Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next-gen approaches

Capturing protein-coding genes across highly divergent species

(2016) Chenhong Li et al.   BIOTECHNIQUES

Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species

(2015) Rajanikanth Govindarajulu et al.   AMERICAN JOURNAL OF BOTANY

The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

(2015) Isabelle Lesur et al.   BMC GENOMICS

De novo sequencing of the Hypericum perforatum L. flower transcriptome to identify potential genes that are related to plant reproduction sensu lato

(2015) Giulio Galla et al.   BMC GENOMICS

An Exploration into Fern Genome Space

(2015) Paul G. Wolf et al.   Genome Biology and 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

Is the extremely rare Iberian endemic plant species Castrilanthemum debeauxii (Compositae, Anthemideae) a ‘living fossil’? Evidence from a multi-locus species tree reconstruction

(2015) Salvatore Tomasello et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment

(2015) Jessica D. Stephens et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome skimming for next-generation biodiversity analysis

(2015) Steven Dodsworth   TRENDS IN PLANT SCIENCE

Coalescent methods for estimating species trees from phylogenomic data

(2015) Liang Liu et al.   Journal of Systematics and Evolution

Expression patterns ofAP1,FUL,FTandLEAFYorthologs in Vitaceae support the homology of tendrils and inflorescences throughout the grape family

(2015) Ning Zhang et al.   Journal of Systematics and Evolution

Using phylogenomics to resolve mega-families: An example from Compositae

(2015) Jennifer R. Mandel et al.   Journal of Systematics and Evolution

Transcriptome Sequencing and Marker Development for Four Underutilized Legumes

(2015) Mark A. Chapman   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

SNP Discovery in Complex Allotetraploid Genomes (Gossypiumspp., Malvaceae) Using Genotyping by Sequencing

(2015) Carla Jo Logan-Young et al.   Applications in Plant Sciences

Isoëtes viridimontana: A Previously Unrecognized Quillwort from Vermont, USA

(2014) Michael A. Rosenthal et al.   AMERICAN FERN JOURNAL

Phylogenomics of the carrot genus (Daucus , Apiaceae)

(2014) Carlos Arbizu et al.   AMERICAN JOURNAL OF BOTANY

Biological invasions, climate change and genomics

(2014) Steven L. Chown et al.   Evolutionary Applications

A novel set of single-copy nuclear DNA markers for the genetic study of Salicaceae

(2014) S.H. Du et al.   GENETICS AND MOLECULAR RESEARCH

Evolutionary Origins and Dynamics of Octoploid Strawberry Subgenomes Revealed by Dense Targeted Capture Linkage Maps

(2014) Jacob A. Tennessen et al.   Genome Biology and Evolution

Comparative Transcriptome Analyses Reveal Core Parasitism Genes and Suggest Gene Duplication and Repurposing as Sources of Structural Novelty

(2014) Zhenzhen Yang 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

Empirical Assessment of RAD Sequencing for Interspecific Phylogeny

(2014) Astrid Cruaud et al.   MOLECULAR BIOLOGY AND EVOLUTION

Application of RAD-based phylogenetics to complex relationships among variously related taxa in a species flock

(2014) Tetsumi Takahashi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Sequencing Degraded DNA from Non-Destructively Sampled Museum Specimens for RAD-Tagging and Low-Coverage Shotgun Phylogenetics

(2014) Mandy Man-Ying Tin et al.   PLoS One

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

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

Phylogenetic Properties of 50 Nuclear Loci in Medicago (Leguminosae) Generated Using Multiplexed Sequence Capture and Next-Generation Sequencing

(2014) Filipe de Sousa 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

Investigation of terpene diversification across multiple sequenced plant genomes

(2014) Alexander M. Boutanaev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide identification and expression analysis of TCP transcription factors in Gossypium raimondii

(2014) Jun Ma et al.   Scientific Reports

Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis

(2014) Linhai Wang et al.   GENOME BIOLOGY

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

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

Development of Novel, Exon-Primed Intron-Crossing (EPIC) Markers from EST Databases and Evaluation of their Phylogenetic Utility inCommiphora(Burseraceae)

(2014) Morgan R. Gostel et al.   Applications in Plant Sciences

Gene Prediction and Annotation inPenstemon(Plantaginaceae): A Workflow for Marker Development from Extremely Low-Coverage Genome Sequencing

(2014) Paul D. Blischak et al.   Applications in Plant Sciences

Geneious! Simplified Genome Skimming Methods for Phylogenetic Systematic Studies: A Case Study inOreocarya(Boraginaceae)

(2014) Lee A. Ripma et al.   Applications in Plant Sciences

Primers for Low-Copy Nuclear Genes in Metrosideros and Cross-Amplification in Myrtaceae

(2014) Yohan Pillon 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

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

The carnivorous plant described asSarracenia alatacontains two cryptic species

(2013) Bryan C. Carstens et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

‘Next generation’ biogeography: towards understanding the drivers of species diversification and persistence

(2013) Christian Lexer et al.   JOURNAL OF BIOGEOGRAPHY

Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics

(2013) A. M. Reitzel et al.   MOLECULAR ECOLOGY

Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing

(2013) X. Q. Wang et al.   Molecular Ecology Resources

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

Significant variance in genetic diversity among populations of Schistosoma haematobium detected using microsatellite DNA loci from a genome-wide database

