Practical considerations for plant phylogenomics

Plastid phylogenomic analysis of green plants: A billion years of evolutionary history

(2018) Matthew A. Gitzendanner et al.   AMERICAN JOURNAL OF BOTANY

A software tool ‘CroCo’ detects pervasive cross-species contamination in next generation sequencing data

(2018) Paul Simion et al.   BMC BIOLOGY

Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the moss family Funariaceae

(2018) Rafael Medina et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Ten simple rules for biologists learning to program

(2018) Maureen A. Carey et al.   PLoS Computational Biology

A protocol for high-throughput, untargeted forest community metabolomics using mass spectrometry molecular networks

(2018) Brian E. Sedio et al.   Applications in Plant Sciences

Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a MediterraneanCampanula(Campanulaceae) clade

(2017) Andrew A. Crowl et al.   EVOLUTION

Detection of individual ploidy levels with genotyping-by-sequencing (GBS) analysis

(2017) Zachariah Gompert et al.   Molecular Ecology Resources

Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci

(2017) Heather R. Kates et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events

(2017) Ya Yang et al.   NEW PHYTOLOGIST

Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium )

(2017) Oscar M. Vargas 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

Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events

(2017) W. C. Thomas Gregg et al.   SYSTEMATIC BIOLOGY

Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics

(2017) Étienne Léveillé-Bourret et al.   SYSTEMATIC BIOLOGY

RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra-arid deserts of Namibia

(2017) Erin A. Tripp et al.   Ecology and Evolution

De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from Total DNA Sequences

(2017) Shairul Izan et al.   Frontiers in Plant Science

Primers for Castilleja and their Utility Across Orobanchaceae: II. Single-Copy Nuclear Loci

(2017) Maribeth Latvis et al.   Applications in Plant Sciences

An Efficient Field and Laboratory Workflow for Plant Phylotranscriptomic Projects

(2017) Ya Yang et al.   Applications in Plant Sciences

The Unexpected Depths of Genome-Skimming Data: A Case Study Examining Goodeniaceae Floral Symmetry Genes

(2017) Brent A. Berger et al.   Applications in Plant Sciences

Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes

(2017) Gitte Petersen et al.   PLoS One

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

(2017) Perrine Cruaud et al.   Scientific Reports

Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor

(2016) Mario Vallejo-Marín et al.   AMERICAN JOURNAL OF BOTANY

Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae)

(2016) Michael R. McKain et al.   AMERICAN JOURNAL OF BOTANY

Targeted capture and sequencing of gene-sized DNA molecules

(2016) Michael Giolai et al.   BIOTECHNIQUES

The next generation of target capture technologies - large DNA fragment enrichment and sequencing determines regional genomic variation of high complexity

(2016) Johannes Dapprich et al.   BMC GENOMICS

A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales

(2016) Michael R. McKain et al.   Genome Biology and Evolution

Importance of incomplete lineage sorting and introgression in the origin of shared genetic variation between two closely related pines with overlapping distributions

(2016) Y Zhou et al.   HEREDITY

GinkgoandWelwitschiaMitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution

(2016) Wenhu Guo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Strategies for complete plastid genome sequencing

(2016) Alex D. Twyford et al.   Molecular Ecology Resources

RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data

(2016) Sandra L. Hoffberg et al.   Molecular Ecology Resources

ddRAD-seq phylogenetics based on nucleotide, indel, and presence–absence polymorphisms: Analyses of two avian genera with contrasting histories

(2016) Jeffrey M. DaCosta et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

(2016) Andreanna J. Welch et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolution of a CAM anatomy predates the origins of Crassulacean acid metabolism in the Agavoideae (Asparagaceae)

(2016) Karolina Heyduk et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing

(2016) Carl J. Rothfels et al.   NEW PHYTOLOGIST

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods

(2016) Huw A. Ogilvie et al.   SYSTEMATIC BIOLOGY

Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus

(2016) Alex Harkess et al.   G3-Genes Genomes Genetics

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

(2016) James B. Pease et al.   PLOS BIOLOGY

An Expanded Nuclear Phylogenomic PCR Toolkit for Sapindales

(2016) Elizabeth S. Collins et al.   Applications in Plant Sciences

Low-Coverage, Whole-Genome Sequencing of Artocarpus camansi (Moraceae) for Phylogenetic Marker Development and Gene Discovery

