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

Sequencing transcriptomes in toto

(2011) Karin S. Kassahn et al.   Integrative Biology

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing

(2011) Ian Bancroft et al.   NATURE BIOTECHNOLOGY

Comparative Evolution of Photosynthetic Genes in Response to Polyploid and Nonpolyploid Duplication

(2011) J. E. Coate et al.   PLANT PHYSIOLOGY

A Two-Stage Poisson Model for Testing RNA-Seq Data

(2011) Paul L. Auer et al.   Statistical Applications in Genetics and Molecular Biology

Quantifying Whole Transcriptome Size, a Prerequisite for Understanding Transcriptome Evolution Across Species: An Example from a Plant Allopolyploid

(2010) Jeremy E. Coate et al.   Genome Biology and Evolution

Uncovering the Complexity of Transcriptomes with RNA-Seq

(2010) Valerio Costa et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

A Comparison of Global, Gene-Specific, and Relaxed Clock Methods in a Comparative Genomics Framework: Dating the Polyploid History of Soybean (Glycine max)

(2010) Ashley N. Egan et al.   SYSTEMATIC BIOLOGY

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Polyploidy and angiosperm diversification

(2009) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

Non-additive gene regulation in a citrus allotetraploid somatic hybrid between C. reticulata Blanco and C. limon (L.) Burm

(2009) J B Bassene et al.   HEREDITY

Molecular and Chromosomal Evidence for Allopolyploidy in Soybean

(2009) N. Gill et al.   PLANT PHYSIOLOGY

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution

(2008) Lex Flagel et al.   BMC BIOLOGY

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

Genome size is a strong predictor of cell size and stomatal density in angiosperms

(2008) Jeremy M. Beaulieu et al.   NEW PHYTOLOGIST

Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean

(2008) R. W. Innes et al.   PLANT PHYSIOLOGY

Sequencing breakthroughs for genomic ecology and evolutionary biology

(2007) MATTHEW E. HUDSON   Molecular Ecology Resources