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

PubWeight™: 1.26‹?› | Rank: Top 10%

🔗 View Article (PMC 3428664)

Published in BMC Genomics on June 15, 2012

Authors

Janet Higgins1, Andreas Magusin, Martin Trick, Fiona Fraser, Ian Bancroft

Author Affiliations

1: John Innes Centre, Norwich Research Park, Norwich, UK.

Articles citing this

Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nat Biotechnol (2012) 1.96

Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat. BMC Genomics (2014) 0.94

Use of digital gene expression to discriminate gene expression differences in early generations of resynthesized Brassica napus and its diploid progenitors. BMC Genomics (2013) 0.93

Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies. Mol Biol Evol (2014) 0.90

Four genes encoding MYB28, a major transcriptional regulator of the aliphatic glucosinolate pathway, are differentially expressed in the allopolyploid Brassica juncea. J Exp Bot (2013) 0.90

SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species. Int J Plant Genomics (2013) 0.87

The legacy of diploid progenitors in allopolyploid gene expression patterns. Philos Trans R Soc Lond B Biol Sci (2014) 0.86

Differential transcriptome analysis between Paulownia fortunei and its synthesized autopolyploid. Int J Mol Sci (2014) 0.85

Associative transcriptomics study dissects the genetic architecture of seed glucosinolate content in Brassica napus. DNA Res (2014) 0.85

Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids. BMC Plant Biol (2015) 0.84

Sixteen cytosolic glutamine synthetase genes identified in the Brassica napus L. genome are differentially regulated depending on nitrogen regimes and leaf senescence. J Exp Bot (2014) 0.84

Genome distribution of differential homoeologue contributions to leaf gene expression in bread wheat. Plant Biotechnol J (2015) 0.84

Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses. BMC Genomics (2014) 0.82

Dissection of the control of anion homeostasis by associative transcriptomics in Brassica napus. Plant Physiol (2014) 0.82

Transcriptome analysis of Brassica napus pod using RNA-Seq and identification of lipid-related candidate genes. BMC Genomics (2015) 0.79

Genomic origin, expression differentiation and regulation of multiple genes encoding CYP83A1, a key enzyme for core glucosinolate biosynthesis, from the allotetraploid Brassica juncea. Planta (2014) 0.79

Elucidation of the genetic basis of variation for stem strength characteristics in bread wheat by Associative Transcriptomics. BMC Genomics (2016) 0.79

Construction of Brassica A and C genome-based ordered pan-transcriptomes for use in rapeseed genomic research. Data Brief (2015) 0.78

Cytonuclear evolution of rubisco in four allopolyploid lineages. Mol Biol Evol (2014) 0.78

Circadian rhythms of sense and antisense transcription in sugarcane, a highly polyploid crop. PLoS One (2013) 0.77

Applications and challenges of next-generation sequencing in Brassica species. Planta (2013) 0.77

Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies. Mol Genet Genomics (2016) 0.76

Transcriptome Analysis of Stem and Globally Comparison with Other Tissues in Brassica napus. Front Plant Sci (2016) 0.76

Comparative genomics of Brassicaceae crops. Breed Sci (2014) 0.76

Class-Specific Evolution and Transcriptional Differentiation of 14-3-3 Family Members in Mesohexaploid Brassica rapa. Front Plant Sci (2016) 0.76

The defence-associated transcriptome of hexaploid wheat displays homoeolog expression and induction bias. Plant Biotechnol J (2016) 0.75

Assembly and comparison of two closely related Brassica napus genomes. Plant Biotechnol J (2017) 0.75

A comparative genomic and transcriptomic analysis at the level of isolated root hair cells reveals new conserved root hair regulatory elements. Plant Mol Biol (2017) 0.75

Extensive homoeologous genome exchanges in allopolyploid crops revealed by mRNAseq-based visualization. Plant Biotechnol J (2016) 0.75

Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae). Genome Biol Evol (2016) 0.75

Articles cited by this

Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44

Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res (2008) 62.07

RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics (2010) 19.86

agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res (2010) 10.53

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res (2008) 10.10

Genome evolution in polyploids. Plant Mol Biol (2000) 9.92

Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc Natl Acad Sci U S A (1995) 7.48

DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci U S A (1997) 7.08

From RNA-seq reads to differential expression results. Genome Biol (2010) 5.77

Polyploidy and angiosperm diversification. Am J Bot (2009) 4.41

Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics (2009) 3.87

Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics (2005) 3.78

The role of hybridization in plant speciation. Annu Rev Plant Biol (2009) 3.68

Evolutionary genetics of genome merger and doubling in plants. Annu Rev Genet (2008) 3.45

Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res (2006) 3.41

Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnol J (2009) 3.22

Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell (2007) 3.21

Genomic plasticity and the diversity of polyploid plants. Science (2008) 3.18

RNA-seq: from technology to biology. Cell Mol Life Sci (2009) 3.03

Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays. PLoS One (2011) 3.01

Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape). Genome (1995) 2.79

RNA-seq: technical variability and sampling. BMC Genomics (2011) 2.19

Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing. Nat Biotechnol (2011) 2.12

Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence. Plant Cell (2009) 2.01

Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing. RNA (2009) 1.96

Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant. Curr Biol (2011) 1.94

Crop genome sequencing: lessons and rationales. Trends Plant Sci (2011) 1.77

Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. Proc Natl Acad Sci U S A (2011) 1.72

The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution. New Phytol (2009) 1.72

Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (gossypium). Genetics (2009) 1.71

Allopolyploidy alters gene expression in the highly stable hexaploid wheat. Plant Mol Biol (2003) 1.71

Genomic expression dominance in allopolyploids. BMC Biol (2009) 1.71

Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing. BMC Genomics (2007) 1.66

