Forest tree genomics: 10 achievements from the past 10 years and future prospects

Aspen pectate lyase PtxtPL1-27 mobilizes matrix polysaccharides from woody tissues and improves saccharification yield

(2014) Ajaya K Biswal et al.   Biotechnology for Biofuels

Analysis of the leaf methylomes of parents and their hybrids provides new insight into hybrid vigor in Populus deltoides

(2014) Ming Gao et al.   BMC GENETICS

Single-base-resolution methylomes of populus trichocarpa reveal the association between DNA methylation and drought stress

(2014) Dan Liang et al.   BMC GENETICS

Plant traits and taxonomy drive host associations in tropical phyllosphere fungal communities

(2014) Steven W. Kembel et al.   Botany

The emerging field of geogenomics: Constraining geological problems with genetic data

(2014) Paul A. Baker et al.   EARTH-SCIENCE REVIEWS

Sequencing and Assembly of the 22-Gb Loblolly Pine Genome

(2014) A. Zimin et al.   GENETICS

Accuracy of genomic selection models in a large population of open-pollinated families in white spruce

(2014) J Beaulieu et al.   HEREDITY

Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars

(2014) Miklós Bálint et al.   MOLECULAR ECOLOGY

Congruent phylogeographical patterns of eight tree species in Atlantic Central Africa provide insights into the past dynamics of forest cover

(2014) G. Dauby et al.   MOLECULAR ECOLOGY

Detecting short spatial scale local adaptation and epistatic selection in climate-related candidate genes in European beech (Fagus sylvatica) populations

(2014) Katalin Csilléry et al.   MOLECULAR ECOLOGY

Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

(2014) Luke M Evans et al.   NATURE GENETICS

Microbial genome-enabled insights into plant–microorganism interactions

(2014) David S. Guttman et al.   NATURE REVIEWS GENETICS

Towards a holistic understanding of the beneficial interactions across thePopulusmicrobiome

(2014) Stéphane Hacquard et al.   NEW PHYTOLOGIST

Early molecular events involved inPinus pinasterAit. somatic embryo development under reduced water availability: transcriptomic and proteomic analyses

(2014) Alexandre Morel et al.   PHYSIOLOGIA PLANTARUM

Adventitious root formation in tree species: involvement of transcription factors

(2014) Valérie Legué et al.   PHYSIOLOGIA PLANTARUM

Complete Proteomic-Based Enzyme Reaction and Inhibition Kinetics Reveal How Monolignol Biosynthetic Enzyme Families Affect Metabolic Flux and Lignin inPopulus trichocarpa

(2014) Jack P. Wang et al.   PLANT CELL

Cotyledonary somatic embryos of Pinus pinaster Ait. most closely resemble fresh, maturing cotyledonary zygotic embryos: biological, carbohydrate and proteomic analyses

(2014) Alexandre Morel et al.   PLANTA

Comparative Phylogeography in Rainforest Trees from Lower Guinea, Africa

(2014) Myriam Heuertz et al.   PLoS One

Oak Root Response to Ectomycorrhizal Symbiosis Establishment: RNA-Seq Derived Transcript Identification and Expression Profiling

(2014) Mónica Sebastiana et al.   PLoS One

Leaf and Root-Associated Fungal Assemblages Do Not Follow Similar Elevational Diversity Patterns

(2014) Aurore Coince et al.   PLoS One

Patterns of Nucleotide Diversity at Photoperiod Related Genes in Norway Spruce [Picea abies (L.) Karst.]

