Testing the Complete Plastome for Species Discrimination, Cryptic Species Discovery and Phylogenetic Resolution in Cephalotaxus (Cephalotaxaceae)

Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron

(2021) Chao‐Nan Fu et al.   Molecular Ecology Resources

Plastid phylogenomic insights into relationships of all flowering plant families

(2021) Hong-Tao Li et al.   BMC BIOLOGY

Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis

(2021) Rory F. Little et al.   NATURAL PRODUCT REPORTS

Large scale genome skimming from herbarium material for accurate plant identification and phylogenomics

(2020) Paul G. Nevill et al.   Plant Methods

Ultra-Barcoding Discovers a Cryptic Species in Paris yunnanensis (Melanthiaceae), a Medicinally Important Plant

(2020) Yunheng Ji et al.   Frontiers in Plant Science

Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China

(2020) Feng Song et al.   BMC PLANT BIOLOGY

Plastome phylogenomics of Cephalotaxus (Cephalotaxaceae) and allied genera

(2020) Yunheng Ji et al.   ANNALS OF BOTANY

Repeated intercontinental migrations and recurring hybridizations characterise the evolutionary history of yew (Taxus L.)

(2020) Michael Möller et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Middle Miocene Cephalotaxus (Taxaceae) from Yunnan, Southwest China, and its implications to taxonomy and evolution of the genus

(2019) Jian-Wei Zhang et al.   Palaeoworld

Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide

(2019) Chao-Nan Fu et al.   Scientific Reports

PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes

(2019) Xiao-Jian Qu et al.   Plant Methods

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

A new species of Amentotaxus (Taxaceae) from China, Vietnam, and Laos

(2019) Lian-Ming Gao et al.   PhytoKeys

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

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

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms

(2018) Jin-Hua Ran et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Accurate authentication of Dendrobium officinale and its closely related species by comparative analysis of complete plastomes

(2018) Shuying Zhu et al.   Acta Pharmaceutica Sinica B

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

(2017) Julio Rozas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Species boundaries in the Astragalus cusickii complex delimited using molecular phylogenetic techniques

(2017) J.C. Zimmers et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics

(2017) Shu-Dong Zhang et al.   NEW PHYTOLOGIST

What can we do with 1000 plastid genomes?

(2017) Julian Tonti-Filippini et al.   PLANT JOURNAL

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

From barcodes to genomes: extending the concept of DNA barcoding

(2016) Eric Coissac et al.   MOLECULAR ECOLOGY

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Telling plant species apart with DNA: from barcodes to genomes

(2016) Peter M. Hollingsworth et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

DNA barcoding of East Asian Amentotaxus (Taxaceae): Potential new species and implications for conservation

(2016) Lian-Ming Gao et al.   Journal of Systematics and Evolution

A new classification and linear sequence of extant gymnosperms

(2016) M. J. M. Christenhusz et al.   Phytotaxa

Development of chloroplast genomic resources for Cynara

(2015) Pasquale L. Curci et al.   Molecular Ecology Resources

Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria ?

(2015) Markus Ruhsam et al.   Molecular Ecology Resources

Plant identification is key to conservation

(2015) Anna Trias-Blasi et al.   NATURE

DNA barcodes for ecology, evolution, and conservation

(2015) W. John Kress et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Plant DNA barcoding: from gene to genome

(2014) Xiwen Li et al.   BIOLOGICAL REVIEWS

Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep?

(2014) Diana M. Percy et al.   MOLECULAR ECOLOGY

DNA barcoding ofRhododendron(Ericaceae), the largest Chinese plant genus in biodiversity hotspots of the Himalaya-Hengduan Mountains

(2014) Li-Jun Yan et al.   Molecular Ecology Resources

A multidisciplinary approach reveals hidden taxonomic diversity in the morphologically challenging Taxus wallichiana complex

(2014) Michael Möller et al.   TAXON

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

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

Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses

(2013) Jun-Bo Yang et al.   BMC EVOLUTIONARY BIOLOGY

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

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

Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead

(2013) Simon Joly et al.   Molecular Ecology Resources

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

A taxonomic revision of the genus Cephalotaxus (Taxaceae)

(2013) XUE-DONG LANG et al.   Phytotaxa

Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA

(2012) Nolan Kane et al.   AMERICAN JOURNAL OF BOTANY

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

(2012) M. Kearse et al.   BIOINFORMATICS

Sampling Strategy and Potential Utility of Indels for DNA Barcoding of Closely Related Plant Species: A Case Study in Taxus

(2012) Jie Liu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

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

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

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

Refining the DNA barcode for land plants

(2011) P. M. Hollingsworth   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants

(2011) et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species

(2010) JIE LIU et al.   Molecular Ecology Resources

Chloroplast genome sequences from total DNA for plant identification

(2010) Catherine J. Nock et al.   PLANT BIOTECHNOLOGY JOURNAL

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

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

Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants

(2009) MICHELLE L. HOLLINGSWORTH et al.   Molecular Ecology Resources

Plant species delimitation: A comparison of morphological and molecular markers

(2009) J. Duminil et al.   PLANT BIOSYSTEMS

Interspecific relationships and origins of Taxaceae and Cephalotaxaceae revealed by partitioned Bayesian analyses of chloroplast and nuclear DNA sequences

(2008) Da Cheng Hao et al.   PLANT SYSTEMATICS AND EVOLUTION