Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploidCoffea arabicagrown at contrasted temperatures

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

Genomic expression dominance in allopolyploids

(2012) Ryan A Rapp et al.   BMC BIOLOGY

Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective

(2012) Aureliano Bombarely et al.   BMC GENOMICS

Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus

(2012) Janet Higgins et al.   BMC GENOMICS

Polyploidy and its effect on evolutionary success: old questions revisited with new tools

(2012) A Madlung   HEREDITY

Homoeolog expression bias and expression level dominance in allopolyploid cotton

(2012) M-J Yoo et al.   HEREDITY

Homoeolog expression bias and expression level dominance in allopolyploids

(2012) C. E. Grover et al.   NEW PHYTOLOGIST

Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids

(2012) Xiaoli Shi et al.   Nature Communications

Hybridization: Expressing Yourself in a Crowd

(2011) Matthew Hegarty   CURRENT BIOLOGY

Transcriptomic Shock Generates Evolutionary Novelty in a Newly Formed, Natural Allopolyploid Plant

(2011) Richard J.A. Buggs et al.   CURRENT BIOLOGY

Homeologous Gene Expression in Response to Growing Temperature in a Recent Allopolyploid (Coffea arabica L.)

(2011) Marie-Christine Combes et al.   JOURNAL OF HEREDITY

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Genomic expression dominance in the natural allopolyploid Coffea arabica is massively affected by growth temperature

(2011) Amélie Bardil et al.   NEW PHYTOLOGIST

Differential contributions to the transcriptome of duplicated genes in response to abiotic stresses in natural and synthetic polyploids

(2011) Shaowei Dong et al.   NEW PHYTOLOGIST

Identification, characterization and interpretation of single-nucleotide sequence variation in allopolyploid crop species

(2011) Sukhjiwan Kaur et al.   PLANT BIOTECHNOLOGY JOURNAL

Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea)

(2011) Qingyi Yu et al.   PLANT JOURNAL

Genome evolution in diploid and tetraploid Coffea species as revealed by comparative analysis of orthologous genome segments

(2011) Alberto Cenci et al.   PLANT MOLECULAR BIOLOGY

Unstable Transcripts in Arabidopsis Allotetraploids Are Associated with Nonadditive Gene Expression in Response to Abiotic and Biotic Stresses

(2011) Eun-Deok Kim et al.   PLoS One

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

Tissue-specific silencing of homoeologs in natural populations of the recent allopolyploid Tragopogon mirus

(2010) Richard J. A. Buggs et al.   NEW PHYTOLOGIST

A High-Throughput Data Mining of Single Nucleotide Polymorphisms in Coffea Species Expressed Sequence Tags Suggests Differential Homeologous Gene Expression in the Allotetraploid Coffea arabica

(2010) R. O. Vidal et al.   PLANT PHYSIOLOGY

Adaptive radiation in Coffea subgenus Coffea L. (Rubiaceae) in Africa and Madagascar

(2010) François Anthony et al.   PLANT SYSTEMATICS AND EVOLUTION

Genetic and physical mapping of the SH3 region that confers resistance to leaf rust in coffee tree (Coffea arabica L.)

(2010) Philippe Lashermes et al.   Tree Genetics & Genomes

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genomic and expression plasticity of polyploidy

(2009) Scott Jackson et al.   CURRENT OPINION IN PLANT BIOLOGY

Reciprocal Silencing, Transcriptional Bias and Functional Divergence of Homeologs in Polyploid Cotton (Gossypium)

(2009) B. Chaudhary et al.   GENETICS

The complex nature of allopolyploid plant genomes

(2009) M J Hegarty et al.   HEREDITY

Coordinated and Fine-Scale Control of Homoeologous Gene Expression in Allotetraploid Cotton

(2009) L. E. Flagel et al.   JOURNAL OF HEREDITY

Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation

(2009) Lex E. Flagel et al.   NEW PHYTOLOGIST

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

Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies in Senecio

(2008) M. J Hegarty et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant

(2008) R. Hovav et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Plasticity and the Diversity of Polyploid Plants

(2008) A. R. Leitch et al.   SCIENCE

Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects

(2008) Reiner A. Veitia et al.   TRENDS IN GENETICS