Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum)

De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens

(2017) Daniel Blande et al.   Scientific Data

Landscape genomic analysis of candidate genes for climate adaptation in a California endemic oak, Quercus lobata

(2016) V. L. Sork et al.   AMERICAN JOURNAL OF BOTANY

De novo transcriptome sequencing and gene expression analysis reveal potential mechanisms of seed abortion in dove tree (Davidia involucrata Baill.)

(2016) Meng Li et al.   BMC PLANT BIOLOGY

Species-wide patterns of DNA methylation variation inQuercus lobataand their association with climate gradients

(2016) Paul F. Gugger et al.   MOLECULAR ECOLOGY

Distribution, function and evolution characterization of microsatellite in Sargassum thunbergii (Fucales, Phaeophyta) transcriptome and their application in marker development

(2016) Fuli Liu et al.   Scientific Reports

Modelization of the Current and Future Habitat Suitability of Rhododendron ferrugineum Using Potential Snow Accumulation

(2016) Benjamin Komac et al.   PLoS One

Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz) Using Next-Generation Sequencing (NGS)

(2016) Adriana Bastías et al.   PLoS One

Population transcriptomics uncovers the regulation of gene expression variation in adaptation to changing environment

(2016) Qin Xu et al.   Scientific Reports

Plants and climate change: complexities and surprises

(2015) C. Parmesan et al.   ANNALS OF BOTANY

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

De novo sequencing and analysis of the cranberry fruit transcriptome to identify putative genes involved in flavonoid biosynthesis, transport and regulation

(2015) Haiyue Sun et al.   BMC GENOMICS

Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks

(2015) Shawn J. Cokus et al.   BMC GENOMICS

De novo transcriptome assembly of the wild relative of tea tree (Camellia taliensis) and comparative analysis with tea transcriptome identified putative genes associated with tea quality and stress response

(2015) Hai-Bin Zhang et al.   BMC GENOMICS

Characterization of the cork oak transcriptome dynamics during acorn development

(2015) Andreia Miguel et al.   BMC PLANT BIOLOGY

Development and Validation of 697 Novel Polymorphic Genomic and EST-SSR Markers in the American Cranberry (Vaccinium macrocarpon Ait.)

(2015) Brandon Schlautman et al.   MOLECULES

Accelerating extinction risk from climate change

(2015) M. C. Urban   SCIENCE

SNP development for genetic diversity analysis in apricot

(2015) Juan Alfonso Salazar et al.   Tree Genetics & Genomes

An Empirical Review: Characteristics of Plant Microsatellite Markers that Confer Higher Levels of Genetic Variation

(2015) Benjamin J. Merritt et al.   Applications in Plant Sciences

Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species

(2015) Maria Teresa Dettori et al.   SpringerPlus

De Novo Transcriptome Assembly in Firmiana danxiaensis, a Tree Species Endemic to the Danxia Landform

(2015) Su-Fang Chen et al.   PLoS One

Genotyping by Sequencing for SNP-Based Linkage Map Construction and QTL Analysis of Chilling Requirement and Bloom Date in Peach [Prunus persica (L.) Batsch]

(2015) Douglas Gary Bielenberg et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Elucidating cold acclimation pathway in blueberry by transcriptome profiling

(2014) Jose V. Die et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Exploiting EST databases for the development and characterization of EST-SSR markers in blueberry (Vaccinium) and their cross-species transferability in Vaccinium spp

(2014) You-chun Liu et al.   SCIENTIA HORTICULTURAE

Development and characterization of genomic microsatellite markers in Rhododendron arboreum

(2014) Shruti Choudhary et al.   Conservation Genetics Resources

Characterization of Microsatellite Markers for Pinedrops,Pterospora andromedea(Ericaceae), from Illumina MiSeq sequencing

(2014) Lisa C. Grubisha et al.   Applications in Plant Sciences

Influence of late Quaternary climate change on present patterns of genetic variation in valley oak,Quercus lobataNée

(2013) Paul F. Gugger et al.   MOLECULAR ECOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

(2013) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties

(2013) Nivedita Singh et al.   PLoS One

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Designing a transcriptome next-generation sequencing project for a nonmodel plant species1

(2012) Susan R. Strickler et al.   AMERICAN JOURNAL OF BOTANY

Assessment of impact of climate change on Rhododendrons in Sikkim Himalayas using Maxent modelling: limitations and challenges

(2012) Pradeep Kumar   BIODIVERSITY AND CONSERVATION

Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR sequencing

(2012) Tyson Koepke et al.   BMC GENOMICS

Deep-sequencing transcriptome analysis of chilling tolerance mechanisms of a subnival alpine plant, Chorispora bungeana

(2012) Zhiguang Zhao et al.   BMC PLANT BIOLOGY

Transcriptome Characterization and Sequencing-Based Identification of Salt-Responsive Genes in Millettia pinnata, a Semi-Mangrove Plant

(2012) J. Huang et al.   DNA RESEARCH

Flowering phenology of tree rhododendron along an elevation gradient in two sites in the Eastern Himalayas

(2012) Sailesh Ranjitkar et al.   INTERNATIONAL JOURNAL OF BIOMETEOROLOGY

Identification and characterization of proanthocyanidins of 16 members of the Rhododendron genus (Ericaceae) by tandem LC-MS

(2012) Rakesh Jaiswal et al.   JOURNAL OF MASS SPECTROMETRY

Sequencing and Characterization of Striped Venus Transcriptome Expand Resources for Clam Fishery Genetics

(2012) Alessandro Coppe et al.   PLoS One

SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing

(2011) ARMANDO GERALDES et al.   Molecular Ecology Resources

Cross-species transferability of SSR loci developed from transciptome sequencing in lodgepole pine

(2011) MARK R. LESSER et al.   Molecular Ecology Resources

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

KEGG for integration and interpretation of large-scale molecular data sets

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

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Genetic variability of relictRhododendron ferrugineumL. populations in the Northern Apennines with some inferences for a conservation strategy

(2011) Ilaria Bruni et al.   PLANT BIOSYSTEMS

Microsatellite markers: an overview of the recent progress in plants

(2010) Rajwant K. Kalia et al.   EUPHYTICA

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

The Melting Himalayas: Cascading Effects of Climate Change on Water, Biodiversity, and Livelihoods

(2009) JIANCHU XU et al.   CONSERVATION BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY