Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism
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Title
Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism
Authors
Keywords
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Journal
PLANT JOURNAL
Volume 83, Issue 2, Pages 189-212
Publisher
Wiley
Online
2015-05-28
DOI
10.1111/tpj.12886
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Note: Only part of the references are listed.- Expression of the β-glucosidase genePgβglu-1underpins natural resistance of white spruce against spruce budworm
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- (2014) J. L. Wegrzyn et al. GENETICS
- Sequencing and Assembly of the 22-Gb Loblolly Pine Genome
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- (2014) Amanda R. De La Torre et al. MOLECULAR ECOLOGY
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- (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
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- (2014) Jill A. Hamilton et al. Tree Genetics & Genomes
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- (2014) David B Neale et al. GENOME BIOLOGY
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- The evolution of phenylpropanoid metabolism in the green lineage
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- 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
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- (2013) A. Hammerbacher et al. PLANT PHYSIOLOGY
- Gene Discovery of Modular Diterpene Metabolism in Nonmodel Systems
- (2013) P. Zerbe et al. PLANT PHYSIOLOGY
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- (2010) Gordon Robertson et al. NATURE METHODS
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- (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
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- Fast and accurate short read alignment with Burrows-Wheeler transform
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- 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
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- InterPro: the integrative protein signature database
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- 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
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