC, Bunce M, Cannell BL et al. (2011) DNA-Based faecal dietary analysis: a comparison of qPCR and High Throughput Sequencing approaches. PLoS ONE, 6, e25776.
    • (2011) PLoS ONE , vol.6 , pp. e25776
    • Murray, D.C.1    Bunce, M.2    Cannell, B.L.3
  • 32
    • 79952305603 scopus 로고    scopus 로고
    • Chloroplast genome sequences from total DNA for plant identification
    • Nock CJ, Waters DL, Edwards MA et al. (2011) Chloroplast genome sequences from total DNA for plant identification. Plant Biotechnology Journal, 9, 328-333.
    • (2011) Plant Biotechnology Journal , vol.9 , pp. 328-333
    • Nock, C.J.1    Waters, D.L.2    Edwards, M.A.3
  • 33
    • 0025230558 scopus 로고
    • DNA damage promotes jumping between templates during enzymatic amplification
    • Paabo S, Irwin DM, Wilson AC (1990) DNA damage promotes jumping between templates during enzymatic amplification. Journal of Biological Chemistry, 265, 4718-4721.
    • (1990) Journal of Biological Chemistry , vol.265 , pp. 4718-4721
    • Paabo, S.1    Irwin, D.M.2    Wilson, A.C.3
  • 34
    • 0025597229 scopus 로고
    • Sandeels in the diets of seals - application of novel and conventional methods of analysis to feces from seals in the Moray Firth area of Scotland
    • Pierce GJ, Boyle PR, Diack JSW, Clark I (1990) Sandeels in the diets of seals - application of novel and conventional methods of analysis to feces from seals in the Moray Firth area of Scotland. Journal of the Marine Biological Association of the United Kingdom, 70, 829-840.
    • (1990) Journal of the Marine Biological Association of the United Kingdom , vol.70 , pp. 829-840
    • Pierce, G.J.1    Boyle, P.R.2    Diack, J.S.W.3    Clark, I.4
  • 36
    • 84875104888 scopus 로고    scopus 로고
    • A DNA Metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range
    • Quéméré E, Hilbert F, Miquel C et al. (2013) A DNA Metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range. PLoS ONE, 8, e58971.
    • (2013) PLoS ONE , vol.8 , pp. e58971
    • Quéméré, E.1    Hilbert, F.2    Miquel, C.3
  • 37
    • 84863304598 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing, Vienna, Austria.
    • R Development Core Team (2011). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/.
    • (2011) R: A Language and Environment for Statistical Computing
  • 38
    • 79951860106 scopus 로고    scopus 로고
    • Detection distance and environmental factors in conservation detection dog surveys
    • Reed SE, Bidlack AL, Hurt A, Getz WM (2011) Detection distance and environmental factors in conservation detection dog surveys. The Journal of Wildlife Management, 75, 243-251.
    • (2011) The Journal of Wildlife Management , vol.75 , pp. 243-251
    • Reed, S.E.1    Bidlack, A.L.2    Hurt, A.3    Getz, W.M.4
  • 39
    • 84859617279 scopus 로고    scopus 로고
    • Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan
    • Shehzad W, Riaz T, Nawaz MA et al. (2012) Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan. Molecular Ecology, 21, 1951-1965.
    • (2012) Molecular Ecology , vol.21 , pp. 1951-1965
    • Shehzad, W.1    Riaz, T.2    Nawaz, M.A.3
  • 40
    • 79957988440 scopus 로고    scopus 로고
    • Increased sampling reveals novel lineages of Entamoeba: consequences of genetic diversity and host specificity for taxonomy and molecular detection
    • Stensvold CR, Lebbad M, Victory EL et al. (2011) Increased sampling reveals novel lineages of Entamoeba: consequences of genetic diversity and host specificity for taxonomy and molecular detection. Protist, 162, 525-541.
    • (2011) Protist , vol.162 , pp. 525-541
    • Stensvold, C.R.1    Lebbad, M.2    Victory, E.L.3
  • 41
    • 0036010821 scopus 로고    scopus 로고
    • Molecular identification of prey in predator diets
    • Symondson WO (2002) Molecular identification of prey in predator diets. Molecular Ecology, 11, 627-641.
    • (2002) Molecular Ecology , vol.11 , pp. 627-641
    • Symondson, W.O.1
  • 42
    • 33847371187 scopus 로고    scopus 로고
    • Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding
    • Taberlet P, Coissac E, Pompanon F et al. (2007) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research, 35, e14.
    • (2007) Nucleic Acids Research , vol.35 , pp. e14
    • Taberlet, P.1    Coissac, E.2    Pompanon, F.3
  • 44
    • 58949104467 scopus 로고    scopus 로고
    • New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach
    • Valentini A, Miquel C, Nawaz MA et al. (2009) New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach. Molecular Ecology Resources, 9, 51-60.
    • (2009) Molecular Ecology Resources , vol.9 , pp. 51-60
    • Valentini, A.1    Miquel, C.2    Nawaz, M.A.3
  • 46
    • 84870930021 scopus 로고    scopus 로고
    • Improving PCR detection of prey in molecular diet studies: importance of group-specific primer set selection and extraction protocol performances
    • Zarzoso-Lacoste D, Corse E, Vidal E (2013) Improving PCR detection of prey in molecular diet studies: importance of group-specific primer set selection and extraction protocol performances. Molecular Ecology Resources, 13, 117-127.
    • (2013) Molecular Ecology Resources , vol.13 , pp. 117-127
    • Zarzoso-Lacoste, D.1    Corse, E.2    Vidal, E.3
  • 47
    • 85006186573 scopus 로고    scopus 로고
    • Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification
    • Zhou X, Li Y, Liu S et al. (2013) Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. Gigascience, 2, 4.
    • (2013) Gigascience , vol.2 , pp. 4
    • Zhou, X.1    Li, Y.2    Liu, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.