Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids

Both maternally and paternally imprinted genes regulate seed development in rice

(2017) Jingya Yuan et al.   NEW PHYTOLOGIST

Similarity between soybean andArabidopsisseed methylomes and loss of non-CG methylation does not affect seed development

(2017) Jer-Young Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of rice root development by a retrotransposon acting as a microRNA sponge

(2017) Jungnam Cho et al.   eLife

Histone Modifications Define Expression Bias of Homoeologous Genomes in Allotetraploid Cotton

(2016) Dewei Zheng et al.   PLANT PHYSIOLOGY

Transcriptome shock invokes disruption of parental expression-conserved genes in tetraploid wheat

(2016) Huakun Zhang et al.   Scientific Reports

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets

(2015) Ying Jin et al.   BIOINFORMATICS

Epigenetic and developmental regulation in plant polyploids

(2015) Qingxin Song et al.   CURRENT OPINION IN PLANT BIOLOGY

Patatin-related phospholipase A, pPLAIIIα, modulates the longitudinal growth of vegetative tissues and seeds in rice

(2015) Guangmeng Liu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-Wide Dosage-Dependent and -Independent Regulation Contributes to Gene Expression and Evolutionary Novelty in Plant Polyploids

(2015) Xiaoli Shi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

(2015) Tianzhen Zhang et al.   NATURE BIOTECHNOLOGY

A re-evaluation of the homoploid hybrid origin ofAegilops tauschii, the donor of the wheat D-subgenome

(2015) Lin-Feng Li et al.   NEW PHYTOLOGIST

Transcriptome asymmetry in synthetic and natural allotetraploid wheats, revealed by RNA-sequencing

(2015) Xutong Wang et al.   NEW PHYTOLOGIST

Genome-specific differential gene expressions in resynthesized Brassica allotetraploids from pair-wise crosses of three cultivated diploids revealed by RNA-seq

(2015) Dawei Zhang et al.   Frontiers in Plant Science

The polyploidy revolution then...and now: Stebbins revisited

(2014) D. E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

The role of small RNAs in wide hybridisation and allopolyploidisation between Brassica rapa and Brassica nigra

(2014) Muhammad Awais Ghani et al.   BMC PLANT BIOLOGY

The chloroplast view of the evolution of polyploid wheat

(2014) Piotr Gornicki et al.   NEW PHYTOLOGIST

Asymmetric Epigenetic Modification and Elimination of rDNA Sequences by Polyploidization in Wheat

(2014) Xiang Guo et al.   PLANT CELL

Evolution of the BBAA Component of Bread Wheat during Its History at the Allohexaploid Level

(2014) Huakun Zhang et al.   PLANT CELL

mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat

(2014) A. Li et al.   PLANT CELL

Ancient hybridizations among the ancestral genomes of bread wheat

(2014) T. Marcussen et al.   SCIENCE

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

Functional genomics based understanding of rice endosperm development

(2013) Shi-Rong Zhou et al.   CURRENT OPINION IN PLANT BIOLOGY

Draft genome of the wheat A-genome progenitor Triticum urartu

(2013) Hong-Qing Ling et al.   NATURE

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation

(2013) Jizeng Jia et al.   NATURE

Intrinsic karyotype stability and gene copy number variations may have laid the foundation for tetraploid wheat formation

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

Rapid, Repeated, and Clustered Loss of Duplicate Genes in Allopolyploid Plant Populations of Independent Origin

(2012) Richard J.A. Buggs et al.   CURRENT BIOLOGY

Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility

(2012) Danny W-K Ng et al.   CURRENT OPINION IN PLANT BIOLOGY

Genomic asymmetry in allopolyploid plants: wheat as a model

(2012) M. Feldman et al.   JOURNAL OF EXPERIMENTAL BOTANY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Gene expression in the developing aleurone and starchy endosperm of wheat

(2012) Susan A. Gillies et al.   PLANT BIOTECHNOLOGY JOURNAL

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds

(2012) J. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Xiaoli Shi et al.   Nature Communications

Wheat Hybridization and Polyploidization Results in Deregulation of Small RNAs

(2011) Michal Kenan-Eichler et al.   GENETICS

Coordinated histone modifications are associated with gene expression variation within and between species

(2011) M. Ha et al.   GENOME RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A Genome-Wide Survey of Imprinted Genes in Rice Seeds Reveals Imprinting Primarily Occurs in the Endosperm

(2011) Ming Luo et al.   PLoS Genetics

Small RNAs, DNA methylation and transposable elements in wheat

(2010) Dario Cantu et al.   BMC GENOMICS

Generality and characteristics of genetic and epigenetic changes in newly synthesized allotetraploid wheat lines

(2010) Bao Qi et al.   Journal of Genetics and Genomics

Rice SUVH Histone Methyltransferase Genes Display Specific Functions in Chromatin Modification and Retrotransposon Repression

(2010) Fu-Jun Qin et al.   Molecular Plant

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

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

(2010) Véronique Chagué et al.   NEW PHYTOLOGIST

Molecular mechanisms of polyploidy and hybrid vigor

(2010) Z. Jeffrey Chen   TRENDS IN PLANT SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

Comparative transcriptomics in the Triticeae

(2009) Andreas W Schreiber et al.   BMC GENOMICS

Genomic and expression plasticity of polyploidy

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

Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis

(2009) Rebecca A. Mosher et al.   NATURE

Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids

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

Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

(2009) M. Gehring et al.   SCIENCE

Genome-Wide Demethylation of Arabidopsis Endosperm

(2009) T.-F. Hsieh et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Evolutionary Genetics of Genome Merger and Doubling in Plants

(2008) Jeff J. Doyle et al.   Annual Review of Genetics

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

(2008) Lex Flagel et al.   BMC BIOLOGY