Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function

SNP genotyping and population genomics from expressed sequences - current advances and future possibilities

(2015) Pierre De Wit et al.   MOLECULAR ECOLOGY

Modular organization of the white spruce (Picea glauca) transcriptome reveals functional organization and evolutionary signatures

(2015) Elie S. M. Raherison et al.   NEW PHYTOLOGIST

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

(2015) René L. Warren et al.   PLANT JOURNAL

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

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

MADS goes genomic in conifers: towards determining the ancestral set of MADS-box genes in seed plants

(2014) Lydia Gramzow et al.   ANNALS OF BOTANY

Transcriptome sequencing and profiling of expressed genes in cambial zone and differentiating xylem of Japanese cedar (Cryptomeria japonica)

(2014) Kentaro Mishima et al.   BMC GENOMICS

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

Plant genome size variation: bloating and purging DNA

(2014) T. P. Michael   Briefings in Functional Genomics

Comparative genetic responses to climate for the varieties of Pinus ponderosa and Pseudotsuga menziesii: Realized climate niches

(2014) Gerald E. Rehfeldt et al.   FOREST ECOLOGY AND MANAGEMENT

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

Population genomics of parallel hybrid zones in the mimetic butterflies,H. melpomeneandH. erato

(2014) Nicola J. Nadeau et al.   GENOME RESEARCH

Large-scale screening of transcription factor–promoter interactions in spruce reveals a transcriptional network involved in vascular development

(2014) Isabelle Duval et al.   JOURNAL OF EXPERIMENTAL BOTANY

The Evolution and Adaptive Potential of Transcriptional Variation in Sticklebacks—Signatures of Selection and Widespread Heritability

(2014) Erica H. Leder et al.   MOLECULAR BIOLOGY AND EVOLUTION

Natural Variation in Abiotic Stress Responsive Gene Expression and Local Adaptation to Climate in Arabidopsis thaliana

(2014) Jesse R. Lasky et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Conservation and divergence of gene expression plasticity followingc. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca × Picea engelmannii)

(2014) Sam Yeaman et al.   NEW PHYTOLOGIST

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

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

Increased genetic divergence between two closely related fir species in areas of range overlap

(2014) Jing Wang et al.   Ecology and Evolution

Extensive Copy-Number Variation of Young Genes across Stickleback Populations

(2014) Frédéric J. J. Chain et al.   PLoS Genetics

A Population Genetic Signal of Polygenic Adaptation

(2014) Jeremy J. Berg et al.   PLoS Genetics

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

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin 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

De novo characterization of Larix gmelinii (Rupr.) Rupr. transcriptome and analysis of its gene expression induced by jasmonates

(2013) Lina Men 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

Human Expression QTLs Are Enriched in Signals of Environmental Adaptation

(2013) Kaixiong Ye et al.   Genome Biology and Evolution

Potential for evolutionary responses to climate change - evidence from tree populations

(2013) Florian J. Alberto et al.   GLOBAL CHANGE BIOLOGY

Evidence for Polygenic Adaptation to Pathogens in the Human Genome

(2013) Josephine T. Daub et al.   MOLECULAR BIOLOGY AND EVOLUTION

Are long-lived trees poised for evolutionary change? Single locus effects in the evolution of gene expression networks in spruce

(2013) Jukka-Pekka Verta et al.   MOLECULAR ECOLOGY

Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners

(2013) Nathalie Pavy et al.   Molecular Ecology Resources

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Transcriptome Characteristics and Six Alternative Expressed Genes Positively Correlated with the Phase Transition of Annual Cambial Activities in Chinese Fir (Cunninghamia lanceolata (Lamb.) Hook)

(2013) Zhanjun Wang et al.   PLoS One

Temperature-driven range expansion of an irruptive insect heightened by weakly coevolved plant defenses

(2013) K. F. Raffa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic rearrangements and the evolution of clusters of locally adaptive loci

(2013) S. Yeaman   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic islands of divergence are not affected by geography of speciation in sunflowers

(2013) S. Renaut et al.   Nature Communications

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

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

Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms

(2012) Emmanuel Buschiazzo et al.   BMC EVOLUTIONARY BIOLOGY

Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms

(2012) Jun Chen 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

Parallel and lineage-specific molecular adaptation to climate in boreal black spruce

(2012) JULIEN PRUNIER et al.   MOLECULAR ECOLOGY

The genetic differentiation at quantitative trait loci under local adaptation

(2012) VALÉRIE LE CORRE et al.   MOLECULAR ECOLOGY

Evidence of widespread selection on standing variation in Europe at height-associated SNPs

(2012) Michael C Turchin et al.   NATURE GENETICS

Ecological and genetic factors linked to contrasting genome dynamics in seed plants

(2012) A. R. Leitch 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

Towards decoding the conifer giga-genome

(2012) John Mackay et al.   PLANT MOLECULAR BIOLOGY

Genomics of a phylum distant from flowering plants: conifers

(2012) Kermit Ritland   Tree Genetics & Genomes

Climate change may cause severe loss in the economic value of European forest land

(2012) Marc Hanewinkel et al.   Nature Climate Change

A comparison of four methods for detecting weak genetic structure from marker data

(2012) Owen R. Jones et al.   Ecology and Evolution

EuroPineDB: a high-coverage web database for maritime pine transcriptome

(2011) Noé Fernández-Pozo et al.   BMC GENOMICS

Transcriptome profiling of Pinus radiata juvenile wood with contrasting stiffness identifies putative candidate genes involved in microfibril orientation and cell wall mechanics

(2011) Xinguo Li et al.   BMC GENOMICS

Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

(2011) W Walter Lorenz et al.   BMC GENOMICS

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

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

Global Transcriptome Analysis of Constitutive Resistance to the White Pine Weevil in Spruce

(2011) Sébastien Verne et al.   Genome Biology and Evolution

Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions

(2011) A. Schlattl et al.   GENOME RESEARCH

Genetic architecture of regulatory variation in Arabidopsis thaliana

(2011) X. Zhang et al.   GENOME RESEARCH

Intra-specific variability and plasticity influence potential tree species distributions under climate change

(2011) Marta Benito Garzón et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

(2011) N Pavy et al.   HEREDITY

Scanning the genome for gene SNPs related to climate adaptation and estimating selection at the molecular level in boreal black spruce

(2011) JULIEN PRUNIER et al.   MOLECULAR ECOLOGY

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Forest tree genomics: growing resources and applications

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

Establishment of new mutations under divergence and genome hitchhiking

(2011) J. L. Feder et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A White Spruce Gene Catalog for Conifer Genome Analyses

(2011) Philippe Rigault et al.   PLANT PHYSIOLOGY

Adventures in the Enormous: A 1.8 Million Clone BAC Library for the 21.7 Gb Genome of Loblolly Pine

(2011) Zenaida V. Magbanua et al.   PLoS One

Clone history shapes Populus drought responses

(2011) S. Raj et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

(2011) R. J. Schmitz et al.   SCIENCE

Comparative analysis of transcript abundance in Pinus sylvestris after challenge with a saprotrophic, pathogenic or mutualistic fungus

(2011) Aleksandra Adomas et al.   TREE PHYSIOLOGY

The genes underlying the process of speciation

(2011) Patrik Nosil et al.   TRENDS IN ECOLOGY & EVOLUTION

What do we need to know about speciation?

(2011)   TRENDS IN ECOLOGY & EVOLUTION

Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery

(2010) Thomas L Parchman et al.   BMC GENOMICS

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

(2010) Allen Kovach et al.   BMC GENOMICS

Molecular Evolution of Regulatory Genes in Spruces from Different Species and Continents: Heterogeneous Patterns of Linkage Disequilibrium and Selection but Correlated Recent Demographic Changes

(2010) Marie-Claire Namroud et al.   JOURNAL OF MOLECULAR EVOLUTION

Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls

(2010)   NATURE

Sudden larch death

(2010) Clive Brasier et al.   NATURE

The population genomics of plant adaptation

(2010) Mathieu Siol et al.   NEW PHYTOLOGIST

Widespread, ecologically relevant genetic markers developed from association mapping of climate-related traits in Sitka spruce (Picea sitchensis)

(2010) Jason A. Holliday et al.   NEW PHYTOLOGIST

MicroRNAs, the epigenetic memory and climatic adaptation in Norway spruce

(2010) Igor A. Yakovlev et al.   NEW PHYTOLOGIST

Molecular events of apical bud formation in white spruce, Picea glauca

(2010) WALID EL KAYAL et al.   PLANT CELL AND ENVIRONMENT

An integrated genomic, proteomic and biochemical analysis of (+)-3-carene biosynthesis in Sitka spruce (Picea sitchensis) genotypes that are resistant or susceptible to white pine weevil

(2010) Dawn E. Hall et al.   PLANT JOURNAL

Differential gene expression related to an epigenetic memory affecting climatic adaptation in Norway spruce

(2010) Igor A. Yakovlev et al.   PLANT SCIENCE

Selection at Linked Sites Shapes Heritable Phenotypic Variation in C. elegans

(2010) M. V. Rockman et al.   SCIENCE

Genomic selection in forest tree breeding

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

Evolutionary conservation of the transcriptional network regulating secondary cell wall biosynthesis

(2010) Ruiqin Zhong et al.   TRENDS IN PLANT SCIENCE

Association Genetics of Coastal Douglas Fir ( Pseudotsuga menziesii var. menziesii , Pinaceae). I. Cold-Hardiness Related Traits

(2009) Andrew J. Eckert et al.   GENETICS

ABySS: A parallel assembler for short read sequence data

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

Local adaptation at the range peripheries of Sitka spruce

(2009) M. MIMURA et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

(2009) Steven Lockton et al.   JOURNAL OF MOLECULAR EVOLUTION

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

The genetics of inbreeding depression

(2009) Deborah Charlesworth et al.   NATURE REVIEWS GENETICS

Evolution of Genome Size and Complexity in Pinus

(2009) Alison M. Morse et al.   PLoS One

Optimization of gene expression by natural selection

(2009) T. Bedford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptation, migration or extirpation: climate change outcomes for tree populations

(2008) Sally N. Aitken et al.   Evolutionary Applications

Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce

(2008) MARIE-CLAIRE NAMROUD et al.   MOLECULAR ECOLOGY

Global monitoring of autumn gene expression within and among phenotypically divergent populations of Sitka spruce (Picea sitchensis)

(2008) Jason A. Holliday 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

Dominance and the evolutionary accumulation of cis- and trans-effects on gene expression

(2008) B. Lemos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conifers have a unique small RNA silencing signature

(2008) E. V. Dolgosheina et al.   RNA

High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.)

(2008) Andrew J. Eckert et al.   Tree Genetics & Genomes

"Contrasting Patterns of Selection at Pinus pinaster Ait. Drought Stress Candidate Genes as Revealed by Genetic Differentiation Analyses"

(2007) E. Eveno et al.   MOLECULAR BIOLOGY AND EVOLUTION