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Volumn 14, Issue 5, 2014, Pages 1049-1059

Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities

Author keywords

454 pyrosequencing; Aquatic community; Cytochrome c oxidase subunit I (COI); Efficiency test; Mitochondrial 16S ribosomal RNA (mt16S); Small subunit ribosomal DNA (18S)

Indexed keywords

CRUSTACEA;

EID: 84905983626     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12254     Document Type: Article
Times cited : (94)

References (47)
  • 1
    • 28244438087 scopus 로고    scopus 로고
    • How many branchiopod crustacean species are there? Quantifying the components of underestimation
    • Adamowicz SJ, Purvis A (2005) How many branchiopod crustacean species are there? Quantifying the components of underestimation. Global Ecology and Biogeography, 14, 455-468.
    • (2005) Global Ecology and Biogeography , vol.14 , pp. 455-468
    • Adamowicz, S.J.1    Purvis, A.2
  • 2
    • 77954336858 scopus 로고    scopus 로고
    • ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases
    • Bellemain E, Carlsen T, Brochmann C et al. (2010) ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiology, 10, 189.
    • (2010) BMC Microbiology , vol.10 , pp. 189
    • Bellemain, E.1    Carlsen, T.2    Brochmann, C.3
  • 3
    • 33749386605 scopus 로고    scopus 로고
    • Development and evaluation of a DNA-barcoding approach for the rapid identification of nematodes
    • Bhadury P, Austen MC, Bilton DT et al. (2006) Development and evaluation of a DNA-barcoding approach for the rapid identification of nematodes. Marine Ecology Progress Series, 320, 1-9.
    • (2006) Marine Ecology Progress Series , vol.320 , pp. 1-9
    • Bhadury, P.1    Austen, M.C.2    Bilton, D.T.3
  • 4
    • 84858617141 scopus 로고    scopus 로고
    • Sequencing our way towards understanding global eukaryotic biodiversity
    • Bik HM, Porazinska DL, Creer S et al. (2012) Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology and Evolution, 27, 233-243.
    • (2012) Trends in Ecology and Evolution , vol.27 , pp. 233-243
    • Bik, H.M.1    Porazinska, D.L.2    Creer, S.3
  • 5
    • 79956059065 scopus 로고    scopus 로고
    • Use of DNA barcoding to detect invertebrate invasive species from diapausing eggs
    • Briski E, Cristescu ME, Bailey SA et al. (2011) Use of DNA barcoding to detect invertebrate invasive species from diapausing eggs. Biological Invasions, 13, 1325-1340.
    • (2011) Biological Invasions , vol.13 , pp. 1325-1340
    • Briski, E.1    Cristescu, M.E.2    Bailey, S.A.3
  • 6
    • 77954834182 scopus 로고    scopus 로고
    • Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing
    • Cheung MK, Au CH, Chu KH et al. (2010) Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing. The ISME Journal, 4, 1053-1059.
    • (2010) The ISME Journal , vol.4 , pp. 1053-1059
    • Cheung, M.K.1    Au, C.H.2    Chu, K.H.3
  • 8
    • 77951929876 scopus 로고    scopus 로고
    • Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises
    • Creer S, Fonseca VG, Porazinska DL et al. (2010) Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Molecular Ecology, 19, 4-20.
    • (2010) Molecular Ecology , vol.19 , pp. 4-20
    • Creer, S.1    Fonseca, V.G.2    Porazinska, D.L.3
  • 9
    • 80053275663 scopus 로고    scopus 로고
    • From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments
    • Darling JA, Mahon AR (2011) From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments. Environmental Research, 111, 978-988.
    • (2011) Environmental Research , vol.111 , pp. 978-988
    • Darling, J.A.1    Mahon, A.R.2
  • 10
    • 65449140394 scopus 로고    scopus 로고
    • Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces
    • Deagle BE, Kirkwood R, Jarman SN (2009) Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces. Molecular Ecology, 18, 2022-2038.
    • (2009) Molecular Ecology , vol.18 , pp. 2022-2038
    • Deagle, B.E.1    Kirkwood, R.2    Jarman, S.N.3
  • 11
    • 33746217392 scopus 로고    scopus 로고
    • Freshwater biodiversity: importance, threats, status and conservation challenges
