Practical innovations for high-throughput amplicon sequencing

By Derek S. Lundberg, Scott M. Yourstone, P. Mieczkowski, Corbin D. Jones, Jeffery L. Dangl. Nature Methods, 2013

854 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/2aaab77934b1a249bd000dad4429ca99e1c59da1

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Citations in the corpus

Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data (2015, neutral): “In this case, other approaches should be developed, for instance, for the estimation of the richness of present taxa using accumulation curves (Lundberg et al. 2013).”
Assembly and ecological function of the root microbiome across angiosperm plant species (2018, methodology): “To reduce host contamination, we used peptide nucleic acids designed to block amplification of host plant plastid and mitochondrial sequences (62).”
Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species (2015, methodology): “There are > 200 species of Agave, and several of these have been cultivated for centuries for the production of alcohols and fiber (Garcia-Moya et al., 2011).”
Root microbiota drive direct integration of phosphate stress and immunity (2017, positive): “Libraries were created using a modified version of the Lundberg et al. 29 .”
The Cucurbita pepo seed microbiome: genotype-specific composition and implications for breeding (2016, methodology): “For PCR amplification, a modified protocol of Lundberg et al. (2013) including synthetic peptide nucleic acid PCR clamps (PNAs) for blocking the amplification of mitochondrial and plastid 16S rRNA gene sequences of plants was applied.”
Simplified and representative bacterial community of maize roots (2017, methodology): “Recently, some alternative techniques have been applied independently or together with NGS to reduce the processing time (26, 53), determine the absolute abundance of bacteria from a given phylum (2, 54), and eliminate the interference of host DNA and PCR bias (55), but it is still not easy to use o”
Conducting a Microbiome Study (2014, background): “In systems with large amounts of host contamination, such as plant endophytic microbiomes, approaches such as PCR clamps can help to reduce unwanted plant plastid contamination (Lundberg et al., 2013).”