Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids

trieFinder: an efficient program for annotating Digital Gene Expression (DGE) tags

(2014) Gabriel Renaud et al.   BMC BIOINFORMATICS

Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids

(2014) M. R. Woodhouse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Coordinate changes in gene expression and triacylglycerol composition in the developing seeds of oilseed rape (Brassica napus) and turnip rape (Brassica rapa)

(2013) Anssi L. Vuorinen et al.   FOOD CHEMISTRY

Differentially Expressed Genes during Flowering and Grain Filling in Common Bean (Phaseolus vulgaris) Grown under Drought Stress Conditions

(2013) Bárbara Salomão de Faria Müller et al.   PLANT MOLECULAR BIOLOGY REPORTER

Transcriptome Profile Analysis of Maize Seedlings in Response to High-salinity, Drought and Cold Stresses by Deep Sequencing

(2013) Xiaohui Shan et al.   PLANT MOLECULAR BIOLOGY REPORTER

Tracing the Transcriptomic Changes in Synthetic Trigenomic allohexaploids of Brassica Using an RNA-Seq Approach

(2013) Qin Zhao et al.   PLoS One

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

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

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

The draft genome of a diploid cotton Gossypium raimondii

(2012) Kunbo Wang et al.   NATURE GENETICS

Accessing complex crop genomes with next-generation sequencing

(2012) David Edwards et al.   THEORETICAL AND APPLIED GENETICS

Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa

(2011) Jun Wang et al.   BMC GENOMICS

Nutritional and nutraceutical potential of rape (Brassica napus L. var. napus) and “tronchuda” cabbage (Brassica oleraceae L. var. costata) inflorescences

(2011) Cátia Batista et al.   FOOD AND CHEMICAL TOXICOLOGY

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

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

(2011) Ian Bancroft et al.   NATURE BIOTECHNOLOGY

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

Genome structure affects the rate of autosyndesis and allosyndesis in AABC, BBAC and CCAB Brassica interspecific hybrids

(2010) Annaliese S. Mason et al.   CHROMOSOME RESEARCH

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

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

The first meiosis of resynthesized Brassica napus, a genome blender

(2010) E. Szadkowski et al.   NEW PHYTOLOGIST

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences

(2009) Martin Trick et al.   BMC PLANT BIOLOGY

Epigenetic regulation of stress responses in plants

(2009) Viswanathan Chinnusamy et al.   CURRENT OPINION IN PLANT BIOLOGY

Genomic and expression plasticity of polyploidy

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

Next-generation tag sequencing for cancer gene expression profiling

(2009) A. S. Morrissy et al.   GENOME RESEARCH

Homoeologous recombination in allopolyploids: the polyploid ratchet

(2009) Robert T. Gaeta et al.   NEW PHYTOLOGIST

Single nucleotide polymorphism (SNP) discovery in the polyploidBrassica napususing Solexa transcriptome sequencing

(2009) Martin Trick et al.   PLANT BIOTECHNOLOGY JOURNAL

Comparative Analysis between Homoeologous Genome Segments of Brassica napus and Its Progenitor Species Reveals Extensive Sequence-Level Divergence

(2009) F. Cheung et al.   PLANT CELL

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

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

Comparative mapping of Brassica juncea and Arabidopsis thaliana using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes

(2008) Priya Panjabi et al.   BMC GENOMICS

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

(2008) Peter A. C. 't Hoen et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Yanhao Xu et al.   PLANTA

Genomic Plasticity and the Diversity of Polyploid Plants

(2008) A. R. Leitch et al.   SCIENCE