    • Dudgeon D, Arthington AH, Gessner MO et al. (2006) Freshwater biodiversity: importance, threats, status and conservation challenges. Biological Reviews, 81, 163-182.
    • (2006) Biological Reviews , vol.81 , pp. 163-182
    • Dudgeon, D.1    Arthington, A.H.2    Gessner, M.O.3
  • 12
    • 79961181125 scopus 로고    scopus 로고
    • UCHIME improves sensitivity and speed of chimera detection
    • Edgar RC, Haas BJ, Clemente JC et al. (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27, 2194-2200.
    • (2011) Bioinformatics , vol.27 , pp. 2194-2200
    • Edgar, R.C.1    Haas, B.J.2    Clemente, J.C.3
  • 13
    • 50349087863 scopus 로고    scopus 로고
    • DNA barcodes for Cladocera and Copepoda from Mexico and Guatemala, highlights and new discoveries
    • Elías-Gutiérrez M, Martínez-Jerónimo F, Ivanova NV et al. (2008) DNA barcodes for Cladocera and Copepoda from Mexico and Guatemala, highlights and new discoveries. Zootaxa, 1849, 1-42.
    • (2008) Zootaxa , vol.1849 , pp. 1-42
    • Elías-Gutiérrez, M.1    Martínez-Jerónimo, F.2    Ivanova, N.V.3
  • 14
    • 77951498638 scopus 로고    scopus 로고
    • Experimental factors affecting PCR-based estimates of microbial species richness and evenness
    • Engelbrektson A, Kunin V, Wrighton K et al. (2010) Experimental factors affecting PCR-based estimates of microbial species richness and evenness. The ISME Journal, 4, 642-647.
    • (2010) The ISME Journal , vol.4 , pp. 642-647
    • Engelbrektson, A.1    Kunin, V.2    Wrighton, K.3
  • 15
    • 0028528103 scopus 로고
    • DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates
    • Folmer O, Black M, Hoeh W et al. (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294-299.
    • (1994) Molecular Marine Biology and Biotechnology , vol.3 , pp. 294-299
    • Folmer, O.1    Black, M.2    Hoeh, W.3
  • 16
    • 84880321899 scopus 로고    scopus 로고
    • Second-generation environmental sequencing unmasks marine metazoan biodiversity
    • Fonseca VG, Carvalho GR, Sung W et al. (2010) Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nature Communications, 1, 98.
    • (2010) Nature Communications , vol.1 , pp. 98
    • Fonseca, V.G.1    Carvalho, G.R.2    Sung, W.3
  • 17
    • 67949086798 scopus 로고    scopus 로고
    • Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing
    • Galand PE, Casamayor EO, Kirchman DL et al. (2009) Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing. The ISME Journal, 3, 860-869.
    • (2009) The ISME Journal , vol.3 , pp. 860-869
    • Galand, P.E.1    Casamayor, E.O.2    Kirchman, D.L.3
  • 18
    • 84881610261 scopus 로고    scopus 로고
    • Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys
    • Geller J, Meyer C, Parker M, Hawk H (2013) Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys. Molecular Ecology Resources, 13, 851-861.
    • (2013) Molecular Ecology Resources , vol.13 , pp. 851-861
    • Geller, J.1    Meyer, C.2    Parker, M.3    Hawk, H.4
  • 19
    • 0003816899 scopus 로고    scopus 로고
    • EcoSim: null models software for ecology
    • Version 7. Acquired Intelligence Inc. and Kesey-Bear. Jericho, VT05465
    • Gotelli NJ, Entsminger GL (2006) EcoSim: null models software for ecology. Version 7. Acquired Intelligence Inc. and Kesey-Bear. Jericho, VT05465. http://garyents-minger.com/ecosim.ht.
    • (2006)
    • Gotelli, N.J.1    Entsminger, G.L.2
  • 20
    • 79451471581 scopus 로고    scopus 로고
    • Extinction rates, extinction-prone habitats, and indicator groups in Britain and at larger scales
    • Hambler C, Henderson PA, Speight MR (2011) Extinction rates, extinction-prone habitats, and indicator groups in Britain and at larger scales. Biological Conservation, 144, 713-721.
    • (2011) Biological Conservation , vol.144 , pp. 713-721
    • Hambler, C.1    Henderson, P.A.2    Speight, M.R.3
  • 22
    • 84863413525 scopus 로고    scopus 로고
    • Conservation priorities for freshwater biodiversity: the key biodiversity area approach refined and tested for continental Africa
    • Holland RA, Darwall WRT, Smith KG (2012) Conservation priorities for freshwater biodiversity: the key biodiversity area approach refined and tested for continental Africa. Biological Conservation, 148, 167-179.
