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

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

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

Phylogeny, divergence times, and historical biogeography of the angiosperm family Saxifragaceae

(2015) Jia-bin Deng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic relationships and character evolution in Heuchera (Saxifragaceae) on the basis of multiple nuclear loci

(2014) R. A. Folk et al.   AMERICAN JOURNAL OF BOTANY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

(2014) Brad R Ruhfel et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

(2014) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Microsatellite Primers for the Gynodioecious Grassland Perennial Saxifraga granulata (Saxifragaceae)

(2014) Sascha van der Meer et al.   Applications in Plant Sciences

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

(2014) Kevin Weitemier 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

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

Polyploidization in Heuchera cylindrica (Saxifragaceae) did not result in a shift in climatic requirements

(2013) William Godsoe et al.   AMERICAN JOURNAL OF BOTANY

One ring to rule them all? Genome sequencing provides new insights into the ‘master circle’ model of plant mitochondrial DNA structure

(2013) Daniel B. Sloan   NEW PHYTOLOGIST

STRAW: Species TRee Analysis Web server

(2013) Timothy I. Shaw et al.   NUCLEIC ACIDS RESEARCH

OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets

(2013) Marc Lohse et al.   NUCLEIC ACIDS RESEARCH

Targeted enrichment strategies for next-generation plant biology

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

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

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

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

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

The Mitochondrial Genome of the Legume Vigna radiata and the Analysis of Recombination across Short Mitochondrial Repeats

(2011) Andrew J. Alverson et al.   PLoS One

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Mitochondrial DNA of Vitis vinifera and the Issue of Rampant Horizontal Gene Transfer

(2008) V. V. Goremykin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient hybridization and mitochondrial capture between two species of chipmunks

(2008) JEFFREY M. GOOD et al.   MOLECULAR ECOLOGY

Resolving an Ancient, Rapid Radiation in Saxifragales

(2008) Shuguang Jian et al.   SYSTEMATIC BIOLOGY