Comparing whole‐genome shotgun sequencing and DNA metabarcoding approaches for species identification and quantification of pollen species mixtures

Metagenomics: A viable tool for reconstructing herbivore diet

(2021) Physilia Y.S. Chua et al.   Molecular Ecology Resources

Relative species abundance estimation in artificial mixtures of insects using mito‐metagenomics and a correction factor for the mitochondrial DNA copy number

(2021) Lidia Garrido‐Sanz et al.   Molecular Ecology Resources

Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes

(2020) Robert A. Petit et al.   mSystems

A Chromosome-Scale Genome Assembly of Paper Mulberry (Broussonetia papyrifera) Provides New Insights into Its Forage and Papermaking Usage

(2019) Xianjun Peng et al.   Molecular Plant

Biosynthesis and Signal Transduction of ABA, JA, and BRs in Response to Drought Stress of Kentucky Bluegrass

(2019) Yajun Chen et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Human contamination in bacterial genomes has created thousands of spurious proteins

(2019) Florian P. Breitwieser et al.   GENOME RESEARCH

The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition

(2019) Youjun Huang et al.   GigaScience

Temperate airborne grass pollen defined by spatio-temporal shifts in community composition

(2019) Georgina L. Brennan et al.   Nature Ecology & Evolution

SPIKEPIPE : A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes

(2019) Yinqiu Ji et al.   Molecular Ecology Resources

Genome‐skimming provides accurate quantification for pollen mixtures

(2019) Dandan Lang et al.   Molecular Ecology Resources

Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden

(2019) Laura Parducci et al.   Frontiers in Ecology and Evolution

The Draft Genome of Kochia scoparia and the Mechanism of Glyphosate Resistance via Transposon-Mediated EPSPS Tandem Gene Duplication

(2019) Eric L Patterson et al.   Genome Biology and Evolution

Semi‐quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet)

(2019) Ned Peel et al.   Methods in Ecology and Evolution

Study of spontaneous mutations in the transmission of poplar chloroplast genomes from mother to offspring

(2018) Sheng Zhu et al.   BMC GENOMICS

Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples

(2018) Iliana Bista et al.   Molecular Ecology Resources

Minimizing polymerase biases in metabarcoding

(2018) Ruth V. Nichols et al.   Molecular Ecology Resources

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

Earth BioGenome Project: Sequencing life for the future of life

(2018) Harris A. Lewin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant-pollinator interactions over time: Pollen metabarcoding from bees in a historic collection

(2018) Annemarie Gous et al.   Evolutionary Applications

Quantitative and qualitative assessment of pollen DNA metabarcoding using constructed species mixtures

(2018) Karen L. Bell et al.   MOLECULAR ECOLOGY

How quantitative is metabarcoding: A meta‐analytical approach

(2018) Philip D. Lamb et al.   MOLECULAR ECOLOGY

Shotgun metagenomics of honey DNA: Evaluation of a methodological approach to describe a multi-kingdom honey bee derived environmental DNA signature

(2018) Samuele Bovo et al.   PLoS One

Multiple introductions, admixture and bridgehead invasion characterize the introduction history of Ambrosia artemisiifolia in Europe and Australia

(2017) Lotte A. van Boheemen et al.   MOLECULAR ECOLOGY

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Mixed-Ploidy Species: Progress and Opportunities in Polyploid Research

(2017) Filip Kolář et al.   TRENDS IN PLANT SCIENCE

AnrbcLReference Library to Aid in the Identification of Plant Species Mixtures by DNA Metabarcoding

(2017) Karen L. Bell et al.   Applications in Plant Sciences

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

(2016) Ravi Ranjan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Pollen DNA barcoding: current applications and future prospects

(2016) Karen L. Bell et al.   GENOME

Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples

(2015) Marta Pawluczyk et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

How Many Plant Species are There, Where are They, and at What Rate are They Going Extinct?

(2015) Stuart L. Pimm et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

(2015) Carmelo Andújar et al.   MOLECULAR ECOLOGY

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Insights into Transcriptomes of Big and Low Sagebrush

(2015) Mark D. Huynh et al.   PLoS One

Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages

(2015) Carola Gómez-Rodríguez et al.   Methods in Ecology and Evolution

High-throughput monitoring of wild bee diversity and abundance via mitogenomics

(2015) Min Tang et al.   Methods in Ecology and Evolution

Rank-Based Characterization of Pollen Assemblages Collected by Honey Bees Using a Multi-Locus Metabarcoding Approach

(2015) Rodney T. Richardson et al.   Applications in Plant Sciences

Application of ITS2 Metabarcoding to Determine the Provenance of Pollen Collected by Honey Bees in an Agroecosystem

(2015) Rodney T. Richardson et al.   Applications in Plant Sciences

Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach

(2015) Wiebke Sickel et al.   BMC ECOLOGY

Using DNA Metabarcoding to Identify the Floral Composition of Honey: A New Tool for Investigating Honey Bee Foraging Preferences

(2015) Jennifer Hawkins et al.   PLoS One

Efficient and sensitive identification and quantification of airborne pollen using next-generation DNA sequencing

(2014) Ken Kraaijeveld et al.   Molecular Ecology Resources

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

(2014) Amrita Srivathsan et al.   Molecular Ecology Resources

Multiplex sequencing of pooled mitochondrial genomes—a crucial step toward biodiversity analysis using mito-metagenomics

(2014) Min Tang et al.   NUCLEIC ACIDS RESEARCH

Evaluating multiplexed next-generation sequencing as a method in palynology for mixed pollen samples

(2014) A. Keller et al.   PLANT BIOLOGY

From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity

(2014) Melania E. Cristescu   TRENDS IN ECOLOGY & EVOLUTION

An introduction to the analysis of shotgun metagenomic data

(2014) Thomas J. Sharpton   Frontiers in Plant Science

New reports of nuclear DNA content for 407 vascular plant taxa from the United States

(2012) Chengke Bai et al.   ANNALS OF BOTANY

Pollen morphology of Campanula (Campanulaceae) and allied genera in Iran with special focus on its systematic implication

(2012) Elmira Khansari et al.   FLORA

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

Who is eating what: diet assessment using next generation sequencing

(2011) FRANCOIS POMPANON et al.   MOLECULAR ECOLOGY

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species

(2010) Shilin Chen et al.   PLoS One

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

(2010) Jenna L. Morgan et al.   PLoS One

Soft Fruit Traceability in Food Matrices using Real-Time PCR

(2009) Luisa Palmieri et al.   Nutrients

Pollen morphology of Stachys (Lamiaceae) in Iran and its systematic implication

(2008) Yasaman Salmaki et al.   FLORA