(2016) Elliot M. Gardner et al.   Applications in Plant Sciences

HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

(2016) Matthew G. Johnson et al.   Applications in Plant Sciences

A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae)

(2016) Simon Uribe-Convers et al.   PLoS One

Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads

(2015) S. Evan Staton et al.   BIOINFORMATICS

PHYLUCE is a software package for the analysis of conserved genomic loci

(2015) Brant C. Faircloth   BIOINFORMATICS

Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline

(2015) Freek T. Bakker et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico

(2015) Loubab Zedane et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Phylogenomic analyses of species relationships in the genusSabal(Arecaceae) using targeted sequence capture

(2015) Karolina Heyduk et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

(2015) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary transitions in the Asteraceae coincide with marked shifts in transposable element abundance

(2015) S. Evan Staton et al.   BMC GENOMICS

ASTRID: Accurate Species TRees from Internode Distances

(2015) Pranjal Vachaspati et al.   BMC GENOMICS

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

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

Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing

(2015) Adam D. Leaché et al.   Genome Biology and Evolution

Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing

(2015) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the GenusCitrus

(2015) Jose Carbonell-Caballero et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary and biogeographical patterns of barnacles from deep-sea hydrothermal vents

(2015) Santiago Herrera et al.   MOLECULAR ECOLOGY

Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern AfricanOxalis(Oxalidaceae)

(2015) Roswitha Schmickl et al.   Molecular Ecology Resources

Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq)

(2015) Carly F. Graham et al.   Molecular Ecology Resources

Microfluidic PCR-based target enrichment: A case study in two rapid radiations ofCommiphora(Burseraceae) from Madagascar

(2015) Morgan R. Gostel et al.   Journal of Systematics and Evolution

Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species

(2015) Kyunghee Kim et al.   Scientific Reports

Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences

(2015) Peterson W. Wambugu et al.   Scientific Reports

Modified CTAB and TRIzol Protocols Improve RNA Extraction from Chemically Complex Embryophyta

(2015) Ingrid E. Jordon-Thaden et al.   Applications in Plant Sciences

MarkerMiner 1.0: A New Application for Phylogenetic Marker Development Using Angiosperm Transcriptomes

(2015) Srikar Chamala et al.   Applications in Plant Sciences

A Protocol for Targeted Enrichment of Intron-Containing Sequence Markers for Recent Radiations: A Phylogenomic Example from Heuchera (Saxifragaceae)

(2015) Ryan A. Folk et al.   Applications in Plant Sciences

Early genome duplications in conifers and other seed plants

(2015) Z. Li et al.   Science Advances

Congruent Deep Relationships in the Grape Family (Vitaceae) Based on Sequences of Chloroplast Genomes and Mitochondrial Genes via Genome Skimming

(2015) Ning Zhang et al.   PLoS One

Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: The tortoise and the hare IV

(2014) Joey Shaw et al.   AMERICAN JOURNAL OF BOTANY

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrusspecies: analysis of chromosome 2

(2014) Franck Curk et al.   BMC GENETICS

Phylogeny of Zebrafish, a “Model Species,” within Danio, a “Model Genus”

(2014) Braedan M. McCluskey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

(2014) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Restriction site-associated DNA sequencing, genotyping error estimation andde novoassembly optimization for population genetic inference

(2014) A. Mastretta-Yanes et al.   Molecular Ecology Resources

Genotyping-by-sequencing as a tool to infer phylogeny and ancestral hybridization: A case study in Carex (Cyperaceae)

(2014) Marcial Escudero et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data

(2014) Andrew L. Hipp et al.   PLoS One

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species Delimitation using Genome-Wide SNP Data

(2014) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

A multi-step comparison of short-read full plastome sequence assembly methods in grasses