(2014) Thomas Källman et al.   PLoS One

Genome-Wide Characterization and Expression Profiling of the AUXIN RESPONSE FACTOR (ARF) Gene Family in Eucalyptus grandis

(2014) Hong Yu et al.   PLoS One

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest

(2014) S. W. Kembel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping the Epigenetic Basis of Complex Traits

(2014) S. Cortijo et al.   SCIENCE

Potential for marker-assisted selection for forest tree breeding: lessons from 20 years of MAS in crops

(2014) H. Muranty et al.   Tree Genetics & Genomes

Temperature-dependent differential transcriptomes during formation of an epigenetic memory in Norway spruce embryogenesis

(2014) Igor A. Yakovlev et al.   Tree Genetics & Genomes

Molecular and physiological responses to abiotic stress in forest trees and their relevance to tree improvement

(2014) A. Harfouche et al.   TREE PHYSIOLOGY

Get your high-quality low-cost genome sequence

(2014) Luigi Faino et al.   TRENDS IN PLANT SCIENCE

Genome-wide association study of Arabidopsis thaliana leaf microbial community

(2014) Matthew W. Horton et al.   Nature Communications

Regulation of secondary cell wall biosynthesis by poplar R2R3 MYB transcription factor PtrMYB152 in Arabidopsis

(2014) Shucai Wang et al.   Scientific Reports

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

(2014) David B Neale et al.   GENOME BIOLOGY

Fire structures pine serotiny at different scales

(2013) Ana Hernández-Serrano et al.   AMERICAN JOURNAL OF BOTANY

Highly local environmental variability promotes intrapopulation divergence of quantitative traits: an example from tropical rain forest trees

(2013) Louise Brousseau et al.   ANNALS OF BOTANY

Plant Protein Interactomes

(2013) Pascal Braun et al.   Annual Review of Plant Biology

The world within: Quantifying the determinants and outcomes of a host's microbiome

(2013) Elizabeth T. Borer et al.   BASIC AND APPLIED ECOLOGY

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

(2013) Inanc Birol et al.   BIOINFORMATICS

High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination

(2013) Emilie Chancerel et al.   BMC BIOLOGY

Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS

(2013) Eli Rodgers-Melnick et al.   BMC GENOMICS

Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola

(2013) Jun-Jun Liu et al.   BMC GENOMICS

Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing

(2013) Saneyoshi Ueno et al.   BMC GENOMICS

Potential link between biotic defense activation and recalcitrance to induction of somatic embryogenesis in shoot primordia from adult trees of white spruce (Picea glauca)

(2013) Robert G Rutledge et al.   BMC PLANT BIOLOGY

Transcriptomic analysis highlights epigenetic and transcriptional regulation during zygotic embryo development of Pinus pinaster

(2013) José J de Vega-Bartol et al.   BMC PLANT BIOLOGY

Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa

(2013) Kelly Vining et al.   BMC PLANT BIOLOGY

Proteomic Analysis of Two Hybrid Aspen Clones Subjected to Long-term Chronic Ozone Exposure in Open Field

(2013) Vivek Pandey et al.   Current Proteomics

Next-generation technologies and data analytical approaches for epigenomics

(2013) Klaas Mensaert et al.   ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

Below-ground fine-scale distribution and soil versus fine root detection of fungal and soil oomycete communities in a French beech forest

(2013) Aurore Coince et al.   Fungal Ecology

The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa

(2013) K B Budde et al.   HEREDITY

Post-GWAS: where next? More samples, more SNPs or more biology?

(2013) P Marjoram et al.   HEREDITY

Molecular regulation of plant somatic embryogenesis

(2013) Mohamed Elhiti et al.   IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-PLANT

Molecular divergence in tropical tree populations occupying environmental mosaics

(2013) D. Audigeos et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Proteomics of model and crop plant species: Status, current limitations and strategic advances for crop improvement

(2013) Hervé Vanderschuren et al.   Journal of Proteomics

Model selection as a tool for phylogeographic inference: an example from the willowSalix melanopsis

(2013) Bryan C. Carstens et al.   MOLECULAR ECOLOGY

Postglacial recolonization history of the European crabapple (Malus sylvestrisMill.), a wild contributor to the domesticated apple

