Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events

Diverse genome organization following 13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns of gene retention

(2017) Terezie Mandáková et al.   PLANT JOURNAL

Genome of wild olive and the evolution of oil biosynthesis

(2017) Turgay Unver et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

(2016)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication

(2016) Luis M. Corrochano et al.   CURRENT BIOLOGY

Ancient WGD events as drivers of key innovations in angiosperms

(2016) Pamela S Soltis et al.   CURRENT OPINION IN PLANT BIOLOGY

Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life

(2016) Antonio Figueras et al.   DNA RESEARCH

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

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

A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives

(2016) Gautier Sarah et al.   Molecular Ecology Resources

Genome sequence and genetic diversity of European ash trees

(2016) Elizabeth S. A. Sollars et al.   NATURE

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

(2016) Massimo Iorizzo et al.   NATURE GENETICS

Double trouble: taxonomy and definitions of polyploidy

(2016) Jeff J. Doyle et al.   NEW PHYTOLOGIST

Homoeologs: What Are They and How Do We Infer Them?

(2016) Natasha M. Glover et al.   TRENDS IN PLANT SCIENCE

Genome sequence of the olive tree, Olea europaea

(2016) Fernando Cruz et al.   GigaScience

Polyploidy and genome evolution in plants

(2015) Pamela S Soltis et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Tree of Life Reveals Clock-Like Speciation and Diversification

(2015) S. Blair Hedges et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcriptomic Analysis of Flower Blooming in Jasminum sambac through De Novo RNA Sequencing

(2015) Yong-Hua Li et al.   MOLECULES

On the relative abundance of autopolyploids and allopolyploids

(2015) Michael S. Barker et al.   NEW PHYTOLOGIST

TheSolanum commersoniiGenome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

(2015) Riccardo Aversano et al.   PLANT CELL

The Tree of Life: Evolution and Classification of Living Organisms.—Edited by Pablo Vargas and Rafael Zardoya; translated by Anne Louise.

(2015) David A. Morrison   SYSTEMATIC BIOLOGY

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage

(2015) Marina Marcet-Houben et al.   PLOS BIOLOGY

The radish genome and comprehensive gene expression profile of tuberous root formation and development

(2015) Yuki Mitsui et al.   Scientific Reports

Phylogeny of Lamiidae

(2014) Nancy F. Refulio-Rodriguez et al.   AMERICAN JOURNAL OF BOTANY

Doubling down on genomes: Polyploidy and crop plants

(2014) Simon Renny-Byfield et al.   AMERICAN JOURNAL OF BOTANY

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution

(2014) Kevin Vanneste et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ancient hybridizations among the ancestral genomes of bread wheat

(2014) T. Marcussen et al.   SCIENCE

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

(2014) F. Denoeud et al.   SCIENCE

Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina)

(2014) Volker U. Schwartze et al.   PLoS Genetics

Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis

(2014) Linhai Wang et al.   GENOME BIOLOGY

Two Evolutionarily Distinct Classes of Paleopolyploidy

(2013) Olivier Garsmeur et al.   MOLECULAR BIOLOGY AND EVOLUTION

Architecture and evolution of a minute plant genome

(2013) Enrique Ibarra-Laclette et al.   NATURE

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

(2013) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing

(2013) U. Hellsten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adding unaligned sequences into an existing alignment using MAFFT and LAST

(2012) Kazutaka Katoh et al.   BIOINFORMATICS

Polyploidy and its effect on evolutionary success: old questions revisited with new tools

(2012) A Madlung   HEREDITY

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Assigning duplication events to relative temporal scales in genome-wide studies

(2010) J. Huerta-Cepas et al.   BIOINFORMATICS

Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences

(2010) Bastian Schäferhoff et al.   BMC EVOLUTIONARY BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

(2010) J. Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Phylogenetics of Olea (Oleaceae) based on plastid and nuclear ribosomal DNA sequences: Tertiary climatic shifts and lineage differentiation times

(2009) Guillaume Besnard et al.   ANNALS OF BOTANY

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The frequency of polyploid speciation in vascular plants

(2009) T. E. Wood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony

(2008) A. Wehe et al.   BIOINFORMATICS

How to usefully compare homologous plant genes and chromosomes as DNA sequences

(2008) Eric Lyons et al.   PLANT JOURNAL