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

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

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

Chloroplast capture and intra- and inter-continental biogeographic diversification in the Asian – New World disjunct plant genus Osmorhiza (Apiaceae)

(2015) Ting-Shuang Yi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2015) Elizabeth A. Zimmer et al.   Journal of Systematics and Evolution

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times

(2014) Liping Zeng et al.   Nature Communications

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

(2014) Kevin Weitemier 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

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

Synopsis of Nekemias Raf., a segregate genus from Ampelopsis Michx. (Vitaceae) disjunct between eastern/southeastern Asia and eastern North America, with ten new combinations

(2014) Jun Wen et al.   PhytoKeys

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

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

Reprint of: Using nuclear gene data for plant phylogenetics: Progress and prospects

(2013) Elizabeth A. Zimmer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeny of the non-monophyletic Cayratia Juss. (Vitaceae) and implications for character evolution and biogeography

(2013) Limin Lu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

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

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Evolution of the intercontinental disjunctions in six continents in the Ampelopsis clade of the grape family (Vitaceae)

(2012) Ze-Long Nie et al.   BMC EVOLUTIONARY BIOLOGY

Molecular phylogeny of Cissus L. of Vitaceae (the grape family) and evolution of its pantropical intercontinental disjunctions

(2012) Xiu-Qun Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms

(2012) Ning Zhang et al.   NEW PHYTOLOGIST

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

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

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

Molecular phylogeny and biogeographic diversification of Parthenocissus (Vitaceae) disjunct between Asia and North America

(2010) Ze-Long Nie et al.   AMERICAN JOURNAL OF BOTANY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME 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

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH