Towards integration of population and comparative genomics in forest trees

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens

(2016) Jing Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Open chromatin reveals the functional maize genome

(2016) Eli Rodgers-Melnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species

(2015) J. Wang et al.   GENETICS

What to compare and how: Comparative transcriptomics for Evo-Devo

(2015) Julien Roux et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies

(2015) Christophe Plomion et al.   Molecular Ecology Resources

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

(2015) Robert VanBuren et al.   NATURE

Evidence for extensive parallelism but divergent genomic architecture of adaptation along altitudinal and latitudinal gradients inPopulus trichocarpa

(2015) Jason A. Holliday et al.   NEW PHYTOLOGIST

Genome-wide patterns of recombination, linkage disequilibrium and nucleotide diversity from pooled resequencing and single nucleotide polymorphism genotyping unlock the evolutionary history ofEucalyptus grandis

(2015) Orzenil B. Silva-Junior et al.   NEW PHYTOLOGIST

The Plant Genome Integrative Explorer Resource: PlantGenIE.org

(2015) David Sundell et al.   NEW PHYTOLOGIST

Comparative interrogation of the developing xylem transcriptomes of two wood-forming species:Populus trichocarpaandEucalyptus grandis

(2015) Charles A. Hefer et al.   NEW PHYTOLOGIST

Exploiting SNPs for biallelic CRISPR mutations in the outcrossing woody perennialPopulusreveals 4-coumarate:CoA ligase specificity and redundancy

(2015) Xiaohong Zhou et al.   NEW PHYTOLOGIST

ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression

(2015) Yuichi Aoki et al.   PLANT AND CELL PHYSIOLOGY

A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation inPopulus

(2015) Lijun Liu et al.   PLANT JOURNAL

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

The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome

(2015) Hiroaki Sakai et al.   Scientific Reports

Using optical mapping data for the improvement of vertebrate genome assemblies

(2015) Kerstin Howe et al.   GigaScience

Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools

(2015) Janna L. Fierst   Frontiers in Genetics

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

CRISPRing into the woods

(2015) Chung-Jui Tsai et al.   GM Crops & Food-Biotechnology in Agriculture and the Food Chain

ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa

(2014) Sergiu Netotea et al.   BMC GENOMICS

The willow genome and divergent evolution from poplar after the common genome duplication

(2014) Xiaogang Dai et al.   CELL RESEARCH

Structural variation and genome complexity: is dispensable really dispensable?

(2014) Fabio Marroni et al.   CURRENT OPINION IN PLANT BIOLOGY

LANDSCAPE GENOMICS OFPOPULUS TRICHOCARPA: THE ROLE OF HYBRIDIZATION, LIMITED GENE FLOW, AND NATURAL SELECTION IN SHAPING PATTERNS OF POPULATION STRUCTURE

(2014) Armando Geraldes et al.   EVOLUTION

A field guide to whole-genome sequencing, assembly and annotation

(2014) Robert Ekblom et al.   Evolutionary Applications

An Arabidopsis gene regulatory network for secondary cell wall synthesis

(2014) M. Taylor-Teeples et al.   NATURE

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

(2014) G Albert Wu et al.   NATURE BIOTECHNOLOGY

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

(2014) Luke M Evans et al.   NATURE GENETICS

High-resolution genetic maps ofEucalyptusimproveEucalyptus grandisgenome assembly

(2014) Jérôme Bartholomé et al.   NEW PHYTOLOGIST

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations ofPopulus trichocarpa

(2014) Athena D. McKown et al.   NEW PHYTOLOGIST

PLAZA 3.0: an access point for plant comparative genomics

(2014) Sebastian Proost et al.   NUCLEIC ACIDS RESEARCH

AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species

(2014) Tak Lee et al.   NUCLEIC ACIDS RESEARCH

Cell Wall-Related Proteins of Unknown Function: Missing Links in Plant Cell Wall Development

(2014) Ritesh Mewalal et al.   PLANT AND CELL PHYSIOLOGY

Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-Based Curation

(2014) Hajime Ohyanagi et al.   PLANT AND CELL PHYSIOLOGY

Insights into Conifer Giga-Genomes

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

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

(2014) F. Denoeud et al.   SCIENCE

The complex jujube genome provides insights into fruit tree biology

(2014) Meng-Jun Liu et al.   Nature Communications

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

Draft genome sequence of the rubber tree Hevea brasiliensis

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

PLANEX: the plant co-expression database

(2013) Won Yim et al.   BMC PLANT BIOLOGY

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

(2013) S. B. Montgomery et al.   GENOME RESEARCH

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

Genomic signatures of selection at linked sites: unifying the disparity among species

(2013) Asher D. Cutter et al.   NATURE REVIEWS GENETICS

Systems genetics approaches to understand complex traits

(2013) Mete Civelek et al.   NATURE REVIEWS GENETICS

Geographical and environmental gradients shape phenotypic trait variation and genetic structure inPopulus trichocarpa

(2013) Athena D. McKown et al.   NEW PHYTOLOGIST

Genomic insights into salt adaptation in a desert poplar

(2013) Tao Ma et al.   Nature Communications

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

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

(2012) Nian Wang et al.   MOLECULAR ECOLOGY

The draft genome of sweet orange (Citrus sinensis)

(2012) Qiang Xu et al.   NATURE GENETICS

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

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

(2012) Gancho T. Slavov 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

BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species

(2012) Rohan V. Patel et al.   PLANT JOURNAL

Feature-by-Feature – Evaluating De Novo Sequence Assembly

(2012) Francesco Vezzi et al.   PLoS One

Revisiting the sequencing of the first tree genome: Populus trichocarpa

(2012) S. D. Wullschleger et al.   TREE PHYSIOLOGY

Current challenges in de novo plant genome sequencing and assembly

(2012) Michael C Schatz et al.   GENOME BIOLOGY

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species

(2011) M. Mutwil et al.   PLANT CELL

Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice

(2011) S. Movahedi et al.   PLANT PHYSIOLOGY

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

Association genetics of complex traits in plants

(2010) Pär K. Ingvarsson et al.   NEW PHYTOLOGIST

CORNET: A User-Friendly Tool for Data Mining and Integration

(2010) S. De Bodt et al.   PLANT PHYSIOLOGY

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

(2008) Ray Ming et al.   NATURE