(2013) Travis C Glenn et al.   Parasites & Vectors

Whole-exome targeted sequencing of the uncharacterized pine genome

(2013) Leandro G. Neves et al.   PLANT JOURNAL

Transcriptome Sequences Resolve Deep Relationships of the Grape Family

(2013) Jun Wen et al.   PLoS One

Transcriptome-Mining for Single-Copy Nuclear Markers in Ferns

(2013) Carl J. Rothfels et al.   PLoS One

Vitis Phylogenomics: Hybridization Intensities from a SNP Array Outperform Genotype Calls

(2013) Allison J. Miller et al.   PLoS One

Phylogenetic utility of 19 low copy nuclear genes in closely related genera and species of caesalpinioid legumes

(2013) Marielle Babineau et al.   SOUTH AFRICAN JOURNAL OF BOTANY

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

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

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

Exon-Primed Intron-Crossing (EPIC) Markers for Evolutionary Studies of Ficus and Other Taxa in the Fig Family (Moraceae)

(2013) Xiaohong Yao et al.   Applications in Plant Sciences

Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree

(2013) Hannah McPherson et al.   BMC ECOLOGY

Targeted enrichment strategies for next-generation plant biology

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

Targeted sequence capture as a powerful tool for evolutionary analysis1

(2012) Corrinne E. Grover et al.   AMERICAN JOURNAL OF BOTANY

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

(2012) Ylenia Chiari et al.   BMC BIOLOGY

Unraveling reticulate evolution in North American Dryopteris (Dryopteridaceae)

(2012) Emily B Sessa et al.   BMC EVOLUTIONARY BIOLOGY

De novo assembly and Characterisation of the Transcriptome during seed development, and generation of genic-SSR markers in Peanut (Arachis hypogaea L.)

(2012) Jianan Zhang et al.   BMC GENOMICS

Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture

(2012) Lecong Zhou et al.   BMC GENOMICS

High-throughput novel microsatellite marker of faba bean via next generation sequencing

(2012) Tao Yang et al.   BMC GENOMICS

RAD tag sequencing as a source of SNP markers in Cynara cardunculus L

(2012) Davide Scaglione et al.   BMC GENOMICS

Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers

(2012) Nian Wang 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

Reticulate evolution on a global scale: A nuclear phylogeny for New World Dryopteris (Dryopteridaceae)

(2012) Emily B. Sessa et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Using nuclear gene data for plant phylogenetics: Progress and prospects

(2012) Elizabeth A. Zimmer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Making next-generation sequencing work for you: approaches and practical considerations for marker development and phylogenetics

(2012) Grant T. Godden et al.   Plant Ecology & Diversity

Broad Phylogenomic Sampling and the Sister Lineage of Land Plants

(2012) Ruth E. Timme et al.   PLoS One

Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach

(2012) Jesse A. Poland et al.   PLoS One

Inferring Phylogenies from RAD Sequence Data

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

Coalescent Simulations Reveal Hybridization and Incomplete Lineage Sorting in Mediterranean Linaria

(2012) José Luis Blanco-Pastor 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

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

Long identical multispecies elements in plant and animal genomes

(2012) J. Reneker 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

Exploring the utility of three nuclear regions to reconstruct reticulate evolution in the fern genusAsplenium

(2012) Harald SCHNEIDER et al.   Journal of Systematics and Evolution

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

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

Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences

(2011) Juan E. Zalapa et al.   AMERICAN JOURNAL OF BOTANY

RADSeq: next-generation population genetics

(2011) J. W. Davey et al.   Briefings in Functional Genomics

Reconciling Gene and Genome Duplication Events: Using Multiple Nuclear Gene Families to Infer the Phylogeny of the Aquatic Plant Family Pontederiaceae

(2011) Rob W. Ness et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resolving the evolutionary relationships of molluscs with phylogenomic tools

(2011) Stephen A. Smith et al.   NATURE

Phylogenomics reveals deep molluscan relationships

(2011) Kevin M. Kocot et al.   NATURE

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

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

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

A Functional Phylogenomic View of the Seed Plants

(2011) Ernest K. Lee et al.   PLoS Genetics

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

(2010) Bret R. Larget et al.   BIOINFORMATICS

Exon-primed intron-crossing (EPIC) markers for non-model teleost fishes

(2010) Chenhong Li et al.   BMC EVOLUTIONARY BIOLOGY

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

(2010) Jill M Duarte et al.   BMC EVOLUTIONARY BIOLOGY

Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life

(2010) C. T. Hittinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolving postglacial phylogeography using high-throughput sequencing

(2010) K. J. Emerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coalescent methods for estimating phylogenetic trees

(2009) Liang Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

New Heuristic Methods for Joint Species Delimitation and Species Tree Inference

(2009) Brian C. O'Meara   SYSTEMATIC BIOLOGY

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Development of COS genes as universally amplifiable markers for phylogenetic reconstructions of closely related plant species

(2008) Mingai Li et al.   CLADISTICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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

The Utility of Nuclear gapCp in Resolving Polyploid Fern Origins

(2008) Eric Schuettpelz et al.   SYSTEMATIC BOTANY

msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design

(2007) BRANT C. FAIRCLOTH   Molecular Ecology Resources