Next‐generation sequencing technologies for environmental DNA research

By S. Shokralla, Jennifer L. Spall, J. Gibson, Mehrdad Hajibabaei. Molecular Ecology, 2012

855 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/f05bd3755dcb8bab8724221753b8fc9a37c683c9

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Citations in the corpus

Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide (2013, background): “For comprehensive reviews of current and future sequencing technologies, see Glenn (2011) and Shokralla et al. (2012).”
Environmental DNA (2012, background): “Additionally, Shokralla et al. (2012) provide an overview of different modifications and additional tools such as oligonucleotide tags (for combining several environmental samples in one sequence run) or capture arrays (to circumvent amplification biases).”
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples (2018, neutral): “Illumina Illumina sequencers were first introduced to the market in 2007 (Shokralla et al. 2012).”
Molecular genetic tools for environmental monitoring of New Zealand's aquatic habitats, past, present and the future (2013, background): “Despite some significant technical challenges associated with these techniques (Shokralla et al. 2012),NGS technologies provide unprecedented opportunities for the development of innovative diagnostic tools able to detect multiple species from a variety of life stages in environmental samples, and…”
Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing (2014, background): “In recent years, the development of next-generation sequencing (NGS) technologies has permitted in-depth sequencing and data analyses of various types of environmental samples [11–15] at a deeper level than possible with standard molecular biological techniques [16].”
The ecology of environmental DNA and implications for conservation genetics (2016, background): “DNA amplification or hybridization can enrich for a target clade prior to sequencing, or direct shotgun sequencing can be used to generate sequence data from all organisms (Shokralla et al. 2012).”
Deciphering microbial interactions and detecting keystone species with co-occurrence networks (2014, background): “These technologies power ever broader and deeper surveys using targeted marker genes such as the 16S rRNA gene as well as shotgun metagenomics and metatranscriptomics (Caporaso et al., 2011; Shokralla et al., 2012).”
FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild (2016, background): “These three datasets were chosen for two primary reasons: (1) to represent a diversity of environments in which researchers may apply the script; and (2) to show that the script is largely independent of upstream issues with sequencing technologies (Shokralla et al., 2012), OTU picking (Lekberg et a”
Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity (2015, background): “…of PCR products and many still do, there is no doubt that the new emerging sequencing technologies will have profound impact on eDNA studies (Shokralla et al., 2012), and become a fully integrated part of ecologists’ toolbox (Baird and Hajibabaei, 2012; Taberlet et al., 2012b; Valentini et…”
Culture-independent molecular tools for soil and rhizosphere microbiology (2013, background): “This system can generate billions of reads per run that range from 25 to 35 bp [154], and the data output is over one Gb per day Heliscope might contribute to genome biology through direct sequencing of nucleic acids.”
Assembling metagenomes, one community at a time (2017, background): “Over the last decade, high throughput sequencing has revolutionised the field of microbial ecology [44].”
Effects of rising CO₂ on the harmful cyanobacterium Microcystis (2016, background): “Alternatively, amplicon sequencing can be used to quantify different cyanobacterial strains (Shokralla et al. , 2012; Poretsky et al. , 2014).”
Applications of next-generation sequencing to the study of biological invasions (2015, background): “NGS has revolutionized DNA barcoding (Shokralla et al., 2012; Shokralla et al., 2014) by decreasing the cost of sequencing, but more importantly has removed the expensive and time-consuming need to clone amplified eDNA into bacteria before sequencing hundreds of thousands of clones (Valentini et…”
Metabarcoding of marine zooplankton: prospects, progress and pitfalls (2016, background): “HTS technologies provide the ability to read millions of DNA sequences in parallel, making them ideally suited for large-scale biodiversity analyses of samples (Shokralla et al., 2012).”
p-Coumaric can alter the composition of cucumber rhizosphere microbial communities and induce negative plant-microbial interactions (2018, methodology): “In this study, we first analyzed the specific rhizosphere microbial taxa in response to p-coumaric acid with high-throughput amplicon sequencing, which can provide a higher taxonomical resolution than PCR-based fingerprinting techniques (Shokralla et al. 2012; Schöler et al. 2017).”
Microbial communities in anammox reactors: a review (2017, methodology): “NGS has allowed the recovery of thousands of reads from complex environmental samples and within a short period of time, and has generated a large amount of data that may be used to evaluate the biodiversity of specific environments and to understand increasingly complex phenotypes [12,13].”