(2013) A. Cornille et al.   MOLECULAR ECOLOGY

Next-Gen phylogeography of rainforest trees: exploring landscape-level cpDNA variation from whole-genome sequencing

(2013) M. van der Merwe et al.   Molecular Ecology Resources

PtrHB7, a class III HD-Zip Gene, Plays a Critical Role in Regulation of Vascular Cambium Differentiation in Populus

(2013) Yingying Zhu et al.   Molecular Plant

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Breeding with rare defective alleles (BRDA): a naturalPopulus nigraHCT mutant with modified lignin as a case study

(2013) Bartel Vanholme et al.   NEW PHYTOLOGIST

Modeling transcriptional networks regulating secondary growth and wood formation in forest trees

(2013) Lijun Liu et al.   PHYSIOLOGIA PLANTARUM

In search of markers for somatic embryo maturation in hybrid larch (Larix×eurolepis): global DNA methylation and proteomic analyses

(2013) Caroline Teyssier et al.   PHYSIOLOGIA PLANTARUM

De novoassembly of maritime pine transcriptome: implications for forest breeding and biotechnology

(2013) Javier Canales et al.   PLANT BIOTECHNOLOGY JOURNAL

LACCASE Is Necessary and Nonredundant with PEROXIDASE for Lignin Polymerization during Vascular Development in Arabidopsis

(2013) Q. Zhao et al.   PLANT CELL

SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa

(2013) Y.-C. Lin et al.   PLANT CELL

Populusendo-beta-mannanase PtrMAN6 plays a role in coordinating cell wall remodeling with suppression of secondary wall thickening through generation of oligosaccharide signals

(2013) Yunjun Zhao et al.   PLANT JOURNAL

A Transcriptomic Network Underlies Microstructural and Physiological Responses to Cadmium in Populus x canescens

(2013) J. He et al.   PLANT PHYSIOLOGY

Poplars with a PtDDM1-RNAi transgene have reduced DNA methylation and show aberrant post-dormancy morphology

(2013) Ruoqing Zhu et al.   PLANTA

Developmental and Environmental Regulation of Aquaporin Gene Expression across Populus Species: Divergence or Redundancy?

(2013) David Cohen et al.   PLoS One

Host Genotype Shapes the Foliar Fungal Microbiome of Balsam Poplar (Populus balsamifera)

(2013) Miklós Bálint et al.   PLoS One

Association Analysis Identifies Melampsora ×columbiana Poplar Leaf Rust Resistance SNPs

(2013) Jonathan La Mantia et al.   PLoS One

Distinct Phyllosphere Bacterial Communities on Arabidopsis Wax Mutant Leaves

(2013) Eva E. Reisberg et al.   PLoS One

Improved saccharification and ethanol yield from field-grown transgenic poplar deficient in cinnamoyl-CoA reductase

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

The post-transcriptional regulation of LaSCL6 by miR171 during maintenance of embryogenic potential in Larix kaempferi (Lamb.) Carr.

(2013) Wan-Feng Li et al.   Tree Genetics & Genomes

Nucleotide diversity and linkage disequilibrium at 58 stress response and phenology candidate genes in a European beech (Fagus sylvatica L.) population from southeastern France

(2013) H. Lalagüe et al.   Tree Genetics & Genomes

Somatic embryogenesis in forestry with a focus on Europe: state-of-the-art, benefits, challenges and future direction

(2013) Marie-Anne Lelu-Walter et al.   Tree Genetics & Genomes

Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate

(2013) V. L. Sork et al.   Tree Genetics & Genomes

Epigenetic regulation of adaptive responses of forest tree species to the environment

(2013) Katharina Bräutigam et al.   Ecology and Evolution

A High-Density Gene Map of Loblolly Pine ( Pinus taeda L.) Based on Exome Sequence Capture Genotyping

(2013) Leandro Gomide Neves et al.   G3-Genes Genomes Genetics

EXCAVATOR: detecting copy number variants from whole-exome sequencing data

(2013) Alberto Magi et al.   GENOME BIOLOGY

Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree

(2013) Hannah McPherson et al.   BMC ECOLOGY

Adaptive Genetic Variation on the Landscape: Methods and Cases

(2012) Sean D. Schoville et al.   Annual Review of Ecology Evolution and Systematics

Translating conservation genetics into management: Pan-European minimum requirements for dynamic conservation units of forest tree genetic diversity

(2012) Jarkko Koskela et al.   BIOLOGICAL CONSERVATION

Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression

(2012) Kelly J Vining et al.   BMC GENOMICS

Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression

(2012) Elie Raherison et al.   BMC GENOMICS

Reprogramming of gene expression during compression wood formation in pine: Coordinated modulation of S-adenosylmethionine, lignin and lignan related genes

(2012) David P Villalobos et al.   BMC PLANT BIOLOGY

Dynamic Conservation of Forest Genetic Resources in 33 European Countries

(2012) FRANÇOIS LEFÈVRE et al.   CONSERVATION BIOLOGY

Spatial variability of phyllosphere fungal assemblages: genetic distance predominates over geographic distance in a European beech stand (Fagus sylvatica)

(2012) Tristan Cordier et al.   Fungal Ecology

Genetic evidence of Quaternary demographic changes in four rain forest tree species sampled across the Isthmus of Panama

(2012) F. Andrew Jones et al.   JOURNAL OF BIOGEOGRAPHY

Amazon diversification and cross-Andean dispersal of the widespread Neotropical tree speciesJacaranda copaia(Bignoniaceae)

(2012) Caroline Scotti-Saintagne et al.   JOURNAL OF BIOGEOGRAPHY

Phylogeography of a species complex of lowland Neotropical rain forest trees (Carapa, Meliaceae)

(2012) Caroline Scotti-Saintagne et al.   JOURNAL OF BIOGEOGRAPHY

Geographical structure and adaptive population differentiation in herbivore defence genes in European aspen (Populus tremulaL., Salicaceae)

(2012) CAROLINA BERNHARDSSON et al.   MOLECULAR ECOLOGY

Outlier loci highlight the direction of introgression in oaks

(2012) E. Guichoux et al.   MOLECULAR ECOLOGY

Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species

(2012) Kai N. Stölting et al.   MOLECULAR ECOLOGY

Demography and speciation history of the homoploid hybrid pinePinus densataon the Tibetan Plateau

(2012) JIE GAO et al.   MOLECULAR ECOLOGY

Phylogeographical patterns shed light on evolutionary process in South America

(2012) A. C. Turchetto-Zolet et al.   MOLECULAR ECOLOGY

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest treePopulus trichocarpa

(2012) Gancho T. Slavov et al.   NEW PHYTOLOGIST

The Class II KNOX gene KNAT7 negatively regulates secondary wall formation in Arabidopsis and is functionally conserved in Populus

(2012) Eryang Li et al.   NEW PHYTOLOGIST

Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees

(2012) Marcos D. V. Resende et al.   NEW PHYTOLOGIST

Methylome of DNase I sensitive chromatin inPopulus trichocarpashoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state

(2012) Clément Lafon-Placette et al.   NEW PHYTOLOGIST

Metabolic engineering of novel lignin in biomass crops

(2012) Ruben Vanholme et al.   NEW PHYTOLOGIST

The composition of phyllosphere fungal assemblages of European beech (Fagus sylvatica ) varies significantly along an elevation gradient

(2012) Tristan Cordier et al.   NEW PHYTOLOGIST

A Systems Biology View of Responses to Lignin Biosynthesis Perturbations in Arabidopsis

(2012) R. Vanholme et al.   PLANT CELL

Transcriptome profiling and in silico analysis of somatic embryos in Japanese larch (Larix leptolepis)

