Phylotranscriptomics reveals extensive gene duplication in the subtribe Gentianinae (Gentianaceae)

Macrosynteny analysis shows the absence of ancient whole-genome duplication in lepidopteran insects

(2019) Yoichiro Nakatani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations

(2019) Yongzhi Yang et al.   BMC BIOINFORMATICS

Fine-Tuning the Expression of Duplicate Genes by Translational Regulation in Arabidopsis and Maize

(2019) Sishuo Wang et al.   Frontiers in Plant Science

Genomic insight into the ‘Sky Islands’ species diversification in a mountainous biodiversity hotspot

(2019) Dan Zhang et al.   Journal of Systematics and Evolution

Phylogenomics identifies an ancestral burst of gene duplications predating the diversification of aphidomorpha

(2019) Irene Julca et al.   MOLECULAR BIOLOGY AND EVOLUTION

One thousand plant transcriptomes and the phylogenomics of green plants

(2019)   NATURE

Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)

(2018) Matthew B. Parks et al.   AMERICAN JOURNAL OF BOTANY

Comparative Chloroplast Genome Analyses of Species in Gentiana section Cruciata (Gentianaceae) and the Development of Authentication Markers

(2018) Tao Zhou et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Shifts in plant distributions in response to climate warming in a biodiversity hotspot, the Hengduan Mountains

(2018) Qianlong Liang et al.   JOURNAL OF BIOGEOGRAPHY

Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval

(2018) Liming Cai et al.   NEW PHYTOLOGIST

Multiple large-scale gene and genome duplications during the evolution of hexapods

(2018) Zheng Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Practical considerations for plant phylogenomics

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

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

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

Analyses of genome-scale variation reveal divergence of two Sinalliaria species (Brassicaceae) with continuous but limited gene flow

(2018) Tian-Jing Wang et al.   Journal of Systematics and Evolution

Nuclear SSR markers are superior to DNA barcodes for identification of closely related Rhododendron species on the same mountain

(2018) Ji Wang et al.   Journal of Systematics and Evolution

Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses

(2018) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Interspecific hybridization causes long-term phylogenetic discordance between nuclear and mitochondrial genomes in freshwater fishes

(2017) Graham P. Wallis et al.   MOLECULAR ECOLOGY

Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events

(2017) Ya Yang et al.   NEW PHYTOLOGIST

Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events

(2017) W. C. Thomas Gregg et al.   SYSTEMATIC BIOLOGY

Has the connection between polyploidy and diversification actually been tested?

(2016) Elizabeth A Kellogg   CURRENT OPINION IN PLANT BIOLOGY

TransRate: reference-free quality assessment of de novo transcriptome assemblies

(2016) Richard Smith-Unna et al.   GENOME RESEARCH

Out-of-Tibet: the spatio-temporal evolution ofGentiana(Gentianaceae)

(2016) Adrien Favre et al.   JOURNAL OF BIOGEOGRAPHY

The Use of DNA Barcoding on Recently Diverged Species in the Genus Gentiana (Gentianaceae) in China

(2016) Juan Liu et al.   PLoS One

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Back to Gondwanaland: can ancient vicariance explain (some) Indian Ocean disjunct plant distributions?: Figure 1.

(2015) Michael D. Pirie et al.   Biology Letters

Explosive Tandem and Segmental Duplications of Multigenic Families in Eucalyptus grandis

(2015) Qiang Li et al.   Genome Biology and Evolution

Dispersal routes between biodiversity hotspots in Asia: the case of the mountain genus Tripterospermum (Gentianinae, Gentianaceae) and its close relatives

(2015) Sabine Matuszak et al.   JOURNAL OF BIOGEOGRAPHY

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)

(2015) Peter A. Hosner et al.   MOLECULAR BIOLOGY AND EVOLUTION

RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography

(2015) Yan Yu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications

(2015) David C. Tank et al.   NEW PHYTOLOGIST

Early genome duplications in conifers and other seed plants

(2015) Z. Li et al.   Science Advances

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan biotas

(2014) Adrien Favre et al.   BIOLOGICAL REVIEWS

Causes, consequences and solutions of phylogenetic incongruence

(2014) A. Som   BRIEFINGS IN BIOINFORMATICS

Genomic evidence for adaptation by gene duplication

(2014) Wenfeng Qian et al.   GENOME RESEARCH

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

(2014) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Integrated Syntenic and Phylogenomic Analyses Reveal an Ancient Genome Duplication in Monocots

(2014) Yuannian Jiao et al.   PLANT CELL

Allopolyploidy, diversification, and the Miocene grassland expansion

(2014) Matt C. Estep et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two new genera of Gentianinae (Gentianaceae): Sinogentiana and Kuepferia supported by molecular phylogenetic evidence

(2014) Adrien Favre et al.   TAXON

Phylogenetic relationships of the mycoheterotrophic genus Voyria and the implications for the biogeographic history of Gentianaceae

(2013) Vincent S.F.T. Merckx et al.   AMERICAN JOURNAL OF BOTANY

Gene duplication as a driver of plant morphogenetic evolution

(2013) Stefan A Rensing   CURRENT OPINION IN PLANT BIOLOGY

Gene duplication as a major force in evolution

(2013) SANTOSHKUMAR MAGADUM et al.   JOURNAL OF GENETICS

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

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

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods

(2013) Thi-Hau Nguyen et al.   PLoS One

Outcomes of Extensive Hybridization and Introgression in Epidendrum (Orchidaceae): Can We Rely on Species Boundaries?

(2013) Yesenia Vega et al.   PLoS One

Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem

(2012) Pawel Górecki et al.   BMC BIOINFORMATICS

Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence

(2012) Ruchi Chaudhary et al.   BMC BIOINFORMATICS

Profiling of gene duplication patterns of sequenced teleost genomes: evidence for rapid lineage-specific genome expansion mediated by recent tandem duplications

(2012) Jianguo Lu et al.   BMC GENOMICS

Rarely successful polyploids and their legacy in plant genomes

(2012) Nils Arrigo et al.   CURRENT OPINION IN PLANT BIOLOGY

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

(2012) Andre J. Aberer et al.   SYSTEMATIC BIOLOGY

Life at the extreme: lessons from the genome

(2012) Dong-Ha Oh et al.   GENOME BIOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The Ecoresponsive Genome of Daphnia pulex

(2011) J. K. Colbourne et al.   SCIENCE

Recently Formed Polyploid Plants Diversify at Lower Rates

(2011) I. Mayrose et al.   SCIENCE

Patterns and causes of incongruence between plastid and nuclear Senecioneae (Asteraceae) phylogenies

(2010) Pieter B. Pelser et al.   AMERICAN JOURNAL OF BOTANY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting

(2009) Simon Joly et al.   AMERICAN NATURALIST

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants

(2009) J.G. Burleigh et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Gene duplication and evolutionary novelty in plants

(2009) Lex E. Flagel et al.   NEW PHYTOLOGIST

Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event

(2009) J. A. Fawcett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY