Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat

Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat

(2013) Tatiana Belova et al.   BMC GENOMICS

HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids

(2013) Aziz Mithani et al.   BMC GENOMICS

Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat

(2013) Huakun Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic expression dominance in allopolyploids

(2012) Ryan A Rapp et al.   BMC BIOLOGY

Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum) lines

(2012) Bao Qi et al.   BMC BIOLOGY

Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat

(2012) Andreas W Schreiber 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

Chromosome arm-specific BAC end sequences permit comparative analysis of homoeologous chromosomes and genomes of polyploid wheat

(2012) Sunish K Sehgal et al.   BMC PLANT BIOLOGY

Integrating cereal genomics to support innovation in the Triticeae

(2012) C. Feuillet et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Analysis of the bread wheat genome using whole-genome shotgun sequencing

(2012) Rachel Brenchley et al.   NATURE

Pericentromeric Effects Shape the Patterns of Divergence, Retention, and Expression of Duplicated Genes in the Paleopolyploid Soybean

(2012) J. Du et al.   PLANT CELL

Biased Gene Fractionation and Dominant Gene Expression among the Subgenomes of Brassica rapa

(2012) Feng Cheng et al.   PLoS One

Polyploidy in fungi: evolution after whole-genome duplication

(2012) W. Albertin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Extensive and Heritable Epigenetic Remodeling and Genetic Stability Accompany Allohexaploidization of Wheat

(2011) Na Zhao et al.   GENETICS

Organ and Cell Type–Specific Complementary Expression Patterns and Regulatory Neofunctionalization between Duplicated Genes in Arabidopsis thaliana

(2011) Shao-Lun Liu et al.   Genome Biology and Evolution

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Changes in Twelve Homoeologous Genomic Regions in Soybean following Three Rounds of Polyploidy

(2011) Andrew J. Severin et al.   PLANT CELL

Frequent Gene Movement and Pseudogene Evolution Is Common to the Large and Complex Genomes of Wheat, Barley, and Their Relatives

(2011) Thomas Wicker et al.   PLANT CELL

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

(2011) J. C. Schnable et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

The collapse of gene complement following whole genome duplication

(2010) David Sankoff et al.   BMC GENOMICS

Homoeolog-specific transcriptional bias in allopolyploid wheat

(2010) Alina R Akhunova et al.   BMC GENOMICS

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

Genome-wide gene expression changes in genetically stable synthetic and natural wheat allohexaploids

(2010) Véronique Chagué et al.   NEW PHYTOLOGIST

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

(2010) Ignacio Medina et al.   NUCLEIC ACIDS RESEARCH

Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces

(2010) Frédéric Choulet et al.   PLANT CELL

Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs

(2010) Margaret R. Woodhouse et al.   PLOS BIOLOGY

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheat

(2009) Cristobal Uauy et al.   BMC PLANT BIOLOGY

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

(2009) B. Chaudhary et al.   GENETICS

A quantitative genomic imbalance gene expression assay in a hexaploid species: wheat (Triticum aestivum)

(2009) K. Stamati et al.   GENOME

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

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

Differential expression of duplicated peroxidase genes in the allotetraploid Brassica napus

(2009) Jianwei Zhao et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Duplicate genes increase expression diversity in closely related species and allopolyploids

(2009) M. Ha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expression profiling of the bottom fermenting yeastSaccharomyces pastorianusorthologous genes using oligonucleotide microarrays

(2009) Toshiko Minato et al.   YEAST

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

(2008) Lex Flagel et al.   BMC BIOLOGY

Nonadditive Expression of Homoeologous Genes Is Established Upon Polyploidization in Hexaploid Wheat

(2008) M. Pumphrey et al.   GENETICS

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Variation for homoeologous gene silencing in hexaploid wheat

(2008) Andrew Bottley et al.   PLANT JOURNAL

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