(2012) Yuan Zhang et al.   PLANT CELL REPORTS

Microarray analysis revealed upregulation of nitrate reductase in juvenile cuttings of Eucalyptus grandis, which correlated with increased nitric oxide production and adventitious root formation

(2012) Mohamad Abu-Abied et al.   PLANT JOURNAL

The AINTEGUMENTA LIKE1 Homeotic Transcription Factor PtAIL1 Controls the Formation of Adventitious Root Primordia in Poplar

(2012) A. Rigal et al.   PLANT PHYSIOLOGY

Genome-wide identification of microRNAs in larch and stage-specific modulation of 11 conserved microRNAs and their targets during somatic embryogenesis

(2012) Junhong Zhang et al.   PLANTA

Deep Annotation of Populus trichocarpa microRNAs from Diverse Tissue Sets

(2012) Joshua R. Puzey et al.   PLoS One

Metatranscriptomics Reveals the Diversity of Genes Expressed by Eukaryotes in Forest Soils

(2012) Coralie Damon 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

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

(2012) M. dos Reis et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

SNP markers trace familial linkages in a cloned population of Pinus taeda—prospects for genomic selection

(2012) Jaime Zapata-Valenzuela et al.   Tree Genetics & Genomes

Efficiency of genomic selection with models including dominance effect in the context of Eucalyptus breeding

(2012) Marie Denis et al.   Tree Genetics & Genomes

Conifer DBMagic: a database housing multiple de novo transcriptome assemblies for 12 diverse conifer species

(2012) W. Walter Lorenz et al.   Tree Genetics & Genomes

Experimental ‘omics’ data in tree research: facing complexity

(2012) Wolfgang zu Castell et al.   TREES-STRUCTURE AND FUNCTION

Development and characterization of microsatellite loci in Pericopsis elata (Fabaceae) using a cost-efficient approach

(2011) Claire Micheneau et al.   AMERICAN JOURNAL OF BOTANY

Low genetic diversity, moderate local adaptation, and phylogeographic insights in Cornus nuttallii (Cornaceae)

(2011) Karolyn R. Keir et al.   AMERICAN JOURNAL OF BOTANY

RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus

(2011) Emilie Villar et al.   BMC GENOMICS

Ecophysiological and transcriptomic responses of oak (Quercus robur) to long-term drought exposure and rewatering

(2011) Nadine Spieß et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Genetic mapping provides evidence for the role of additive and non-additive QTLs in the response of inter-specific hybrids of Eucalyptus to Puccinia psidii rust infection

(2011) Alexandre Alonso Alves et al.   EUPHYTICA

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice

(2011) Claudia Knief et al.   ISME Journal

Metabolomics demonstrates divergent responses of two Eucalyptus species to water stress

(2011) Charles R. Warren et al.   Metabolomics

Testing species delimitation in sympatric species complexes: The case of an African tropical tree, Carapa spp. (Meliaceae)

(2011) Jérôme Duminil et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Forest tree genomics: growing resources and applications

(2011) David B. Neale et al.   NATURE REVIEWS GENETICS

Qualitative and quantitative resistances to leaf rust finely mapped within two nucleotide-binding site leucine-rich repeat (NBS-LRR)-rich genomic regions of chromosome 19 in poplar

(2011) Aloïs Bresson et al.   NEW PHYTOLOGIST

Salt stress induces the formation of a novel type of ‘pressure wood’ in two Populus species

(2011) Dennis Janz et al.   NEW PHYTOLOGIST

Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments

(2011) M. F. R. Resende et al.   NEW PHYTOLOGIST

Controlling for non-independence in comparative analysis of patterns across populations within species

(2011) G. N. Stone et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Variations of DNA methylation in Eucalyptus urophylla×Eucalyptus grandis shoot tips and apical meristems of different physiological ages

(2011) François Mankessi et al.   PHYSIOLOGIA PLANTARUM

Proteomics research on forest trees, the most recalcitrant and orphan plant species

