Homoeolog expression bias and expression level dominance in resynthesized allopolyploid Brassica napus

Creating favourable morphological and yield variations for rapeseed by interspecific crosses between Brassica rapa and Brassica oleracea

(2018) Jinjin Jiang et al.   PLANT BREEDING

Assembly and comparison of two closely related Brassica napus genomes

(2017) Philipp E. Bayer et al.   PLANT BIOTECHNOLOGY JOURNAL

The high-quality genome of Brassica napus cultivar ‘ZS11’ reveals the introgression history in semi-winter morphotype

(2017) Fengming Sun et al.   PLANT JOURNAL

Cytogenetics and germplasm enrichment in Brassica allopolyploids in China

(2017) Zai-yun LI et al.   Journal of Integrative Agriculture

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

(2016) Jinghua Yang et al.   NATURE GENETICS

The defence-associated transcriptome of hexaploid wheat displays homoeolog expression and induction bias

(2016) Jonathan J. Powell et al.   PLANT BIOTECHNOLOGY JOURNAL

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

(2016) Nathan M. Springer et al.   PLANT CELL

Distinct subgenome stabilities in synthesized Brassica allohexaploids

(2016) Jiannan Zhou et al.   THEORETICAL AND APPLIED GENETICS

Analysis of cytosine methylation in early generations of resynthesized Brassica napus

(2016) Li-ping RAN et al.   Journal of Integrative Agriculture

Comparative transcriptomic analysis uncovers the complex genetic network for resistance to Sclerotinia sclerotiorum in Brassica napus

(2016) Jian Wu et al.   Scientific Reports

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

(2015) Tianzhen Zhang et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

(2014) B. Chalhoub et al.   SCIENCE

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

(2014) Shengyi Liu et al.   Nature Communications

Use of digital gene expression to discriminate gene expression differences in early generations of resynthesized Brassica napus and its diploid progenitors

(2013) Jinjin Jiang et al.   BMC GENOMICS

Hybridization and speciation

(2013) R. Abbott et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Allopolyploidy has a moderate impact on restructuring at three contrasting transposable element insertion sites in resynthesizedBrassica napusallotetraploids

(2013) Véronique Sarilar et al.   NEW PHYTOLOGIST

Nucleolar dominance and different genome behaviors in hybrids and allopolyploids

(2013) Xian-Hong Ge et al.   PLANT CELL REPORTS

Cytoplasmic and Genomic Effects on Non-Meiosis-Driven Genetic Changes in Brassica Hybrids and Allotetraploids from Pairwise Crosses of Three Cultivated Diploids

(2013) Cheng Cui et al.   PLoS One

Genomic expression dominance in allopolyploids

(2012) Ryan A Rapp et al.   BMC BIOLOGY

Cytoplasmic and Genomic Effects on Meiotic Pairing in Brassica Hybrids and Allotetraploids from Pair Crosses of Three Cultivated Diploids

(2012) Cheng Cui et al.   GENETICS

Homoeolog expression bias and expression level dominance in allopolyploid cotton

(2012) M-J Yoo et al.   HEREDITY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Cole Trapnell et al.   Nature Protocols

Homoeolog expression bias and expression level dominance in allopolyploids

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

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

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

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

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

Polyploid formation pathways have an impact on genetic rearrangements in resynthesized Brassica napus

(2011) E. Szadkowski et al.   NEW PHYTOLOGIST

Proteomic Changes in Newly Synthesized Brassica napus Allotetraploids and Their Early Generations

(2011) Fang Kong et al.   PLANT MOLECULAR BIOLOGY REPORTER

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploids

(2011) R. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus

(2011) Z. Xiong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Homoeolog-specific transcriptional bias in allopolyploid wheat

(2010) Alina R Akhunova et al.   BMC GENOMICS

The first meiosis of resynthesized Brassica napus, a genome blender

(2010) E. Szadkowski et al.   NEW PHYTOLOGIST

Analysis of gene expression in resynthesized Brassica napus allotetraploids: transcriptional changes do not explain differential protein regulation

(2010) Anne Marmagne et al.   NEW PHYTOLOGIST

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genomic and expression plasticity of polyploidy

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

Analysis of Gene Expression in Resynthesized Brassica napus Allopolyploids Using Arabidopsis 70mer Oligo Microarrays

(2009) Robert T. Gaeta et al.   PLoS One

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

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

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids

(2008) Yanhao Xu et al.   PLANTA