The Apostasia genome and the evolution of orchids

The evolutionary significance of polyploidy

(2017) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

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

Orchid historical biogeography, diversification, Antarctica and the paradox of orchid dispersal

(2016) Thomas J. Givnish et al.   JOURNAL OF BIOGEOGRAPHY

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

(2016) Jeanine L. Olsen et al.   NATURE

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

A hybrid approach for de novo human genome sequence assembly and phasing

(2016) Yulia Mostovoy et al.   NATURE METHODS

The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution

(2016) Guo-Qiang Zhang et al.   Scientific Reports

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The pineapple genome and the evolution of CAM photosynthesis

(2015) Ray Ming et al.   NATURE GENETICS

Orchid phylogenomics and multiple drivers of their extraordinary diversification

(2015) Thomas J. Givnish et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

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

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

(2014) Andrew Adey et al.   GENOME RESEARCH

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

(2014) Kevin Vanneste et al.   GENOME RESEARCH

The genome sequence of the orchid Phalaenopsis equestris

(2014) Jing Cai et al.   NATURE GENETICS

The velamen protects photosynthetic orchid roots against UV-B damage, and a large dated phylogeny implies multiple gains and losses of this function during the Cenozoic

(2014) Guillaume Chomicki et al.   NEW PHYTOLOGIST

Flower development ofPhalaenopsisorchid involves functionally divergentSEPALLATA-like genes

(2014) Zhao-Jun Pan et al.   NEW PHYTOLOGIST

SMART: recent updates, new developments and status in 2015

(2014) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Yuannian Jiao et al.   PLANT CELL

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Land plant evolutionary timeline: Gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates

(2013) Susana Magallón et al.   AMERICAN JOURNAL OF BOTANY

De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana

(2013) Stephen M Gross et al.   BMC GENOMICS

Genome size variation in Orchidaceae subfamily Apostasioideae: filling the phylogenetic gap

(2013) Jana Jersáková et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Architecture and evolution of a minute plant genome

(2013) Enrique Ibarra-Laclette et al.   NATURE

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

Aerial roots of epiphytic orchids: the velamen radicum and its role in water and nutrient uptake

(2013) Gerhard Zotz et al.   OECOLOGIA

Functional Conservation of MIKC*-Type MADS Box Genes in Arabidopsis and Rice Pollen Maturation

(2013) Y. Liu et al.   PLANT CELL

Transcriptome sequencing to produce SNP-based genetic maps of onion

(2013) J. Duangjit et al.   THEORETICAL AND APPLIED GENETICS

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Inference of Genome Duplications from Age Distributions Revisited

(2012) Kevin Vanneste et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

(2012) Angélique D’Hont et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales

(2012) Z. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists

(2011) Jan Fostier et al.   BIOINFORMATICS

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

How MIKC* MADS-Box Genes Originated and Evidence for Their Conserved Function Throughout the Evolution of Vascular Plant Gametophytes

(2011) M. Kwantes et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

(2011) Eman K Al-Dous et al.   NATURE BIOTECHNOLOGY

Establishing a time-scale for plant evolution

(2011) John T. Clarke et al.   NEW PHYTOLOGIST

i-ADHoRe 3.0—fast and sensitive detection of genomic homology in extremely large data sets

(2011) Sebastian Proost et al.   NUCLEIC ACIDS RESEARCH

The Emerging Importance of Type I MADS Box Transcription Factors for Plant Reproduction

(2011) S. Masiero et al.   PLANT CELL

Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation

(2011) Joseph Heled et al.   SYSTEMATIC BIOLOGY

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants

(2010) S. A. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana

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

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Why are orchid flowers so diverse? Reduction of evolutionary constraints by paralogues of class B floral homeotic genes

(2009) Mariana Mondragón-Palomino et al.   ANNALS OF BOTANY

Genome size diversity in orchids: consequences and evolution

(2009) I. J. Leitch et al.   ANNALS OF BOTANY

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

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

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

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

(2009) G. Ostlund et al.   NUCLEIC ACIDS RESEARCH

Orchids

(2008) David L. Roberts et al.   CURRENT BIOLOGY

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

An AGAMOUS-Related MADS-Box Gene, XAL1 (AGL12), Regulates Root Meristem Cell Proliferation and Flowering Transition in Arabidopsis

(2008) R. Tapia-Lopez et al.   PLANT PHYSIOLOGY