High‐throughput sequencing of 5S‐IGS in oaks: Exploring intragenomic variation and algorithms to recognize target species in pure and mixed samples

5S Ribosomal DNA of Distantly Related Quercus Species: Molecular Organization and Taxonomic Application

(2020) Y. O. Tynkevich et al.   Cytology and Genetics

ddRAD Sequencing-Based Identification of Genomic Boundaries and Permeability in Quercus ilex and Q. suber Hybrids

(2020) Unai López de Heredia et al.   Frontiers in Plant Science

Uncovering the genomic signature of ancient introgression between white oak lineages ( Quercus )

(2019) Andrew A. Crowl et al.   NEW PHYTOLOGIST

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Integrative rDNAomics—Importance of the Oldest Repetitive Fraction of the Eukaryote Genome

(2019) Symonová   Genes

East Asian origins of European holly oaks ( Quercus section Ilex Loudon) via the Tibet‐Himalaya

(2019) Xiao‐Long Jiang et al.   JOURNAL OF BIOGEOGRAPHY

Testing and using complete plastomes and ribosomal DNA sequences as the next generation DNA barcodes in Panax (Araliaceae)

(2019) Yunheng Ji et al.   Molecular Ecology Resources

Genomic Identity of White Oak Species in an Eastern North American Syngameon

(2019) Andrew L. Hipp et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

The oak syngameon: more than the sum of its parts

(2019) Charles H. Cannon et al.   NEW PHYTOLOGIST

Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers

(2019) Thibault Leroy et al.   NEW PHYTOLOGIST

Ancient events and climate adaptive capacity shaped distinct chloroplast genetic structure in the oak lineages

(2019) Mengxiao Yan et al.   BMC EVOLUTIONARY BIOLOGY

Genomic landscape of the global oak phylogeny

(2019) Andrew L. Hipp et al.   NEW PHYTOLOGIST

Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies

(2019) Ryan P. Kelly et al.   Scientific Reports

Oaks: an evolutionary success story

(2019) Antoine Kremer et al.   NEW PHYTOLOGIST

Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis

(2018) Teresita M. Porter et al.   MOLECULAR ECOLOGY

A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

(2018) Elisabeth Fitzek et al.   Ecology and Evolution

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

Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation

(2018) Marco Cosimo Simeone et al.   PeerJ

A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny

(2017) Kasey K. Pham et al.   GENOME

Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in western North America

(2017) John D. McVay et al.   GENOME

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

Extensive recent secondary contacts between four European white oak species

(2017) Thibault Leroy et al.   NEW PHYTOLOGIST

Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity

(2017) Andrew L. Hipp et al.   NEW PHYTOLOGIST

A genetic legacy of introgression confounds phylogeny and biogeography in oaks

(2017) John D. McVay et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Sequencing of whole plastid genomes and nuclear ribosomal DNA ofDiospyrosspecies (Ebenaceae) endemic to New Caledonia: many species, little divergence

(2016) Barbara Turner et al.   ANNALS OF BOTANY

Diverse evolutionary pathways shaped 5S rDNA of species of tribe Anemoneae (Ranunculaceae) and reveal phylogenetic signal

(2016) Jelena Mlinarec et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Phylogeographic structuring of plastome diversity in Mediterranean oaks (Quercus Group Ilex, Fagaceae)

(2016) Martina Vitelli et al.   Tree Genetics & Genomes

Plastome data reveal multiple geographic origins ofQuercusGroup Ilex

(2016) Marco Cosimo Simeone et al.   PeerJ

Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb

(2015) Wencai Wang et al.   CHROMOSOMA

Next-generation sequencing reveals differentially amplified tandem repeats as a major genome component of Northern Europe’s oldest Camellia japonica

(2015) Tony Heitkam et al.   CHROMOSOME RESEARCH

Historical introgression among the American live oaks and the comparative nature of tests for introgression

