Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae)

A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species

(2012) Daniel C. Ilut et al.   AMERICAN JOURNAL OF BOTANY

Next-generation sequencing and genome evolution in allopolyploids

(2012) Richard J. A. Buggs et al.   AMERICAN JOURNAL OF BOTANY

Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies

(2012) Robert Ekblom et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

Proteomic analyses of apoplastic proteins from germinating Arabidopsis thaliana pollen

(2011) Weina Ge et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Global characterization of the root transcriptome of a wild species of rice, Oryza longistaminata, by deep sequencing

(2011) Haiyuan Yang et al.   BMC GENOMICS

Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing

(2011) Susanne U Franssen et al.   BMC GENOMICS

Transcriptomic analysis of grain amaranth (Amaranthus hypochondriacus) using 454 pyrosequencing: comparison with A. tuberculatus, expression profiling in stems and in response to biotic and abiotic stress

(2011) John P Délano-Frier et al.   BMC GENOMICS

De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)

(2011) Maria D Logacheva et al.   BMC GENOMICS

De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification

(2011) R. Garg et al.   DNA RESEARCH

Spartina alterniflora Loisel., a halophyte grass model to dissect salt stress tolerance

(2011) Prasanta K Subudhi et al.   IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-PLANT

Identification of NaCl stress-responsive apoplastic proteins in rice shoot stems by 2D-DIGE

(2011) Yun Song et al.   Journal of Proteomics

Differential Expression of the Transcripts of Spartina alterniflora Loisel (Smooth Cordgrass) Induced in Response to Petroleum Hydrocarbon

(2011) Mangu Venkata RamanaRao et al.   MOLECULAR BIOTECHNOLOGY

Analysis of Leaf and Root Transcriptomes of Soil-Grown Avena barbata Plants

(2011) Stéphanie M. Swarbreck et al.   PLANT AND CELL PHYSIOLOGY

Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae)

(2010) Jin Koh et al.   BMC GENOMICS

De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis

(2010) Chao Sun et al.   BMC GENOMICS

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

(2010) Thomas L Parchman et al.   BMC GENOMICS

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

(2010) R Ekblom et al.   HEREDITY

Transcriptome divergence between the hexaploid salt-marsh sister species Spartina maritima and Spartina alterniflora (Poaceae)

(2010) H. CHELAIFA et al.   MOLECULAR ECOLOGY

Characterization of duplicate gene evolution in the recent natural allopolyploidTragopogon miscellusby next-generation sequencing and Sequenom iPLEX MassARRAY genotyping

(2010) RICHARD J. A. BUGGS et al.   MOLECULAR ECOLOGY

Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina × townsendii and Spartina anglica (Poaceae)

(2010) Houda Chelaifa et al.   NEW PHYTOLOGIST

Pyrosequencing of Mytilus galloprovincialis cDNAs: Tissue-Specific Expression Patterns

(2010) John A. Craft et al.   PLoS One

Investigation of the Transcriptome of Prairie Cord Grass, a New Cellulosic Biomass Crop

(2010) Kristene Gedye et al.   Plant Genome

Applications of New Sequencing Technologies for Transcriptome Analysis

(2009) Olena Morozova et al.   Annual Review of Genomics and Human Genetics

Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species

(2009) Diana Bellin et al.   BMC GENOMICS

Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing

(2009) Julio C Vega-Arreguín et al.   BMC GENOMICS

Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery

(2009) Matthew C Hale et al.   BMC GENOMICS

Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development

(2009) Fiammetta Alagna et al.   BMC GENOMICS

Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection

(2009) Abdelali Barakat et al.   BMC PLANT BIOLOGY

On the road to diploidization? Homoeolog loss in independently formed populations of the allopolyploid Tragopogon miscellus (Asteraceae)

(2009) Jennifer A Tate et al.   BMC PLANT BIOLOGY

Spartina alterniflora invasions in the Yangtze River estuary, China: An overview of current status and ecosystem effects

(2009) Bo Li et al.   ECOLOGICAL ENGINEERING

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Diversity in leaf anatomy, and stomatal distribution and conductance, between salt marsh and freshwater species in the C4 genus Spartina (Poaceae)

(2009) Brian R. Maricle et al.   NEW PHYTOLOGIST

Homoeologous recombination in allopolyploids: the polyploid ratchet

(2009) Robert T. Gaeta et al.   NEW PHYTOLOGIST

Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina

(2009) Christian Parisod et al.   NEW PHYTOLOGIST

Genetic regulation of meiosis in polyploid species: new insights into an old question

(2009) Marta Cifuentes et al.   NEW PHYTOLOGIST

Homoeologous nonreciprocal recombination in polyploid cotton

(2009) Armel Salmon et al.   NEW PHYTOLOGIST

Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing

(2009) Peter C. Bundock et al.   PLANT BIOTECHNOLOGY JOURNAL

Evolutionary Genetics of Genome Merger and Doubling in Plants

(2008) Jeff J. Doyle et al.   Annual Review of Genetics

Mechanisms of Salinity Tolerance

(2008) Rana Munns et al.   Annual Review of Plant Biology

Differential proteomic analysis of soluble extracellular proteins reveals the cysteine protease and cystatin involved in suspension-cultured cell proliferation in rice

(2008) Lihong Tian et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Hybridization, polyploidy and invasion: lessons from Spartina (Poaceae)

(2008) M. L. Ainouche et al.   BIOLOGICAL INVASIONS

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

(2008) Evandro Novaes et al.   BMC GENOMICS

Primary responses to salt stress in a halophyte, smooth cordgrass (Spartina alterniflora Loisel.)

(2008) Niranjan Baisakh et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing

(2008) Christopher W. Wheat   GENETICA

The new paradigm of flow cell sequencing

(2008) R. A. Holt et al.   GENOME RESEARCH

Evolution of C4 Phosphoenolpyruvate Carboxykinase in Grasses, from Genotype to Phenotype

(2008) Pascal-Antoine Christin et al.   MOLECULAR BIOLOGY AND EVOLUTION

The enigmatic invasiveSpartina densiflora: A history of hybridizations in a polyploidy context

(2008) P. M. FORTUNE et al.   MOLECULAR ECOLOGY

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Growth and photosynthetic responses to zinc stress of an invasive cordgrass,Spartina densiflora

(2008) E. Mateos-Naranjo et al.   PLANT BIOLOGY

Oligocene CO2 Decline Promoted C4 Photosynthesis in Grasses

(2007) Pascal-Antoine Christin et al.   CURRENT BIOLOGY

Efficiency of antioxidant response in Spartina densiflora: An adaptative success in a polluted environment

(2007) D. Martínez-Domínguez et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Sequencing breakthroughs for genomic ecology and evolutionary biology

(2007) MATTHEW E. HUDSON   Molecular Ecology Resources