(2011) Nieves Abril et al.   PHYTOCHEMISTRY

The Predicted Arabidopsis Interactome Resource and Network Topology-Based Systems Biology Analyses

(2011) M. Lin et al.   PLANT CELL

Proteomic plasticity of two Eucalyptus genotypes under contrasted water regimes in the field

(2011) FRANK BEDON et al.   PLANT CELL AND ENVIRONMENT

Cell-specific chemotyping and multivariate imaging by combined FT-IR microspectroscopy and orthogonal projections to latent structures (OPLS) analysis reveals the chemical landscape of secondary xylem

(2011) András Gorzsás et al.   PLANT JOURNAL

A NAC domain protein family contributing to the regulation of wood formation in poplar

(2011) Misato Ohtani et al.   PLANT JOURNAL

Climate change and forest diseases

(2011) R. N. Sturrock et al.   PLANT PATHOLOGY

Dissection of the Transcriptional Program Regulating Secondary Wall Biosynthesis during Wood Formation in Poplar

(2011) R. Zhong et al.   PLANT PHYSIOLOGY

Transcriptome Response to Embolism Formation in Stems of Populus trichocarpa Provides Insight into Signaling and the Biology of Refilling

(2011) F. Secchi et al.   PLANT PHYSIOLOGY

Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics

(2011) Xiaohan Yang et al.   PLANT SCIENCE

Influence of over-expression of the FLOWERING PROMOTING FACTOR 1 gene (FPF1) from Arabidopsis on wood formation in hybrid poplar (Populus tremula L. × P. tremuloides Michx.)

(2011) Hans Hoenicka et al.   PLANTA

The Populus Class III HD ZIP Transcription Factor POPCORONA Affects Cell Differentiation during Secondary Growth of Woody Stems

(2011) Juan Du et al.   PLoS One

Evidence for Network Evolution in an Arabidopsis Interactome Map

(2011) et al.   SCIENCE

QTL mapping of resistance to leaf rust in Salix

(2011) Berit Samils et al.   Tree Genetics & Genomes

Prospects for genomic selection in conifer breeding: a simulation study of Cryptomeria japonica

(2011) Hiroyoshi Iwata et al.   Tree Genetics & Genomes

DNA methylation and histone acetylation: genotypic variations in hybrid poplars, impact of water deficit and relationships with productivity

(2010) Delphine Gourcilleau et al.   ANNALS OF FOREST SCIENCE

The Genetics of Lignin Biosynthesis: Connecting Genotype to Phenotype

(2010) Nicholas D. Bonawitz et al.   Annual Review of Genetics

Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes

(2010) David Cohen et al.   BMC GENOMICS

Pathway analysis of the transcriptome and metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms

(2010) Dennis Janz et al.   BMC PLANT BIOLOGY

Wood formation in Angiosperms

(2010) Annabelle Déjardin et al.   COMPTES RENDUS BIOLOGIES

The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves

(2010) Amanda J. Redford et al.   ENVIRONMENTAL MICROBIOLOGY

The physiological, transcriptional and genetic responses of an ozone- sensitive and an ozone tolerant poplar and selected extremes of their F 2 progeny

(2010) Nathaniel Robert Street et al.   ENVIRONMENTAL POLLUTION

High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland

(2010) W Wachowiak et al.   HEREDITY

Molecular Footprints of Local Adaptation in Two Mediterranean Conifers

(2010) D. Grivet et al.   MOLECULAR BIOLOGY AND EVOLUTION

The ‘New Wave’ in plant demographic inference: more loci and more individuals

(2010) MARTIN LASCOUX et al.   MOLECULAR ECOLOGY

Genomic diversity, population structure, and migration following rapid range expansion in the Balsam Poplar,Populus balsamifera

(2010) STEPHEN R. KELLER et al.   MOLECULAR ECOLOGY

The Strait of Gibraltar as a major biogeographic barrier in Mediterranean conifers: a comparative phylogeographic survey

