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

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

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

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

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

Pivoting the Plant Immune System from Dissection to Deployment

(2013) J. L. Dangl et al.   SCIENCE

Caffeoyl Shikimate Esterase (CSE) Is an Enzyme in the Lignin Biosynthetic Pathway in Arabidopsis

(2013) R. Vanholme et al.   SCIENCE

Web Apollo: a web-based genomic annotation editing platform

(2013) Eduardo Lee et al.   GENOME BIOLOGY

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

(2013) Alberto Magi et al.   GENOME BIOLOGY

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

(2012) A. R. Leitch et al.   NEW PHYTOLOGIST

Hemisphere-scale differences in conifer evolutionary dynamics

(2012) A. B. Leslie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Structures of COPI-Coated Vesicles Reveal Alternate Coatomer Conformations and Interactions

(2012) M. Faini et al.   SCIENCE

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Comprehensive genetic dissection of wood properties in a widely-grown tropical tree: Eucalyptus

(2011) Jean-Marc Gion 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

Adaptation to drought in two wild tomato species: the evolution of the Asr gene family

(2011) Iris Fischer et al.   NEW PHYTOLOGIST

Phytozome: a comparative platform for green plant genomics

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

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Chalcone synthase and its functions in plant resistance

(2011) T. T. H. Dao et al.   PHYTOCHEMISTRY REVIEWS

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Hemicelluloses

(2010) Henrik Vibe Scheller et al.   Annual Review of Plant Biology

A genomic map enriched for markers linked to Avr1 in Cronartium quercuum f.sp. fusiforme

(2010) Thomas L. Kubisiak et al.   FUNGAL GENETICS AND BIOLOGY

Convergent Evolution of Syringyl Lignin Biosynthesis via Distinct Pathways in the LycophyteSelaginellaand Flowering Plants

(2010) Jing-Ke Weng et al.   PLANT CELL

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

(2009) Matthew Parks et al.   BMC BIOLOGY

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Patterns of polymorphism resulting from long-range colonization in the Mediterranean conifer Aleppo pine

(2009) Delphine Grivet et al.   NEW PHYTOLOGIST

Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes

(2009) Rui Shi et al.   PLANT AND CELL PHYSIOLOGY

Conserved Functions of Membrane Active GTPases in Coated Vesicle Formation

(2009) T. J. Pucadyil et al.   SCIENCE

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

Flowering-time genes modulate meristem determinacy and growth form in Arabidopsis thaliana

(2008) Siegbert Melzer et al.   NATURE GENETICS

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

"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