(2014) William P. Wysocki et al.   TAXON

Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

(2014) Kevin Weitemier et al.   Applications in Plant Sciences

A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae

(2014) Jennifer R. Mandel et al.   Applications in Plant Sciences

Data access for the 1,000 Plants (1KP) project

(2014) Naim Matasci et al.   GigaScience

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

The miniature genome of a carnivorous plant Genlisea aurea contains a low number of genes and short non-coding sequences

(2013) Evgeny V Leushkin et al.   BMC GENOMICS

The Gut Microbiotassay: a high-throughput qPCR approach combinable with next generation sequencing to study gut microbial diversity

(2013) Marie Hermann-Bank et al.   BMC GENOMICS

Highly multiplexed quantitation of gene expression on single cells

(2013) Maria H. Dominguez et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis

(2013) Victoria Moignard et al.   NATURE CELL BIOLOGY

Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke

(2013) Dan G. Bock et al.   NEW PHYTOLOGIST

The First Symbiont-Free Genome Sequence of Marine Red Alga, Susabi-nori (Pyropia yezoensis)

(2013) Yoji Nakamura et al.   PLoS One

Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens

(2013) Martijn Staats et al.   PLoS One

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

(2013) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array™ system for simplified amplicon library preparation

(2013) P. V. Moonsamy et al.   TISSUE ANTIGENS

Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

(2013) Marie Cariou et al.   Ecology and Evolution

A Targeted Enrichment Strategy for Massively Parallel Sequencing of Angiosperm Plastid Genomes

(2013) Gregory W. Stull et al.   Applications in Plant Sciences

A Method for Extracting High-Quality RNA from Diverse Plants for Next-Generation Sequencing and Gene Expression Analyses

(2013) Roxana Yockteng et al.   Applications in Plant Sciences

ezRAD: a simplified method for genomic genotyping in non-model organisms

(2013) Robert J. Toonen et al.   PeerJ

Targeted enrichment strategies for next-generation plant biology

(2012) Richard Cronn et al.   AMERICAN JOURNAL OF BOTANY

Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae

(2012) P. Roxanne Steele et al.   AMERICAN JOURNAL OF BOTANY

The Rectal Cancer microRNAome - microRNA Expression in Rectal Cancer and Matched Normal Mucosa

(2012) J. Gaedcke et al.   CLINICAL CANCER RESEARCH

DNA Methylation Profiling Defines Clinically Relevant Biological Subsets of Non-Small Cell Lung Cancer

(2012) K. Walter et al.   CLINICAL CANCER RESEARCH

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide patterns of divergence and gene flow across a butterfly radiation

(2012) Nicola J. Nadeau et al.   MOLECULAR ECOLOGY

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis

(2012) Pierre De Wit et al.   Molecular Ecology Resources

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

(2012) Kanchon K. Dasmahapatra et al.   NATURE

Genome-wide association study in Han Chinese identifies four new susceptibility loci for coronary artery disease

(2012) Xiangfeng Lu et al.   NATURE GENETICS

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Inferring Phylogenies from RAD Sequence Data

(2012) Benjamin E. R. Rubin et al.   PLoS One

The Effect of Input DNA Copy Number on Genotype Call and Characterising SNP Markers in the Humpback Whale Genome Using a Nanofluidic Array

(2012) Somanath Bhat et al.   PLoS One

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

How to Open the Treasure Chest? Optimising DNA Extraction from Herbarium Specimens

(2012) Tiina Särkinen et al.   PLoS One

Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes

(2012) Marc T. J. Johnson et al.   PLoS One

Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing

(2012) J. G. Lohr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

Development and mapping of SNP assays in allotetraploid cotton

(2012) Robert L. Byers et al.   THEORETICAL AND APPLIED GENETICS

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

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

Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing

(2011) Kerry A Lutz et al.   BMC BIOTECHNOLOGY

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

DNA Damage in Plant Herbarium Tissue

(2011) Martijn Staats et al.   PLoS One

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

(2010) Bret R. Larget et al.   BIOINFORMATICS

The largest eukaryotic genome of them all?

(2010) JAUME PELLICER et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

(2010) J. Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

(2009) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One