(2010) J. P. JARAMILLO-CORREA et al.   MOLECULAR ECOLOGY

Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae)

(2010) ANDREW J. ECKERT et al.   MOLECULAR ECOLOGY

Spatially explicit Bayesian clustering models in population genetics

(2010) OLIVIER FRANÇOIS et al.   Molecular Ecology Resources

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments

(2010) A. Jumpponen et al.   NEW PHYTOLOGIST

Increased gelling agent concentration promotes somatic embryo maturation in hybrid larch (Larix×eurolepsis): a 2-DE proteomic analysis

(2010) Caroline Teyssier et al.   PHYSIOLOGIA PLANTARUM

Transcriptome changes in the cambial region of poplar (Populus alba L.) in response to water deficit

(2010) M. Berta et al.   PLANT BIOLOGY

Intraspecific variation in the Populus balsamifera drought transcriptome

(2010) ERIN T. HAMANISHI et al.   PLANT CELL AND ENVIRONMENT

Potential of Eurasian poplar rust to overcome a major quantitative resistance factor

(2010) A. Dowkiw et al.   PLANT PATHOLOGY

Xyloglucan endo-Transglycosylase-Mediated Xyloglucan Rearrangements in Developing Wood of Hybrid Aspen

(2010) N. Nishikubo et al.   PLANT PHYSIOLOGY

Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants

(2010) P. Zhang et al.   PLANT PHYSIOLOGY

Mass Spectrometry-Based Sequencing of Lignin Oligomers

(2010) K. Morreel et al.   PLANT PHYSIOLOGY

Initiation of somatic embryos and regeneration of plants from primordial shoots of 10-year-old somatic white spruce and expression profiles of 11 genes followed during the tissue culture process

(2010) Krystyna Klimaszewska et al.   PLANTA

Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus

(2010) D. R. Drost et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conservation and divergence of methylation patterning in plants and animals

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

Activation tagging is an effective gene tagging system in Populus

(2010) Victor Busov et al.   Tree Genetics & Genomes

Important processes during differentiation and early development of somatic embryos of Norway spruce as revealed by changes in global gene expression

(2010) Daniel Vestman et al.   Tree Genetics & Genomes

Genomic selection in forest tree breeding

(2010) Dario Grattapaglia et al.   Tree Genetics & Genomes

Pathogenesis-related genes and proteins in forest tree species

(2010) Radha Veluthakkal et al.   TREES-STRUCTURE AND FUNCTION

Plant phenotypic plasticity in a changing climate

(2010) A.B. Nicotra et al.   TRENDS IN PLANT SCIENCE

Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil

(2010) Stéphane Uroz et al.   Environmental Microbiology Reports

Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

(2009) Stefanie De Bodt et al.   BMC GENOMICS

Poplar and Pathogen Interactions: Insights fromPopulusGenome-Wide Analyses of Resistance and Defense Gene Families and Gene Expression Profiling

(2009) Sébastien Duplessis et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Breeding without breeding

(2009) YOUSRY A. El-KASSABY et al.   Genetics Research

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Statistical inferences in phylogeography

(2009) RASMUS NIELSEN et al.   MOLECULAR ECOLOGY

Identification of Lignin and Polysaccharide Modifications in Populus Wood by Chemometric Analysis of 2D NMR Spectra from Dissolved Cell Walls

(2009) Mattias Hedenström et al.   Molecular Plant

Xyloglucan for Generating Tensile Stress to Bend Tree Stem

(2009) Kei'ichi Baba et al.   Molecular Plant

Selective histories of poplar protease inhibitors: elevated polymorphism, purifying selection, and positive selection driving divergence of recent duplicates

(2009) Maurine Neiman et al.   NEW PHYTOLOGIST

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

(2009) M. Buée et al.   NEW PHYTOLOGIST

Fungal ecology catches fire

(2009) David S. Hibbett et al.   NEW PHYTOLOGIST

Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperateQuercus macrocarpaphyllosphere

(2009) A. Jumpponen et al.   NEW PHYTOLOGIST

Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest

(2009) M. Öpik et al.   NEW PHYTOLOGIST

Physiological and proteomic responses of two contrastingPopulus cathayanapopulations to drought stress

(2009) Xiangwen Xiao et al.   PHYSIOLOGIA PLANTARUM

Genetic variation and drought response in two Populus×euramericana genotypes through 2-DE proteomic analysis of leaves from field and glasshouse cultivated plants

(2009) Ludovic Bonhomme et al.   PHYTOCHEMISTRY

Predicting the regenerative capacity of conifer somatic embryogenic cultures by metabolomics

(2009) Andrew R. Robinson et al.   PLANT BIOTECHNOLOGY JOURNAL

The Populus homeobox gene ARBORKNOX2 regulates cell differentiation during secondary growth

(2009) Juan Du et al.   PLANT JOURNAL

The Ectomycorrhizal Fungus Laccaria bicolor Stimulates Lateral Root Formation in Poplar and Arabidopsis through Auxin Transport and Signaling

(2009) J. Felten et al.   PLANT PHYSIOLOGY

The Cytokinin Type-B Response Regulator PtRR13 Is a Negative Regulator of Adventitious Root Development in Populus

(2009) G. A. Ramirez-Carvajal et al.   PLANT PHYSIOLOGY

Sucrose synthase affects carbon partitioning to increase cellulose production and altered cell wall ultrastructure

(2009) H. D. Coleman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular phylogenetics reveal multiple tertiary vicariance origins of the African rain forest trees

(2008) Thomas LP Couvreur et al.   BMC BIOLOGY

Few Mendelian Genes Underlie the Quantitative Response of a Forest Tree, Eucalyptus globulus , to a Natural Fungal Epidemic

(2008) Jules S. Freeman et al.   GENETICS

Phylogeographical structure and temporal complexity in American sweetgum (Liquidambar styraciflua; Altingiaceae)

(2008) ASHLEY B. MORRIS et al.   MOLECULAR ECOLOGY

A phylogeographical analysis of the range disjunction for foxtail pine (Pinus balfouriana, Pinaceae): the role of Pleistocene glaciation

(2008) ANDREW J. ECKERT et al.   MOLECULAR ECOLOGY

Personal genomes: The case of the missing heritability

(2008) Brendan Maher   NATURE

Gene expression inEucalyptusbranch wood with marked variation in cellulose microfibril orientation and lacking G-layers

(2008) Deyou Qiu et al.   NEW PHYTOLOGIST

Molecular and phenotypic profiling from the base to the crown in maritime pine wood-forming tissue

(2008) Jorge A.P. Paiva et al.   NEW PHYTOLOGIST

Plasticity of maritime pine (Pinus pinaster) wood-forming tissues during a growing season

(2008) J. A. P. Paiva et al.   NEW PHYTOLOGIST

Genome-wide identification of NBS resistance genes in Populus trichocarpa

(2008) Annegret Kohler et al.   PLANT MOLECULAR BIOLOGY

Differential Response of Gray Poplar Leaves and Roots Underpins Stress Adaptation during Hypoxia

(2008) J. Kreuzwieser et al.   PLANT PHYSIOLOGY

HPCE quantification of 5-methyl-2′-deoxycytidine in genomic DNA: Methodological optimization for chestnut and other woody species

(2008) Rodrigo Hasbún et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

DNA barcodes: Genes, genomics, and bioinformatics

(2008) W. J. Kress et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequencing and annotation of the evergrowing locus in peach [Prunus persica (L.) Batsch] reveals a cluster of six MADS-box transcription factors as candidate genes for regulation of terminal bud formation

(2008) Douglas Gary Bielenberg et al.   Tree Genetics & Genomes