Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing

De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum

(2013) Joshua P Der et al.   BMC GENOMICS

Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures

(2012) Michael L Hayes et al.   BMC EVOLUTIONARY BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing

(2012) Steven B. Roberts et al.   PLoS One

mRNA-Seq Analysis of the Pseudoperonospora cubensis Transcriptome During Cucumber (Cucumis sativus L.) Infection

(2012) Elizabeth A. Savory et al.   PLoS One

De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing

(2011) Purushothaman Natarajan et al.   BMC GENOMICS

Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance

(2011) Barbara Feldmeyer et al.   BMC GENOMICS

Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery

(2011) Sukhjiwan Kaur 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

Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds

(2011) Cheng-Ying Shi et al.   BMC GENOMICS

Transcriptomes of the Parasitic Plant Family Orobanchaceae Reveal Surprising Conservation of Chlorophyll Synthesis

(2011) Norman J. Wickett et al.   CURRENT BIOLOGY

De novo transcriptome sequencing in Salvia miltiorrhiza to identify genes involved in the biosynthesis of active ingredients

(2011) Hua Wenping et al.   GENOMICS

Critical assessment of assembly strategies for non-model species mRNA-Seq data and application of next-generation sequencing to the comparison of C3 and C4 species

(2011) Andrea Bräutigam et al.   JOURNAL OF EXPERIMENTAL BOTANY

De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next-generation sequencing techniques

(2011) F. ANGELONI et al.   Molecular Ecology Resources

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

The evolution of RNA editing and pentatricopeptide repeat genes

(2011) Sota Fujii et al.   NEW PHYTOLOGIST

Whole-transcriptome RNAseq analysis from minute amount of total RNA

(2011) Muhammad A. Tariq et al.   NUCLEIC ACIDS RESEARCH

Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae)

(2011) J. Chris Blazier et al.   PLANT MOLECULAR BIOLOGY

Gene Discovery and Tissue-Specific Transcriptome Analysis in Chickpea with Massively Parallel Pyrosequencing and Web Resource Development

(2011) R. Garg et al.   PLANT PHYSIOLOGY

Transcriptome Sequencing and De Novo Analysis for Yesso Scallop (Patinopecten yessoensis) Using 454 GS FLX

(2011) Rui Hou et al.   PLoS One

Transcriptome Sequencing, and Rapid Development and Application of SNP Markers for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)

(2011) Venu M. Margam et al.   PLoS One

High-throughput DNA sequencing - concepts and limitations

(2010) Martin Kircher et al.   BIOESSAYS

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

(2010) Jill M Duarte et al.   BMC EVOLUTIONARY BIOLOGY

Differences in transcription between free-living and CO2-activated third-stage larvae of Haemonchus contortus

(2010) Cinzia Cantacessi et al.   BMC GENOMICS

De novo characterization of a whitefly transcriptome and analysis of its gene expression during development

(2010) Xiao-Wei Wang et al.   BMC GENOMICS

Comparing de novo assemblers for 454 transcriptome data

(2010) Sujai Kumar et al.   BMC GENOMICS

Extensive Loss of RNA Editing Sites in Rapidly Evolving Silene Mitochondrial Genomes: Selection vs. Retroprocessing as the Driving Force

(2010) D. B. Sloan et al.   GENETICS

Extreme Reconfiguration of Plastid Genomes in the Angiosperm Family Geraniaceae: Rearrangements, Repeats, and Codon Usage

(2010) M. M. Guisinger et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Editing of accD and ndhF chloroplast transcripts is partially affected in the Arabidopsis vanilla cream1 mutant

(2010) Ching-Chih Tseng et al.   PLANT MOLECULAR BIOLOGY

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae

(2009) Daniel B Sloan et al.   BMC EVOLUTIONARY BIOLOGY

Comparison of next generation sequencing technologies for transcriptome characterization

(2009) P Kerr Wall 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

Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx

(2009) Eli Meyer et al.   BMC GENOMICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Pentatricopeptide Repeat Proteins with the DYW Motif Have Distinct Molecular Functions in RNA Editing and RNA Cleavage in Arabidopsis Chloroplasts

(2009) K. Okuda et al.   PLANT CELL

A Study of New Arabidopsis Chloroplast RNA Editing Mutants Reveals General Features of Editing Factors and Their Target Sites

(2009) K. Hammani et al.   PLANT CELL

AtECB2, a pentatricopeptide repeat protein, is required for chloroplast transcriptaccDRNA editing and early chloroplast biogenesis inArabidopsis thaliana

(2009) Qing-Bo Yu et al.   PLANT JOURNAL

LPA66 Is Required for Editing psbF Chloroplast Transcripts in Arabidopsis

(2009) W. Cai et al.   PLANT PHYSIOLOGY

A comparative genomics approach identifies a PPR-DYW protein that is essential for C-to-U editing of the Arabidopsis chloroplast accD transcript

(2009) J. C. Robbins et al.   RNA

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

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

(2008) Evandro Novaes et al.   BMC GENOMICS

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

(2008) Christopher W. Wheat   GENETICA

Characterizing the mouse ES cell transcriptome with Illumina sequencing

(2008) Ruben Rosenkranz et al.   GENOMICS

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

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

CLB19, a pentatricopeptide repeat protein required for editing ofrpoAandclpPchloroplast transcripts

(2008) Anne-Laure Chateigner-Boutin et al.   PLANT JOURNAL

The Arabidopsis gene YS1 encoding a DYW protein is required for editing of rpoB transcripts and the rapid development of chloroplasts during early growth

(2008) Wenbin Zhou et al.   PLANT JOURNAL

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions

(2008) M. M. Guisinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

Pentatricopeptide repeat proteins: a socket set for organelle gene expression

(2008) C SCHMITZLINNEWEBER et al.   TRENDS IN PLANT SCIENCE