    • (2012) Biological Conservation , vol.148 , pp. 167-179
    • Holland, R.A.1    Darwall, W.R.T.2    Smith, K.G.3
  • 23
    • 65349091290 scopus 로고    scopus 로고
    • Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure
    • Huber JA, Morrison HG, Huse SM et al. (2009) Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. Environmental Microbiology, 11, 1292-1302.
    • (2009) Environmental Microbiology , vol.11 , pp. 1292-1302
    • Huber, J.A.1    Morrison, H.G.2    Huse, S.M.3
  • 24
    • 79956082889 scopus 로고    scopus 로고
    • Species diversity and phylogeographical affinities of the Branchiopoda (Crustacea) of Churchill, Manitoba, Canada
    • Jeffery NW, Eías-Gutiérrez M, Adamowicz SJ (2011) Species diversity and phylogeographical affinities of the Branchiopoda (Crustacea) of Churchill, Manitoba, Canada. PLoS ONE, 6, e18364.
    • (2011) PLoS ONE , vol.6
    • Jeffery, N.W.1    Eías-Gutiérrez, M.2    Adamowicz, S.J.3
  • 25
    • 79956216816 scopus 로고    scopus 로고
    • CLOTU: an online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation
    • Kumar S, Carlsen T, Mevik B et al. (2011) CLOTU: an online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation. BMC Bioinformatics, 12, 182.
    • (2011) BMC Bioinformatics , vol.12 , pp. 182
    • Kumar, S.1    Carlsen, T.2    Mevik, B.3
  • 26
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 27
    • 84861537650 scopus 로고    scopus 로고
    • Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA
    • Lodge DM, Turner CR, Jerde CL et al. (2012) Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA. Molecular Ecology, 21, 2555-2558.
    • (2012) Molecular Ecology , vol.21 , pp. 2555-2558
    • Lodge, D.M.1    Turner, C.R.2    Jerde, C.L.3
  • 28
    • 70349871220 scopus 로고    scopus 로고
    • Zooplankton diversity analysis through single-gene sequencing of a community sample
    • Machida RJ, Hashiguchi Y, Nishida M et al. (2009) Zooplankton diversity analysis through single-gene sequencing of a community sample. BMC Genomics, 10, 438.
    • (2009) BMC Genomics , vol.10 , pp. 438
    • Machida, R.J.1    Hashiguchi, Y.2    Nishida, M.3
  • 29
    • 84862133318 scopus 로고    scopus 로고
    • Fungicide-induced declines of freshwater biodiversity modify ecosystem functions and services
    • McMahon TA, Halstead NT, Johnson S et al. (2012) Fungicide-induced declines of freshwater biodiversity modify ecosystem functions and services. Ecology Letters, 15, 714-722.
    • (2012) Ecology Letters , vol.15 , pp. 714-722
    • McMahon, T.A.1    Halstead, N.T.2    Johnson, S.3
  • 30
    • 44449171351 scopus 로고    scopus 로고
    • A universal DNA mini-barcode for biodiversity analysis
    • Meusnier I, Singer GAC, Landry J et al. (2008) A universal DNA mini-barcode for biodiversity analysis. BMC Genomics, 9, 214.
    • (2008) BMC Genomics , vol.9 , pp. 214
    • Meusnier, I.1    Singer, G.A.C.2    Landry, J.3
  • 31
    • 67349093866 scopus 로고    scopus 로고
    • Identification of animal species using the partial sequences in the mitochondrial 16S rRNA gene
    • Mitani T, Akane A, Tokiyasu T et al. (2009) Identification of animal species using the partial sequences in the mitochondrial 16S rRNA gene. Legal Medicine, 11, S449-S450.
    • (2009) Legal Medicine , vol.11
    • Mitani, T.1    Akane, A.2    Tokiyasu, T.3
  • 32
    • 77956578390 scopus 로고    scopus 로고
    • Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome
    • Nossa CW, Oberdorf WE, Yang L et al. (2010) Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. World Journal of Gastroenterology, 16, 4135-4144.
    • (2010) World Journal of Gastroenterology , vol.16 , pp. 4135-4144
    • Nossa, C.W.1    Oberdorf, W.E.2    Yang, L.3
  • 33
    • 36148937913 scopus 로고    scopus 로고
    • A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing
    • Parameswaran P, Jalili R, Tao L et al. (2007) A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Research, 35, e130.
    • (2007) Nucleic Acids Research , vol.35
    • Parameswaran, P.1    Jalili, R.2    Tao, L.3
  • 35
    • 84865060813 scopus 로고    scopus 로고
    • PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets
    • Pinto AJ, Raskin L (2012) PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS ONE, 7, e43093.
    • (2012) PLoS ONE , vol.7
    • Pinto, A.J.1    Raskin, L.2
  • 36
    • 84883319585 scopus 로고    scopus 로고
    • Evaluating detection limits of next-generation sequencing for the surveillance and monitoring of international marine pests
    • Pochon X, Bott NJ, Smith KF, Wood SA (2013) Evaluating detection limits of next-generation sequencing for the surveillance and monitoring of international marine pests. PLoS ONE, 8, e73935.
    • (2013) PLoS ONE , vol.8
    • Pochon, X.1    Bott, N.J.2    Smith, K.F.3    Wood, S.A.4
  • 38
    • 65349171889 scopus 로고    scopus 로고
    • DNA barcoding of marine crustaceans from the Estuary and Gulf of St Lawrence: a regional-scale approach
    • Radulovici AE, Sainte-Marie B, Dufresn F (2009) DNA barcoding of marine crustaceans from the Estuary and Gulf of St Lawrence: a regional-scale approach. Molecular Ecology Resources, 9, 181-187.
    • (2009) Molecular Ecology Resources , vol.9 , pp. 181-187
    • Radulovici, A.E.1    Sainte-Marie, B.2    Dufresn, F.3
  • 39
    • 0032877922 scopus 로고    scopus 로고
    • Extinction rates of North American freshwater fauna
    • Ricciardi A, Rasmussen JB (1999) Extinction rates of North American freshwater fauna. Conservation Biology, 13, 1220-1222.
    • (1999) Conservation Biology , vol.13 , pp. 1220-1222
    • Ricciardi, A.1    Rasmussen, J.B.2
  • 40
    • 73449103883 scopus 로고    scopus 로고
    • Population structure of the Monocelis lineata (Proseriata, Monocelididae) species complex assessed by phylogenetic analysis of the mitochondrial Cytochrome c Oxidase subunit I (COI) gene
    • Sanna D, Lai T, Francalacci P et al. (2009) Population structure of the Monocelis lineata (Proseriata, Monocelididae) species complex assessed by phylogenetic analysis of the mitochondrial Cytochrome c Oxidase subunit I (COI) gene. Genetics and Molecular Biology, 32, 864-867.
    • (2009) Genetics and Molecular Biology , vol.32 , pp. 864-867
    • Sanna, D.1    Lai, T.2    Francalacci, P.3
  • 41
    • 72949107142 scopus 로고    scopus 로고
    • Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
    • Schloss PD, Westcott SL, Ryabin T et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75, 7537-7541.
    • (2009) Applied and Environmental Microbiology , vol.75 , pp. 7537-7541
    • Schloss, P.D.1    Westcott, S.L.2    Ryabin, T.3
  • 42
  • 43
    • 3042743588 scopus 로고    scopus 로고
    • Plankton of the Baltic estuarine ecosystems with emphasis on Neva Estuary: a review of present knowledge and research perspectives
    • Telesh IV (2004) Plankton of the Baltic estuarine ecosystems with emphasis on Neva Estuary: a review of present knowledge and research perspectives. Marine Pollution Bulletin, 49, 206-219.
    • (2004) Marine Pollution Bulletin , vol.49 , pp. 206-219
    • Telesh, I.V.1
  • 44
    • 84861563592 scopus 로고    scopus 로고
    • Monitoring endangered freshwater biodiversity using environmental DNA
    • Thomsen PF, Kielgast J, Iversen LL et al. (2012) Monitoring endangered freshwater biodiversity using environmental DNA. Molecular Ecology, 21, 2565-2573.
    • (2012) Molecular Ecology , vol.21 , pp. 2565-2573
    • Thomsen, P.F.1    Kielgast, J.2    Iversen, L.L.3
  • 46
    • 84888007223 scopus 로고    scopus 로고
    • Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED
    • Větrovský T, Baldrian P (2013) Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED. Biology and Fertility of Soils, 49, 1027-1037.
    • (2013) Biology and Fertility of Soils , vol.49 , pp. 1027-1037
    • Větrovský, T.1    Baldrian, P.2
  • 47
    • 84878914141 scopus 로고    scopus 로고
    • High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities
    • Zhan A, Hulák M, Sylvester F et al. (2013) High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities. Methods in Ecology and Evolution, 4, 558-565.
    • (2013) Methods in Ecology and Evolution , vol.4 , pp. 558-565
    • Zhan, A.1    Hulák, M.2    Sylvester, F.3


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