Phylogenetics and comparative plastome genomics of two of the largest genera of angiosperms, Piper and Peperomia (Piperaceae)

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

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

Target Nuclear and Off-Target Plastid Hybrid Enrichment Data Inform a Range of Evolutionary Depths in the Orchid Genus Epidendrum

(2020) Carolina Granados Mendoza et al.   Frontiers in Plant Science

Insights into phylogeny, age and evolution of Allium (Amaryllidaceae) based on the whole plastome sequences

(2020) Deng-Feng Xie et al.   ANNALS OF BOTANY

Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L.

(2020) Craig F. Barrett   PeerJ

Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes

(2020) Shuyu Zheng et al.   Frontiers in Genetics

Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation

(2019) Zhang-Hai Li et al.   BMC EVOLUTIONARY BIOLOGY

Origin and evolution of the genus Piper in Peninsular India

(2019) Sandeep Sen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes

(2019) Stephan Greiner et al.   NUCLEIC ACIDS RESEARCH

Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species

(2019) Mahmoud Magdy et al.   Horticulture Research

The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis

(2019) Lisong Hu et al.   Nature Communications

Intraspecific Variation within the Utricularia amethystina Species Morphotypes Based on Chloroplast Genomes

(2019) Saura R. Silva et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

(2019) Andrew D. Young et al.   SYSTEMATIC ENTOMOLOGY

IRscope: an online program to visualize the junction sites of chloroplast genomes

(2018) Ali Amiryousefi et al.   BIOINFORMATICS

Practical considerations for plant phylogenomics

(2018) Michael R. McKain et al.   Applications in Plant Sciences

Shedding new light on the origin and spread of the brinjal eggplant (Solanum melongena L.) and its wild relatives

(2018) Xavier Aubriot et al.   AMERICAN JOURNAL OF BOTANY

Phylogenetic relationships in Malesian-Pacific Piper (Piperaceae) and their implications for systematics

(2018) Rani Asmarayani   TAXON

First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L. (Moraceae)

(2017) Sam Bruun-Lund et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Comparative plastome genomics and phylogenomics of Brachypodium : flowering time signatures, introgression and recombination in recently diverged ecotypes

(2017) Rubén Sancho et al.   NEW PHYTOLOGIST

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

Diversification rates, host plant shifts and an updated molecular phylogeny of Andean Eois moths (Lepidoptera: Geometridae)

(2017) Patrick Strutzenberger et al.   PLoS One

The Emergence of Earliest Angiosperms May be Earlier than Fossil Evidence Indicates

(2017) Karsten Salomo et al.   SYSTEMATIC BOTANY

Intraspecific and heteroplasmic variations, gene losses and inversions in the chloroplast genome of Astragalus membranaceus

(2016) Wanjun Lei et al.   Scientific Reports

A Late Cretaceous Piper (Piperaceae) from Colombia and diversification patterns for the genus

(2015) Camila Martínez et al.   AMERICAN JOURNAL OF BOTANY

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

Collections-based research in the genomic era

(2015) Sven Buerki et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Phytochemical diversity drives plant–insect community diversity

(2015) Lora A. Richards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A revised infrageneric classification of the genus Peperomia (Piperaceae)

(2015) Lena Frenzke et al.   TAXON

Genome skimming for next-generation biodiversity analysis

(2015) Steven Dodsworth   TRENDS IN PLANT SCIENCE

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

(2015) Kyunghee Kim et al.   Scientific Reports

ycf1, the most promising plastid DNA barcode of land plants

(2015) Wenpan Dong et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Phylogenetic studies of Piper and Peperomia: Reconstruction of secondary metabolites evolution

(2014) APM Egydio et al.   PLANTA MEDICA

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

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

Phylogenetics and diversification of morning glories (tribe Ipomoeeae, Convolvulaceae) based on whole plastome sequences

(2013) Lauren A. Eserman et al.   AMERICAN JOURNAL OF BOTANY

Chloroplast genome analysis of Australian eucalypts – Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae)

(2013) Michael J. Bayly et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

The potential of genomics in plant systematics

(2013) Douglas E. Soltis et al.   TAXON

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Host conservatism, host shifts and diversification across three trophic levels in two Neotropical forests

(2012) J. S. WILSON et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Highly Variable Chloroplast Markers for Evaluating Plant Phylogeny at Low Taxonomic Levels and for DNA Barcoding

(2012) Wenpan Dong et al.   PLoS One

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

The extraordinary journey of Peperomia subgenus Tildenia (Piperaceae): insights into diversification and colonization patterns from its cradle in Peru to the Trans-Mexican Volcanic Belt

(2011) Lars Symmank et al.   JOURNAL OF BIOGEOGRAPHY

Parallelization of the MAFFT multiple sequence alignment program

(2010) Kazutaka Katoh et al.   BIOINFORMATICS

pegas: an R package for population genetics with an integrated-modular approach

(2010) E. Paradis   BIOINFORMATICS

Intraspecific Inversions Pose a Challenge for the trnH-psbA Plant DNA Barcode

(2010) Barbara A. Whitlock et al.   PLoS One

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

(2009) Matthew Parks et al.   BMC BIOLOGY

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III

(2009)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots

(2008) Rui-Jiang Wang et al.   BMC EVOLUTIONARY BIOLOGY

Placing the origin of two species-rich genera in the late cretaceous with later species divergence in the tertiary: a phylogenetic, biogeographic and molecular dating analysis of Piper and Peperomia (Piperaceae)

(2008) James F. Smith et al.   PLANT SYSTEMATICS AND EVOLUTION

A Phylogeny of the Tropical Genus Piper Using ITS and the Chloroplast Intron psbJ–petA

(2008) M. Alejandra Jaramillo et al.   SYSTEMATIC BOTANY