Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms

Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms

(2012) Emmanuel Buschiazzo et al.   BMC EVOLUTIONARY BIOLOGY

Advances in plant genome sequencing

(2012) John P. Hamilton et al.   PLANT JOURNAL

De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)

(2011) Zhangying Wang 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

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

(2011) R. Garg et al.   DNA RESEARCH

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

(2011) E. Moritsuka et al.   GENETICS

Factors that Contribute to Variation in Evolutionary Rate among Arabidopsis Genes

(2011) L. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

454-pyrosequencing of Coffea arabica leaves infected by the rust fungus Hemileia vastatrix reveals in planta-expressed pathogen-secreted proteins and plant functions in a late compatible plant-rust interaction

(2011) DIANA FERNANDEZ et al.   MOLECULAR PLANT PATHOLOGY

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

A White Spruce Gene Catalog for Conifer Genome Analyses

(2011) Philippe Rigault et al.   PLANT PHYSIOLOGY

The First Insight into the Tissue Specific Taxus Transcriptome via Illumina Second Generation Sequencing

(2011) Da Cheng Hao et al.   PLoS One

Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules

(2011) Sergei A. Filichkin et al.   PLoS One

A Functional Phylogenomic View of the Seed Plants

(2011) Ernest K. Lee et al.   PLoS Genetics

The contribution of recombination to heterozygosity differs among plant evolutionary lineages and life-forms

(2010) Juan P Jaramillo-Correa et al.   BMC EVOLUTIONARY BIOLOGY

High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus

(2010) Sofia Berlin 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

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

The Positive Correlation between dN/dS and dS in Mammals Is Due to Runs of Adjacent Substitutions

(2010) Nina Stoletzki et al.   MOLECULAR BIOLOGY AND EVOLUTION

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

New insights on the speciation history and nucleotide diversity of three boreal spruce species and a Tertiary relict

(2009) J Chen et al.   HEREDITY

RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing

(2009) Brian T. Wilhelm et al.   METHODS

Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci

(2009) Yuan Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis)

(2008) Steven G Ralph et al.   BMC GENOMICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Patterns of Divergence among Conifer ESTs and Polymorphism in Pinus sylvestris Identify Putative Selective Sweeps

(2008) A. E. Palme et al.   MOLECULAR BIOLOGY AND EVOLUTION

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Rates of Molecular Evolution Are Linked to Life History in Flowering Plants

(2008) S. A. Smith et al.   SCIENCE