Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism

Expression of the β-glucosidase genePgβglu-1underpins natural resistance of white spruce against spruce budworm

(2015) Melissa H. Mageroy et al.   PLANT JOURNAL

DIDA: Distributed Indexing Dispatched Alignment

(2015) Hamid Mohamadi et al.   PLoS One

Changes in tracheid and ray traits in fire scars of North American conifers and their ecophysiological implications

(2014) Estelle Arbellay et al.   ANNALS OF BOTANY

Molecular cloning and characterization of a cytochrome P450 taxoid 9á-hydroxylase in Ginkgo biloba cells

(2014) Nan Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size

(2014) Juliana Stival Sena et al.   BMC PLANT BIOLOGY

Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation

(2014) J. L. Wegrzyn et al.   GENETICS

Sequencing and Assembly of the 22-Gb Loblolly Pine Genome

(2014) A. Zimin et al.   GENETICS

Plasticity and Evolution of (+)-3-Carene Synthase and (−)-Sabinene Synthase Functions of a Sitka Spruce Monoterpene Synthase Gene Family Associated with Weevil Resistance

(2014) Christopher R. Roach et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-wide admixture and ecological niche modelling reveal the maintenance of species boundaries despite long history of interspecific gene flow

(2014) Amanda R. De La Torre et al.   MOLECULAR ECOLOGY

Cloning and characterization of chitinases from interior spruce and lodgepole pine

(2014) N. Kolosova et al.   PHYTOCHEMISTRY

Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes

(2014) MeiYee Law et al.   PLANT PHYSIOLOGY

Flavan-3-ols in Norway Spruce: Biosynthesis, Accumulation, and Function in Response to Attack by the Bark Beetle-Associated Fungus Ceratocystis polonica

(2014) A. Hammerbacher et al.   PLANT PHYSIOLOGY

Insights into Conifer Giga-Genomes

(2014) A. R. De La Torre et al.   PLANT PHYSIOLOGY

Species-Specific Expansion and Molecular Evolution of the 3-hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Plants

(2014) Wei Li et al.   PLoS One

Investigation of terpene diversification across multiple sequenced plant genomes

(2014) Alexander M. Boutanaev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Signatures of Specialized Metabolism in Plants

(2014) L. Chae et al.   SCIENCE

Fine-scale environmental variation contributes to introgression in a three-species spruce hybrid complex

(2014) Jill A. Hamilton et al.   Tree Genetics & Genomes

Distinct evolutionary strategies in the GGPPS family from plants

(2014) Diana Coman et al.   Frontiers in Plant Science

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

(2014) David B Neale et al.   GENOME BIOLOGY

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

(2013) Inanc Birol et al.   BIOINFORMATICS

Transcriptome resources and functional characterization of monoterpene synthases for two host species of the mountain pine beetle, lodgepole pine (Pinus contorta) and jack pine (Pinus banksiana)

(2013) Dawn E Hall et al.   BMC PLANT BIOLOGY

The evolution of phenylpropanoid metabolism in the green lineage

(2013) Takayuki Tohge et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

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

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

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

(2013) Ignazio Verde et al.   NATURE GENETICS

Activities at the Universal Protein Resource (UniProt)

(2013)   NUCLEIC ACIDS RESEARCH

Plant P450s as versatile drivers for evolution of species-specific chemical diversity

(2013) B. Hamberger et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Overexpression of an Isoprenyl Diphosphate Synthase in Spruce Leads to Unexpected Terpene Diversion Products That Function in Plant Defense

(2013) R. Nagel et al.   PLANT PHYSIOLOGY

A Common Fungal Associate of the Spruce Bark Beetle Metabolizes the Stilbene Defenses of Norway Spruce

(2013) A. Hammerbacher et al.   PLANT PHYSIOLOGY

Gene Discovery of Modular Diterpene Metabolism in Nonmodel Systems

(2013) P. Zerbe et al.   PLANT PHYSIOLOGY

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences

(2013) Jill L. Wegrzyn et al.   PLoS One

Recent burning of boreal forests exceeds fire regime limits of the past 10,000 years

(2013) R. Kelly et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Impacts of Diversification of Cytochrome P450 on Plant Metabolism

(2012) Masaharu Mizutani   BIOLOGICAL & PHARMACEUTICAL BULLETIN

Exploiting sparseness in de novo genome assembly

(2012) Chengxi Ye et al.   BMC BIOINFORMATICS

A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers

(2012) Nathalie Pavy et al.   BMC BIOLOGY

ISOPRENE SYNTHASE GENES FORM A MONOPHYLETIC CLADE OF ACYCLIC TERPENE SYNTHASES IN THE TPS-B TERPENE SYNTHASE FAMILY

(2012) Thomas D. Sharkey et al.   EVOLUTION

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

(2012) M. Lohse et al.   NUCLEIC ACIDS RESEARCH

Evolution of Conifer Diterpene Synthases: Diterpene Resin Acid Biosynthesis in Lodgepole Pine and Jack Pine Involves Monofunctional and Bifunctional Diterpene Synthases

(2012) D. E. Hall et al.   PLANT PHYSIOLOGY

Succinct data structures for assembling large genomes

(2011) Thomas C. Conway et al.   BIOINFORMATICS

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments

(2011) Betty Pelgas et al.   BMC GENOMICS

Defense mechanisms against herbivory in Picea: sequence evolution and expression regulation of gene family members in the phenylpropanoid pathway

(2011) Ilga Porth et al.   BMC GENOMICS

Transcriptome mining, functional characterization, and phylogeny of a large terpene synthase gene family in spruce (Picea spp.)

(2011) Christopher I Keeling et al.   BMC PLANT BIOLOGY

Phenolic compounds that confer resistance to spruce budworm

(2011) Nathalie Delvas et al.   ENTOMOLOGIA EXPERIMENTALIS ET APPLICATA

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

Biochemical Characterization and Homology Modeling of Methylbutenol Synthase and Implications for Understanding Hemiterpene Synthase Evolution in Plants

(2011) Dennis W. Gray et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Primary Diterpene Synthase Products ofPicea abiesLevopimaradiene/Abietadiene Synthase (PaLAS) Are Epimers of a Thermally Unstable Diterpenol

(2011) Christopher I. Keeling et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A P450-centric view of plant evolution

(2011) David Nelson et al.   PLANT JOURNAL

The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom

(2011) Feng Chen et al.   PLANT JOURNAL

Biosynthesis of the Major Tetrahydroxystilbenes in Spruce, Astringin and Isorhapontin, Proceeds via Resveratrol and Is Enhanced by Fungal Infection

(2011) A. Hammerbacher et al.   PLANT PHYSIOLOGY

A White Spruce Gene Catalog for Conifer Genome Analyses

(2011) Philippe Rigault et al.   PLANT PHYSIOLOGY

Evolution of Diterpene Metabolism: Sitka Spruce CYP720B4 Catalyzes Multiple Oxidations in Resin Acid Biosynthesis of Conifer Defense against Insects

(2011) B. Hamberger et al.   PLANT PHYSIOLOGY

A raison d’être for two distinct pathways in the early steps of plant isoprenoid biosynthesis?

(2011) Andréa Hemmerlin et al.   PROGRESS IN LIPID RESEARCH

Efficient construction of an assembly string graph using the FM-index

(2010) J. T. Simpson et al.   BIOINFORMATICS

Functional Annotation, Genome Organization and Phylogeny of the Grapevine (Vitis vinifera) Terpene Synthase Gene Family Based on Genome Assembly, FLcDNA Cloning, and Enzyme Assays

(2010) Diane M Martin et al.   BMC PLANT BIOLOGY

Cytochrome P450 metabolizing fatty acids in plants: characterization and physiological roles

(2010) Franck Pinot et al.   FEBS Journal

Phylogeographic History of White Spruce During the Last Glacial Maximum: Uncovering Cryptic Refugia

(2010) Lynn L. Anderson et al.   JOURNAL OF HEREDITY

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Identification and Functional Characterization of Monofunctional ent-Copalyl Diphosphate and ent-Kaurene Synthases in White Spruce Reveal Different Patterns for Diterpene Synthase Evolution for Primary and Secondary Metabolism in Gymnosperms

(2010) C. I. Keeling et al.   PLANT PHYSIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Discordant mtDNA and cpDNA phylogenies indicate geographic speciation and reticulation as driving factors for the diversification of the genus Picea

(2010) Marie Bouillé et al.   Tree Genetics & Genomes

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome

(2009) Björn Hamberger et al.   BMC PLANT BIOLOGY

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Characterization of 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate synthase (HDS) gene from Ginkgo biloba

(2009) Sang-Min Kim et al.   MOLECULAR BIOLOGY REPORTS

A Bifunctional Geranyl and Geranylgeranyl Diphosphate Synthase Is Involved in Terpene Oleoresin Formation in Picea abies

(2009) A. Schmidt et al.   PLANT PHYSIOLOGY

A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis)

(2008) Steven G Ralph et al.   BMC GENOMICS

Genetic consequences of glacial survival and postglacial colonization in Norway spruce: combined analysis of mitochondrial DNA and fossil pollen

(2008) MARI METTE TOLLEFSRUD et al.   MOLECULAR ECOLOGY

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Two copies of 4-(cytidine 5′-diphospho)-2-C-methyl-d-erythritol kinase (CMK) gene in Ginkgo biloba: molecular cloning and functional characterization

(2008) Sang-Min Kim et al.   PLANTA

Does egg deposition by herbivorous pine sawflies affect transcription of sesquiterpene synthases in pine?

(2008) Diana Köpke et al.   PLANTA

Functional plasticity of paralogous diterpene synthases involved in conifer defense

(2008) C. I. Keeling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cloning and characterization of two different types of geranyl diphosphate synthases from Norway spruce (Picea abies)

(2007) Axel Schmidt et al.   PHYTOCHEMISTRY