High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers

(2014) Jun Wu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq

(2014) M.-J. Karam et al.   Molecular Ecology Resources

A High-Density SNP Map of Sunflower Derived from RAD-Sequencing Facilitating Fine-Mapping of the Rust Resistance Gene R12

(2014) Zahirul I. Talukder et al.   PLoS One

The genetic diversity and introgression of Juglans regia and Juglans sigillata in Tibet as revealed by SSR markers

(2014) Hua Wang et al.   Tree Genetics & Genomes

A grass-fire cycle eliminates an obligate-seeding tree in a tropical savanna

(2014) David M. J. S. Bowman et al.   Ecology and Evolution

Genetic Differentiation and Evolutionary Adaptation in Cryptomeria japonica

(2014) Yoshihiko Tsumura et al.   G3-Genes Genomes 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

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

A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae)

(2013) Ryo Kakioka et al.   BMC GENOMICS

Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

(2013) Judson A Ward et al.   BMC GENOMICS

De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach

(2013) Venkatramana Pegadaraju et al.   BMC GENOMICS

DIVERGENCE IS FOCUSED ON FEW GENOMIC REGIONS EARLY IN SPECIATION: INCIPIENT SPECIATION OF SUNFLOWER ECOTYPES

(2013) Rose L. Andrew et al.   EVOLUTION

Marker Density and Read Depth for Genotyping Populations Using Genotyping-by-Sequencing

(2013) T. M. Beissinger et al.   GENETICS

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold 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

Arabidopsis meiotic crossover hot spots overlap with H2A.Z nucleosomes at gene promoters

(2013) Kyuha Choi et al.   NATURE GENETICS

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grassMiscanthus sinensis

(2013) Gancho T. Slavov et al.   NEW PHYTOLOGIST

Climate, not Aboriginal landscape burning, controlled the historical demography and distribution of fire-sensitive conifer populations across Australia

(2013) S. Sakaguchi et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Combination of multipoint maximum likelihood (MML) and regression mapping algorithms to construct a high-density genetic linkage map for loblolly pine (Pinus taeda L.)

(2013) Pedro J. Martínez-García et al.   Tree Genetics & Genomes

Conservative water management in the widespread conifer genus Callitris

(2013) T. J. Brodribb et al.   AoB Plants

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

The construction of a high-density linkage map for identifying SNP markers that are tightly linked to a nuclear-recessive major gene for male sterility in Cryptomeria japonica D. Don

(2012) Yoshinari Moriguchi et al.   BMC GENOMICS

A transcriptome map of perennial ryegrass (Lolium perenne L.)

(2012) Bruno Studer et al.   BMC GENOMICS

The effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Distribution of living Cupressaceae reflects the breakup of Pangea

(2012) K. Mao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Hypomethylated Partial Restriction (HMPR) method reduces the repetitive content of genomic libraries in Norway spruce (Picea abies)

(2012) Hanna Larsson et al.   Tree Genetics & Genomes

Isolation and characterization of 52 polymorphic EST-SSR markers for Callitris columellaris (Cupressaceae)

(2011) Shota Sakaguchi et al.   AMERICAN JOURNAL OF BOTANY

Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley

(2011) Yada Chutimanitsakun et al.   BMC GENOMICS

Population structures of the widespread Australian conifer Callitris columellaris are a bio-indicator of continental environmental change

(2011) Lynda D. Prior et al.   FOREST ECOLOGY AND MANAGEMENT

Extended Linkage Disequilibrium in Noncoding Regions in a Conifer, Cryptomeria japonica

(2011) E. Moritsuka et al.   GENETICS

A high-density genetic linkage map of a black spruce (Picea mariana) × red spruce (Picea rubens) interspecific hybrid

(2011) Bum-Yong Kang et al.   GENOME

A reduced representation approach to population genetic analyses and applications to human evolution

(2011) F. Luca et al.   GENOME RESEARCH

Potential chromosomal introgression barriers revealed by linkage analysis in a hybrid of Pinus massoniana and P. hwangshanensis

(2010) Shuxian Li et al.   BMC PLANT BIOLOGY

Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae)

(2010) A. J. Eckert et al.   GENETICS

Population genetic inference from genomic sequence variation

(2010) J. E. Pool et al.   GENOME RESEARCH

Ascertainment Biases in SNP Chips Affect Measures of Population Divergence

(2010) A. Albrechtsen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph

(2008) Yonghui Wu et al.   PLoS Genetics