(2015) Deren A. R. Eaton et al.   EVOLUTION

Phylogeny and biogeography of the American live oaks (QuercussubsectionVirentes): a genomic and population genetics approach

(2015) Jeannine Cavender-Bares et al.   MOLECULAR ECOLOGY

Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks

(2015) C. Lepoittevin et al.   Molecular Ecology Resources

Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA inAsclepias(Apocynaceae)

(2015) Kevin Weitemier et al.   PeerJ

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

A metagenetic approach for revealing community structure of marine planktonic copepods

(2014) J. Hirai et al.   Molecular Ecology Resources

Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family

(2014) Pierre-Jean G. Malé et al.   Molecular Ecology Resources

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

(2014) A. Keller et al.   PLANT BIOLOGY

Multiple nuclear genes stabilize the phylogenetic backbone of the genusQuercus

(2014) François Hubert et al.   SYSTEMATICS AND BIODIVERSITY

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Dancing together and separate again: gymnosperms exhibit frequent changes of fundamental 5S and 35S rRNA gene (rDNA) organisation

(2013) S Garcia et al.   HEREDITY

Contrasting Patterns of Evolution of 45S and 5S rDNA Families Uncover New Aspects in the Genome Constitution of the Agronomically Important Grass Thinopyrum intermedium (Triticeae)

(2013) Václav Mahelka et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Intra-Genomic Variation in the Ribosomal Repeats of Nematodes

(2013) Holly M. Bik et al.   PLoS One

Constructing Phylogenies in the Presence Of Intra-Individual Site Polymorphisms (2ISPs) with a Focus on the Nuclear Ribosomal Cistron

(2013) Alastair J. Potts et al.   SYSTEMATIC BIOLOGY

Partial Sequence Homogenization in the 5S Multigene Families May Generate Sequence Chimeras and Spurious Results in Phylogenetic Reconstructions

(2013) José A. Galián et al.   SYSTEMATIC BIOLOGY

Strength and variability of postmating reproductive isolating barriers between four European white oak species

(2013) O. Lepais et al.   Tree Genetics & Genomes

Trichome types, foliar indumentum and epicuticular wax in the Mediterranean gall oaks, Quercus subsection Galliferae (Fagaceae): implications for taxonomy, ecology and evolution

(2012) GEORG F. TSCHAN et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Accession-Specific Haplotypes of the Internal Transcribed Spacer Region in Arabidopsis thaliana--A Means for Barcoding Populations

(2012) U. K. Simon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Extensive Pyrosequencing Reveals Frequent Intra-Genomic Variations of Internal Transcribed Spacer Regions of Nuclear Ribosomal DNA

(2012) Jingyuan Song et al.   PLoS One

Genomics of Fagaceae

(2012) Antoine Kremer et al.   Tree Genetics & Genomes

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos

(2011) Mehrdad Hajibabaei et al.   PLoS One

Choosing and Using a Plant DNA Barcode

(2011) Peter M. Hollingsworth et al.   PLoS One

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

Evolution of rDNA FISH patterns in the Fagaceae

(2011) Teresa Ribeiro et al.   Tree Genetics & Genomes

Detecting interspecific and geographic differentiation patterns in two interfertile oak species (Quercus petraea (Matt.) Liebl. and Q. robur L.) using small sets of microsatellite markers

(2010) C. Neophytou et al.   FOREST ECOLOGY AND MANAGEMENT

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Progress in phylogenetic analysis and a new infrageneric classification of the barley genus Hordeum (Poaceae: Triticeae)

(2009) Frank R. Blattner   BREEDING SCIENCE

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

New generation sequencers as a tool for genotyping of highly polymorphic multilocus MHC system

(2009) WIESŁAW BABIK et al.   Molecular Ecology Resources

General functions to transform associate data to host data, and their use in phylogenetic inference from sequences with intra-individual variability

(2008) Markus Göker et al.   BMC EVOLUTIONARY BIOLOGY