Plastome sequences fail to resolve shallow level relationships within the rapidly radiated genus Isodon (Lamiaceae)

Plastome structure, phylogenomics and evolution of plastid genes in Swertia (Gentianaceae) in the Qing-Tibetan Plateau

(2022) Qian Cao et al.   BMC PLANT BIOLOGY

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

(2022) Jie Wang et al.   Frontiers in Plant Science

An updated tribal classification of Lamiaceae based on plastome phylogenomics

(2021) Fei Zhao et al.   BMC BIOLOGY

Phylogenomic and ecological analyses reveal the spatiotemporal evolution of global pines

(2021) Wei-Tao Jin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Target enrichment improves phylogenetic resolution in the genus Zanthoxylum (Rutaceae) and indicates both incomplete lineage sorting and hybridization events

(2021) Niklas Reichelt et al.   ANNALS OF BOTANY

Can plastome data resolve recent radiations? Rhodiola (Crassulaceae) as a case study

(2021) Dan-Ni Zhao et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Capturing single‐copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

(2021) Bin‐Bin Liu et al.   Journal of Systematics and Evolution

Phylogenomic and Macroevolutionary Evidence for an Explosive Radiation of a Plant Genus in the Miocene

(2021) Hanghui Kong et al.   SYSTEMATIC BIOLOGY

Plastid phylogenomic insights into relationships of all flowering plant families

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

Spatiotemporal Evolution of the Global Species Diversity of Rhododendron

(2021) Xiao-Mei Xia et al.   MOLECULAR BIOLOGY AND EVOLUTION

An updated phylogenetic and biogeographic analysis based on genome skimming data reveals convergent evolution of shrubby habit in Clematis in the Pliocene and Pleistocene

(2021) Jian He et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae

(2020) Rong Zhang et al.   SYSTEMATIC BIOLOGY

Plastome Sequences Help to Resolve Deep-Level Relationships of Populus in the Family Salicaceae

(2019) Dan Zong et al.   Frontiers in Plant Science

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

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

Taxonomic notes on Isodon (Lamiaceae) in China, III: resurrection of I. brachythyrsus , I. chionanthus and I. kangtingensis

(2019) Ya‐Ping Chen et al.   NORDIC JOURNAL OF BOTANY

Frequent chloroplast capture among Isodon (Lamiaceae) species in Japan revealed by phylogenies based on variation in chloroplast and nuclear DNA

(2019) Miho Ogishima et al.   PLANT SPECIES BIOLOGY

Revisiting the phylogeny of Dipsacales: new insights from phylogenomic analyses of complete plastomic sequences

(2019) Chun-Lei Xiang et al.   Journal of Systematics and Evolution

Characterizing gene tree conflict in plastome-inferred phylogenies

(2019) Joseph F. Walker et al.   PeerJ

Plastid phylogenomics and biogeographic analysis support a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous

(2019) Chao-Nan Fu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

(2019) Yunheng Ji et al.   BMC PLANT BIOLOGY

Isodon hsiwenii (Lamiaceae: Nepetoideae), A New Species From Yunnan, China

(2019) Ya-Ping Chen et al.   SYSTEMATIC BOTANY

Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea )

(2018) Charles S.P. Foster et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Chloroplast variation is incongruent with classification of the Australian bloodwood eucalypts (genus Corymbia, family Myrtaceae)

(2018) Tanja M. Schuster et al.   PLoS One

An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus )

(2018) Julie A. Lee-Yaw et al.   NEW PHYTOLOGIST

A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny

(2017) Kasey K. Pham et al.   GENOME

Diterpenoids from Isodon species: an update

(2017) Miao Liu et al.   NATURAL PRODUCT REPORTS

Insights into the historical assembly of East Asian subtropical evergreen broadleaved forests revealed by the temporal history of the tea family

(2017) Xiang-Qin Yu et al.   NEW PHYTOLOGIST

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

(2016) Robert Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resolving the phylogenetic position of Ombrocharis (Lamiaceae), with reference to the molecular phylogeny of tribe Elsholtzieae

(2016) Ya-Ping Chen et al.   TAXON

Widespread adaptive evolution during repeated evolutionary radiations in New World lupins

(2016) Bruno Nevado et al.   Nature Communications

Isodon villosus (Nepetoideae, Lamiaceae), a new species from Guangxi, China

(2016) YA-PING CHEN et al.   Phytotaxa

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

(2015) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

TreSpEx–-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information

(2014) Torsten H. Struck   Evolutionary Bioinformatics

Phylogeny and historical biogeography of Isodon (Lamiaceae): Rapid radiation in south-west China and Miocene overland dispersal into Africa

(2014) Xiang-Qin Yu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2012) M. Kearse et al.   BIOINFORMATICS

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Horizontal transfer of chloroplast genomes between plant species

(2012) S. Stegemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

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

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

Geographic and phylogenetic patterns in Silene section Melandrium (Caryophyllaceae) as inferred from chloroplast and nuclear DNA sequences

(2010) Anja Rautenberg et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Molecular phylogeny of Isodon (Lamiaceae) in Japan using chloroplast DNA sequences: recent rapid radiations or ancient introgressive hybridization?

(2010) MASAYUKI MAKI et al.   PLANT SPECIES BIOLOGY

Phylogeny of Isodon (Schrad. ex Benth.) Spach (Lamiaceae) and Related Genera Inferred from Nuclear Ribosomal ITS, trnL–trnF Region, and rps16 Intron Sequences and Morphology

(2010) Jin-Shun Zhong et al.   SYSTEMATIC BOTANY

Micromorphology and Character Evolution of Nutlets in Tribe Mentheae (Nepetoideae, Lamiaceae)

(2009) Hye-Kyoung Moon et al.   SYSTEMATIC BOTANY