What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research. Plant Biol (Stuttg) (2010) 1.46

Genomic and expression plasticity of polyploidy. Curr Opin Plant Biol (2009) 1.44

Phylogenetic analysis of Brassiceae based on the nucleotide sequences of the S-locus related gene, SLR1. Theor Appl Genet (2002) 1.41

Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation. Mol Ecol (2005) 1.40

Numerous and rapid nonstochastic modifications of gene products in newly synthesized Brassica napus allotetraploids. Genetics (2006) 1.32

Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina x townsendii and Spartina anglica (Poaceae). New Phytol (2010) 1.26

A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences. BMC Plant Biol (2009) 1.20

Differential contributions to the transcriptome of duplicated genes in response to abiotic stresses in natural and synthetic polyploids. New Phytol (2011) 1.09

Analysis of gene expression in resynthesized Brassica napus Allopolyploids using arabidopsis 70mer oligo microarrays. PLoS One (2009) 1.02

Analysis of gene expression in resynthesized Brassica napus allotetraploids: transcriptional changes do not explain differential protein regulation. New Phytol (2010) 0.99

Sequencing crop genomes: approaches and applications. New Phytol (2011) 0.95

Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localization. BMC Genomics (2007) 0.92

Articles by these authors

The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23

Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature (2012) 5.67

Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics (2005) 4.28

Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnol J (2009) 3.22

Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell (2006) 3.10

An integrated physical and genetic map of the rice genome. Plant Cell (2002) 3.07

Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature (2009) 2.97

Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa. Plant Cell (2006) 2.45

CATMA: a complete Arabidopsis GST database. Nucleic Acids Res (2003) 2.34

Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol (2009) 2.17

Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing. Nat Biotechnol (2011) 2.12

Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives. Plant J (2004) 2.07

Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence. Plant Cell (2009) 2.01

Expression profiling reveals COI1 to be a key regulator of genes involved in wound- and methyl jasmonate-induced secondary metabolism, defence, and hormone interactions. Plant Mol Biol (2005) 2.00

Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nat Biotechnol (2012) 1.96

Unraveling the complex trait of crop yield with quantitative trait loci mapping in Brassica napus. Genetics (2009) 1.84

A nuclear protease required for flowering-time regulation in Arabidopsis reduces the abundance of SMALL UBIQUITIN-RELATED MODIFIER conjugates. Plant Cell (2003) 1.83

Anthocyanins double the shelf life of tomatoes by delaying overripening and reducing susceptibility to gray mold. Curr Biol (2013) 1.68

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol (2014) 1.56

Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa. BMC Genomics (2009) 1.49

An SSR-based genetic linkage map of the model grass Brachypodium distachyon. Genome (2010) 1.41

Sequence and structure of Brassica rapa chromosome A3. Genome Biol (2010) 1.35

Six new recombinant inbred populations for the study of quantitative traits in Arabidopsis thaliana. Theor Appl Genet (2008) 1.26

Natural variation for seed oil composition in Arabidopsis thaliana. Phytochemistry (2003) 1.21

A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences. BMC Plant Biol (2009) 1.20

Characterization of the centromere and peri-centromere retrotransposons in Brassica rapa and their distribution in related Brassica species. Plant J (2006) 1.14

Integration of Brassica A genome genetic linkage map between Brassica napus and B. rapa. Genome (2008) 1.11

Origin and maintenance of a broad-spectrum disease resistance locus in Arabidopsis. Mol Biol Evol (2004) 1.02

Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysis. BMC Genomics (2009) 1.02

The Plasmodium translocon of exported proteins (PTEX) component thioredoxin-2 is important for maintaining normal blood-stage growth. Mol Microbiol (2013) 1.02

BACFinder: genomic localisation of large insert genomic clones based on restriction fingerprinting. Nucleic Acids Res (2002) 1.00

RNA 3' processing functions of Arabidopsis FCA and FPA limit intergenic transcription. Proc Natl Acad Sci U S A (2011) 0.99

A Survey of the Brassica rapa genome by BAC-end sequence analysis and comparison with Arabidopsis thaliana. Mol Cells (2006) 0.95

Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea. BMC Genomics (2013) 0.93

Sequence-level comparative analysis of the Brassica napus genome around two stearoyl-ACP desaturase loci. Plant J (2009) 0.91

Genome-wide investigation of genetic changes during modern breeding of Brassica napus. Theor Appl Genet (2014) 0.89

Wheat blast: histopathology and transcriptome reprogramming in response to adapted and nonadapted Magnaporthe isolates. New Phytol (2009) 0.89

Sequencing-based variant detection in the polyploid crop oilseed rape. BMC Plant Biol (2013) 0.86

The transcriptome of Euglena gracilis reveals unexpected metabolic capabilities for carbohydrate and natural product biochemistry. Mol Biosyst (2015) 0.84

Methionine regulates copper/hydrogen peroxide oxidation products of Abeta. J Pept Sci (2005) 0.83

Methods to study PAMP-triggered immunity in Brassica species. Mol Plant Microbe Interact (2014) 0.78

Identification of a gene controlling variation in the salt tolerance of rapeseed (Brassica napus L.). Planta (2015) 0.78

Two high linolenic mutants of Arabidopsis thaliana contain megabase-scale genome duplications encompassing the FAD3 locus. Plant J (2011) 0.77

Computational tools for Brassica-Arabidopsis comparative genomics. Comp Funct Genomics (2005) 0.77

Mental health care training for practitioners in remote and rural areas. Clin Teach (2013) 0.75

GARNet, the Genomic Arabidopsis Resource Network. Trends Plant Sci (2002) 0.75