High-throughput sequencing of multiple amplicons for barcoding and integrative taxonomy.

PubWeight™: 0.77‹?›

🔗 View Article (PMID 28165046)

Published in Sci Rep on February 06, 2017

Authors

Perrine Cruaud1, Jean-Yves Rasplus1, Lillian Jennifer Rodriguez1,2, Astrid Cruaud1

Author Affiliations

1: INRA, UMR1062 CBGP, F-34988 Montferrier-sur-Lez, France.
2: Institute of Biology, University of the Philippines Diliman, Quezon City, Philippines.

Articles cited by this

Biological identifications through DNA barcodes. Proc Biol Sci (2003) 54.14

CAP3: A DNA sequence assembly program. Genome Res (1999) 50.04

DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol (1994) 49.81

MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol (2013) 34.34

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics (2014) 28.04

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol (1994) 24.04

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol (2016) 14.16

Quality control and preprocessing of metagenomic datasets. Bioinformatics (2011) 13.84

FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics (2011) 13.71

Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol (2013) 8.53

DNA barcoding: error rates based on comprehensive sampling. PLoS Biol (2005) 7.81

DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst Biol (2006) 5.79

Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol (1995) 4.88

Evaluating alternative hypotheses for the early evolution and diversification of ants. Proc Natl Acad Sci U S A (2006) 4.67

Assessment of the universality and utility of a set of conserved mitochondrial COI primers in insects. Insect Mol Biol (1997) 3.65

Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proc Natl Acad Sci U S A (2008) 3.56

DNA barcodes for 1/1000 of the animal kingdom. Biol Lett (2009) 3.46

TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics (2010) 3.38

A universal DNA mini-barcode for biodiversity analysis. BMC Genomics (2008) 3.16

Missing data, incomplete taxa, and phylogenetic accuracy. Syst Biol (2003) 2.82

Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Appl Environ Microbiol (2011) 2.52

Towards next-generation biodiversity assessment using DNA metabarcoding. Mol Ecol (2012) 2.43

An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome (2014) 2.27

The effect of geographical scale of sampling on DNA barcoding. Syst Biol (2012) 2.22

An extreme case of plant-insect codiversification: figs and fig-pollinating wasps. Syst Biol (2012) 2.20

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res (2015) 2.04

Comparative performances of DNA barcoding across insect orders. BMC Bioinformatics (2010) 1.86

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics. Am J Bot (2011) 1.82

Four years of DNA barcoding: current advances and prospects. Infect Genet Evol (2008) 1.82

DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae). Proc Biol Sci (2007) 1.76

The role of replicates for error mitigation in next-generation sequencing. Nat Rev Genet (2013) 1.66

Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proc Biol Sci (2010) 1.66

A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Front Zool (2013) 1.63

How to fail at species delimitation. Mol Ecol (2013) 1.60

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecol Lett (2013) 1.56

Profiling phylogenetic informativeness. Syst Biol (2007) 1.56

Wolbachia and DNA barcoding insects: patterns, potential, and problems. PLoS One (2012) 1.46

Quantitative evolutionary dynamics using high-resolution lineage tracking. Nature (2015) 1.41

Elongation factor-1 alpha occurs as two copies in bees: implications for phylogenetic analysis of EF-1 alpha sequences in insects. Mol Biol Evol (1998) 1.40

The cytochrome b region in the mitochondrial DNA of the ant Tetraponera rufoniger: sequence divergence in Hymenoptera may be associated with nucleotide content. J Mol Evol (1994) 1.29

Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens. Mol Ecol Resour (2014) 1.25

Molecular detection of trophic links in a complex insect host-parasitoid food web. Mol Ecol Resour (2011) 1.21

Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Mol Ecol (2012) 1.19

From barcodes to genomes: extending the concept of DNA barcoding. Mol Ecol (2016) 1.00

Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ (2015) 0.96

Mitochondrial heteroplasmy and DNA barcoding in Hawaiian Hylaeus (Nesoprosopis) bees (Hymenoptera: Colletidae). BMC Evol Biol (2010) 0.94

Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Sci Rep (2015) 0.93

Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing. PLoS One (2015) 0.92

A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes. Front Microbiol (2015) 0.87

Obligate mutualism within a host drives the extreme specialization of a fig wasp genome. Genome Biol (2013) 0.87

The occurrence of mtDNA heteroplasmy in multiple cetacean species. Curr Genet (2011) 0.84

Discrimination of grasshopper (Orthoptera: Acrididae) diet and niche overlap using next-generation sequencing of gut contents. Ecol Evol (2015) 0.81

A new method to prevent carry-over contaminations in two-step PCR NGS library preparations. Nucleic Acids Res (2015) 0.80

Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics. Genome Biol Evol (2015) 0.80

Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers. PLoS One (2016) 0.80

Articles by these authors

RADIS: analysis of RAD-seq data for interspecific phylogeny. Bioinformatics (2016) 0.75

Testing cospeciation through large-scale cophylogenetic studies. Curr Opin Insect Sci (2016) 0.75