A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae

Evolution at the tips: Asclepias phylogenomics and new perspectives on leaf surfaces

(2018) Mark Fishbein et al.   AMERICAN JOURNAL OF BOTANY

Evolution of pyrrolizidine alkaloid biosynthesis in Apocynaceae: revisiting the defence de-escalation hypothesis

(2018) Tatyana Livshultz et al.   NEW PHYTOLOGIST

Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea , a Producer of Anticancer and Antimalarial Cardenolides

(2017) Genevieve M. Hoopes et al.   G3-Genes Genomes Genetics

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

(2016) Massimo Iorizzo et al.   NATURE GENETICS

Transcriptome and Metabolite analysis reveal candidate genes of the cardiac glycoside biosynthetic pathway from Calotropis procera

(2016) Akansha Pandey et al.   Scientific Reports

Genome sequence of the olive tree, Olea europaea

(2016) Fernando Cruz et al.   GigaScience

The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae

(2016) Jamal S. M. Sabir et al.   Scientific Reports

Development and evolution of extreme synorganization in angiosperm flowers and diversity: a comparison of Apocynaceae and Orchidaceae

(2015) Peter K. Endress   ANNALS OF BOTANY

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Identification of a Fungal 1,8-Cineole Synthase fromHypoxylonsp. with Specificity Determinants in Common with the Plant Synthases

(2015) Jeffrey J. Shaw et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Iridoid Synthase Activity Is Common among the Plant Progesterone 5β-Reductase Family

(2015) Jennifer Munkert et al.   Molecular Plant

Genomic Characterization Reveals Insights Into Patulin Biosynthesis and Pathogenicity in Penicillium Species

(2015) Boqiang Li et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Genome-guided investigation of plant natural product biosynthesis

(2015) Franziska Kellner et al.   PLANT JOURNAL

A Revised Time Tree of the Asterids: Establishing a Temporal Framework For Evolutionary Studies of the Coffee Family (Rubiaceae)

(2015) Niklas Wikström et al.   PLoS One

The butterfly plant arms-race escalated by gene and genome duplications

(2015) Patrick P. Edger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1

(2015) Andrea Firrincieli et al.   Frontiers in Microbiology

Cysteine Protease Profiles of the Medicinal Plant Calotropis procera R. Br. Revealed by De Novo Transcriptome Analysis

(2015) Chang Woo Kwon et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Complete sequences of organelle genomes from the medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids

(2014) Seongjun Park et al.   BMC GENOMICS

The temporal foliar transcriptome of the perennial C3 desert plant Rhazya stricta in its natural environment

(2014) Steven A Yates et al.   BMC PLANT BIOLOGY

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

PLAZA 3.0: an access point for plant comparative genomics

(2014) Sebastian Proost et al.   NUCLEIC ACIDS RESEARCH

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Polyploidy-associated genome modifications during land plant evolution

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

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

(2014) Robert Riley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) F. Denoeud et al.   SCIENCE

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

(2014) James F. Denton et al.   PLoS Computational Biology

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

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

Draft genome sequence of the rubber tree Hevea brasiliensis

(2013) Ahmad Yamin Abdul Rahman et al.   BMC GENOMICS

Horizontal Transfer of DNA from the Mitochondrial to the Plastid Genome and Its Subsequent Evolution in Milkweeds (Apocynaceae)

(2013) Shannon C.K. Straub et al.   Genome Biology and Evolution

Transcriptome analysis based on next-generation sequencing of non-model plants producing specialized metabolites of biotechnological interest

(2013) Mei Xiao et al.   JOURNAL OF BIOTECHNOLOGY

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

Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

(2013) MARC LOHSE et al.   PLANT CELL AND ENVIRONMENT

TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

(2013) Michiel Van Bel et al.   GENOME BIOLOGY

New reports of nuclear DNA content for 407 vascular plant taxa from the United States

(2012) Chengke Bai et al.   ANNALS OF BOTANY

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

(2012) M. Kearse et al.   BIOINFORMATICS

Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer

(2012) Jinnan Hu et al.   BMC GENOMICS

Sequencing of Cladosporium sphaerospermum, a Dematiaceous Fungus Isolated from Blood Culture

(2012) Kee Peng Ng et al.   EUKARYOTIC CELL

Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers

(2012) Nian Wang et al.   MOLECULAR ECOLOGY

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A multivariate analysis of variation in genome size and endoreduplication in angiosperms reveals strong phylogenetic signal and association with phenotypic traits

(2012) Jillian D. Bainard et al.   NEW PHYTOLOGIST

Toxic cardenolides: chemical ecology and coevolution of specialized plant-herbivore interactions

(2012) Anurag A. Agrawal et al.   NEW PHYTOLOGIST

Development of Transcriptomic Resources for Interrogating the Biosynthesis of Monoterpene Indole Alkaloids in Medicinal Plant Species

(2012) Elsa Góngora-Castillo et al.   PLoS One

The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

(2012) D. Floudas et al.   SCIENCE

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

(2012) Robin A. Ohm et al.   PLoS Pathogens

BadiRate: estimating family turnover rates by likelihood-based methods

(2011) P. Librado et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

An automated homology-based approach for identifying transposable elements

(2011) Ryan C Kennedy et al.   BMC BIOINFORMATICS

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

(2011) Shannon CK Straub et al.   BMC GENOMICS

The Monarch Butterfly Genome Yields Insights into Long-Distance Migration

(2011) Shuai Zhan et al.   CELL

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform

(2011) M. Van Bel et al.   PLANT PHYSIOLOGY

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes

(2011) Maria Anisimova et al.   SYSTEMATIC BIOLOGY

Phylogenetic Relationships of Asclepias (Apocynaceae) Inferred from Non-coding Chloroplast DNA Sequences

(2011) Mark Fishbein et al.   SYSTEMATIC BOTANY

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

(2011) Joelle Amselem et al.   PLoS Genetics

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Direct and indirect root defences of milkweed (Asclepias syriaca): trophic cascades, trade-offs and novel methods for studying subterranean herbivory

(2010) Sergio Rasmann et al.   JOURNAL OF ECOLOGY

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Highly conserved progesterone 5β-reductase genes (P5βR) from 5β-cardenolide-free and 5β-cardenolide-producing angiosperms

(2010) Peter Bauer et al.   PHYTOCHEMISTRY

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Cardenolides, induced responses, and interactions between above- and belowground herbivores of milkweed (Asclepiasspp.)

(2009) Sergio Rasmann et al.   ECOLOGY

Digitalis purpurea P5βR2, encoding steroid 5β-reductase, is a novel defense-related gene involved in cardenolide biosynthesis

(2009) Pedro Pérez-Bermúdez et al.   NEW PHYTOLOGIST

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

(2009) S. Proost et al.   PLANT CELL

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

(2008) Diego Martinez et al.   NATURE BIOTECHNOLOGY

Phylogenetic escalation and decline of plant defense strategies

(2008) A. A. Agrawal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY