Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias

作者: Laurence J. Clarke , Julien Soubrier , Laura S. Weyrich , Alan Cooper

DOI: 10.1111/1755-0998.12265

关键词: Pcr biasComputational biologyEcologyBiologyIn silico PCRCytochrome oxidase cEnvironmental DNAAmplicon sequencingIn silicoPrimer (molecular biology)

摘要: Studies of insect assemblages are suited to the simultaneous DNA‐based identification of multiple taxa known as metabarcoding. To obtain accurate estimates of diversity …

参考文章(43)
R. H. GLOVER, D. W. COLLINS, K. WALSH, N. BOONHAM, Assessment of loci for DNA barcoding in the genus Thrips (Thysanoptera:Thripidae). Molecular Ecology Resources. ,vol. 10, pp. 51- 59 ,(2010) , 10.1111/J.1755-0998.2009.02723.X
MATT R. K. ZEALE, ROGER K. BUTLIN, GARY L. A. BARKER, DAVID C. LEES, GARETH JONES, Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces Molecular Ecology Resources. ,vol. 11, pp. 236- 244 ,(2011) , 10.1111/J.1755-0998.2010.02920.X
Douglas W. Yu, Yinqiu Ji, Brent C. Emerson, Xiaoyang Wang, Chengxi Ye, Chunyan Yang, Zhaoli Ding, Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring Methods in Ecology and Evolution. ,vol. 3, pp. 613- 623 ,(2012) , 10.1111/J.2041-210X.2012.00198.X
NATALIA V. IVANOVA, JEREMY R. DEWAARD, PAUL D. N. HEBERT, An inexpensive, automation-friendly protocol for recovering high-quality DNA Molecular Ecology Notes. ,vol. 6, pp. 998- 1002 ,(2006) , 10.1111/J.1471-8286.2006.01428.X
Rita Sipos, Anna J. Székely, Márton Palatinszky, Sára Révész, Károly Márialigeti, Marcell Nikolausz, Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene‐targetting bacterial community analysis FEMS Microbiology Ecology. ,vol. 60, pp. 341- 350 ,(2007) , 10.1111/J.1574-6941.2007.00283.X
J. H. SØNSTEBØ, L. GIELLY, A. K. BRYSTING, R. ELVEN, M. EDWARDS, J. HAILE, E. WILLERSLEV, E. COISSAC, D. RIOUX, J. SANNIER, P. TABERLET, C. BROCHMANN, Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate. Molecular Ecology Resources. ,vol. 10, pp. 1009- 1018 ,(2010) , 10.1111/J.1755-0998.2010.02855.X
STEPHANE A. P. DEROCLES, MANUEL PLANTEGENEST, JEAN‐CHRISTOPHE SIMON, PIERRE TABERLET, ANNE LE RALEC, A universal method for the detection and identification of Aphidiinae parasitoids within their aphid hosts. Molecular Ecology Resources. ,vol. 12, pp. 634- 645 ,(2012) , 10.1111/J.1755-0998.2012.03131.X
Laurence J. Clarke, Paul Czechowski, Julien Soubrier, Mark I. Stevens, Alan Cooper, Modular tagging of amplicons using a single PCR for high-throughput sequencing. Molecular Ecology Resources. ,vol. 14, pp. 117- 121 ,(2014) , 10.1111/1755-0998.12162
E. Willerslev, E. Cappellini, W. Boomsma, R. Nielsen, M. B. Hebsgaard, T. B. Brand, M. Hofreiter, M. Bunce, H. N. Poinar, D. Dahl-Jensen, S. Johnsen, J. P. Steffensen, O. Bennike, J.-L. Schwenninger, R. Nathan, S. Armitage, C.-J. de Hoog, V. Alfimov, M. Christl, J. Beer, R. Muscheler, J. Barker, M. Sharp, K. E. H. Penkman, J. Haile, P. Taberlet, M. T. P. Gilbert, A. Casoli, E. Campani, M. J. Collins, Ancient Biomolecules from Deep Ice Cores Reveal a Forested Southern Greenland Science. ,vol. 317, pp. 111- 114 ,(2007) , 10.1126/SCIENCE.1141758
Margaret M. DeAngelis, David G. Wang, Trevor L. Hawkins, Solid-phase reversible immobilization for the isolation of PCR products Nucleic Acids Research. ,vol. 23, pp. 4742- 4743 ,(1995) , 10.1093/NAR/23.22.4742